Contacts of the helix formed by residues 49 - 76 (chain B) in PDB entry 2NQB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 49 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PRO* 3.6 27.9 - - + +
47B SER* 3.2 4.1 + - - +
48B GLY* 1.3 76.1 - - - +
50B ILE* 1.3 64.4 + - - +
51B TYR 3.3 0.6 + - - -
52B GLU* 3.6 8.1 + - + +
53B GLU* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A PHE* 4.2 15.7 - - + -
519A ILE* 3.5 26.9 - - + +
520A MET* 3.4 33.9 - - - +
521A PRO* 3.7 1.8 - - + -
524A ILE* 3.6 21.1 - - + -
34B ILE* 4.6 5.8 - - + -
46B ILE* 3.6 20.9 - - + -
47B SER* 3.1 18.6 + - - +
49B LEU* 1.3 79.0 - - - +
51B TYR* 1.3 57.6 + - + +
53B GLU* 3.0 4.1 + - - +
54B THR* 2.7 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 3.5 56.8 - - + -
34B ILE* 3.6 31.4 - - + +
35B ARG* 3.0 35.0 + - + -
46B ILE* 3.6 24.6 + - + +
47B SER 3.9 11.4 - - - -
48B GLY* 3.1 30.5 - - - +
49B LEU 3.3 0.6 - - - -
50B ILE* 1.3 76.0 - - - +
52B GLU* 1.3 62.6 + - + +
54B THR 3.4 0.2 + - - -
55B ARG* 3.1 46.5 + - - +
228J A 4.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 3.1 25.2 + - - +
48B GLY 4.9 0.6 + - - -
49B LEU* 3.6 9.6 + - + +
50B ILE 3.4 0.4 - - - -
51B TYR* 1.3 73.7 - - + +
53B GLU* 1.3 66.2 + - - +
55B ARG* 2.7 33.1 + - - +
56B GLY* 3.2 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PRO* 3.5 24.4 - - + +
524A ILE* 3.9 26.4 - - + +
525A GLN* 3.6 29.1 + - - +
528A ARG* 6.0 0.2 + - - -
534A ARG* 4.7 6.2 + - - -
49B LEU 3.3 11.8 + - - +
50B ILE* 3.0 12.3 + - - +
52B GLU* 1.3 79.1 - - - +
54B THR* 1.3 61.2 + - - +
56B GLY* 3.3 3.0 + - - -
57B VAL* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LEU* 4.2 25.6 - - + -
504A PHE* 3.5 33.2 - - + -
524A ILE* 4.1 6.7 - - - +
29B ILE* 6.1 1.6 - - + -
34B ILE* 4.0 21.7 - - + +
37B LEU* 5.5 0.4 - - + -
50B ILE* 2.7 29.4 + - - +
51B TYR 3.6 4.5 - - - -
53B GLU* 1.3 70.9 - - - +
55B ARG* 1.3 56.2 + - - +
57B VAL* 3.0 8.5 + - - +
58B LEU* 2.7 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.3 43.6 + - + +
27B GLN* 3.5 33.9 + - - +
29B ILE* 2.8 31.1 + - + +
30B THR* 3.9 2.4 - - - +
31B LYS* 3.7 21.0 - - - +
34B ILE* 4.1 11.2 - - + +
51B TYR* 3.1 37.8 + - - +
52B GLU* 2.7 34.6 + - - +
53B GLU 3.4 0.2 - - - -
54B THR* 1.3 77.2 - - - +
56B GLY* 1.3 58.9 + - - +
58B LEU* 3.3 6.4 + - - +
59B LYS* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU 3.2 11.7 + - - -
53B GLU 3.8 3.4 - - - -
54B THR 3.2 0.2 - - - -
55B ARG* 1.3 78.7 - - - +
57B VAL* 1.3 61.7 + - - +
59B LYS* 3.4 8.2 + - - +
60B VAL* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TYR* 3.7 22.1 + - + +
500A LEU* 4.2 5.2 - - + -
503A LEU* 3.6 25.4 - - + -
524A ILE* 4.1 15.0 - - + -
528A ARG* 3.8 32.7 + - - +
534A ARG* 6.3 0.2 - - - +
53B GLU* 3.0 21.1 + - - +
54B THR* 3.0 11.1 + - - +
56B GLY* 1.3 74.3 - - - +
58B LEU* 1.3 64.9 + - - +
60B VAL* 3.3 7.2 + - - +
61B PHE* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 4.4 7.4 - - + -
467A PHE* 4.7 2.2 - - + -
470A LEU* 4.3 8.3 - - + -
496A SER* 3.8 23.3 - - - +
500A LEU* 4.2 28.9 - - + +
26B ILE* 4.9 1.1 - - + -
29B ILE* 4.1 38.4 - - + -
54B THR* 2.7 20.2 + - + +
55B ARG* 3.7 7.0 - - - +
57B VAL* 1.3 74.2 - - - +
59B LYS* 1.3 57.9 + - - +
61B PHE* 3.3 9.8 + - + -
62B LEU* 2.9 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A LEU* 5.8 2.0 - - + -
473A GLU* 5.4 7.8 + - - -
474A ILE* 4.5 16.3 - - + +
26B ILE* 4.6 19.2 - - + +
55B ARG 2.8 18.1 + - - +
56B GLY* 3.6 9.0 - - - +
57B VAL 3.2 0.2 - - - -
58B LEU* 1.3 79.0 - - - +
60B VAL* 1.3 57.4 + - + +
62B LEU* 3.8 4.6 - - - +
63B GLU* 2.9 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ARG* 4.2 21.5 - - - +
56B GLY 3.1 14.7 + - - +
57B VAL* 3.3 9.2 + - - +
59B LYS* 1.3 72.8 - - + +
61B PHE* 1.3 69.4 + - - +
63B GLU* 3.8 15.4 - - - +
64B ASN* 3.1 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 5.2 1.3 - - + -
495A ALA* 4.0 11.2 - - + -
496A SER* 3.8 37.2 - - - -
499A TYR* 3.5 58.1 - + + +
57B VAL 3.0 13.6 + - - +
58B LEU* 3.5 10.5 - - + +
60B VAL* 1.3 80.3 - - - +
62B LEU* 1.3 66.7 + - + +
64B ASN* 3.4 5.3 + - - +
65B VAL* 3.1 49.4 + - + +
90B LEU* 4.2 11.0 - - + -
95B ARG* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 4.0 18.4 - - + -
470A LEU* 4.0 22.9 - - + -
471A VAL* 4.6 4.7 - - + -
474A ILE* 3.7 20.0 - - + -
492A LEU* 4.3 20.4 - - + -
496A SER* 3.1 22.7 - - - +
58B LEU* 2.9 41.3 + - + +
61B PHE* 1.3 79.8 - - + +
63B GLU* 1.3 60.5 + - - +
65B VAL* 4.8 1.8 - - + -
66B ILE* 2.7 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 3.9 24.5 - - + +
478A PHE* 3.7 7.8 - - + -
59B LYS* 2.9 57.4 + - + +
60B VAL* 3.8 18.7 - - - +
62B LEU* 1.3 74.8 - - - +
64B ASN* 1.3 59.6 + - - +
67B ARG* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 3.1 34.3 + - - +
61B PHE* 3.8 6.3 - - - +
63B GLU* 1.3 81.1 - - - +
65B VAL* 1.3 61.1 + - + +
67B ARG* 3.0 28.9 + - - +
68B ASP* 3.5 24.4 + - - +
93B GLN* 3.9 24.3 + - - +
895C LYS* 5.0 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 3.9 22.7 - - + -
61B PHE* 3.1 36.8 + - + +
62B LEU* 4.1 3.4 - - - +
64B ASN* 1.3 75.1 - - + +
66B ILE* 1.3 62.5 + - - +
68B ASP 3.2 1.9 + - - -
69B ALA* 2.8 26.3 + - + +
86B VAL* 4.5 2.0 - - + +
89B ALA* 3.5 15.7 - - + +
90B LEU* 3.7 38.6 - - + +
93B GLN* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A VAL* 3.8 36.3 - - + +
474A ILE* 3.9 14.4 - - + -
475A ALA* 3.8 31.9 - - + +
478A PHE* 4.1 5.2 - - + -
484A PHE* 5.1 4.0 - - + -
492A LEU* 4.2 21.5 - - + -
62B LEU* 2.7 40.5 + - + +
63B GLU 4.1 1.3 - - - +
65B VAL* 1.3 69.4 - - - +
67B ARG* 1.3 57.4 + - - +
69B ALA* 3.6 7.4 - - + +
70B VAL* 2.7 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE* 3.4 47.0 - - + +
63B GLU* 2.9 32.8 + - - +
64B ASN* 3.0 37.0 + - - +
66B ILE* 1.3 76.4 - - - +
68B ASP* 1.3 65.9 + - - +
70B VAL* 3.8 2.1 - - - +
71B THR* 2.8 35.5 + - - +
895C LYS* 5.9 1.8 - - - +
1296D ARG 6.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN 3.5 7.2 + - - +
65B VAL 3.2 3.7 + - - +
66B ILE 3.2 0.4 - - - -
67B ARG* 1.3 86.5 - - - +
69B ALA* 1.3 66.5 + - - +
71B THR* 3.2 4.1 + - - -
72B TYR* 3.1 26.6 + - + -
89B ALA* 3.6 21.3 - - + -
92B ARG* 2.6 38.6 + - - +
93B GLN* 2.9 21.4 + - - +
1296D ARG 5.4 0.7 - - - +
1297D LEU* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 5.7 1.1 - - + -
65B VAL* 2.8 22.0 + - + +
66B ILE* 3.1 10.3 + - + +
68B ASP* 1.3 72.0 - - - +
70B VAL* 1.3 64.2 + - + +
72B TYR* 3.1 6.9 + - - +
73B THR* 3.0 24.3 + - - -
81B VAL* 4.3 9.9 - - + -
85B ASP* 3.7 31.0 - - - +
86B VAL* 4.2 16.2 - - + +
89B ALA* 3.5 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ALA* 4.5 1.8 - - + -
478A PHE* 4.2 18.4 - - + -
479A LYS* 3.9 27.6 - - + -
482A LEU* 3.8 24.7 - - + -
66B ILE* 2.7 38.8 + - + +
67B ARG 3.8 3.6 - - - +
69B ALA* 1.3 70.2 - - + +
71B THR* 1.3 60.1 + - - +
73B THR* 3.0 8.8 + - - -
74B GLU* 2.9 41.1 + - + +
81B VAL* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 2.8 27.2 + - - +
68B ASP* 3.2 6.4 + - - -
70B VAL* 1.3 78.6 - - - +
72B TYR* 1.3 60.8 + - - +
74B GLU* 3.6 9.6 + - + +
75B HIS* 3.1 22.5 + - - +
1293D THR* 3.7 26.5 - - + +
1296D ARG* 4.6 17.2 + - + +
1297D LEU* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP 3.1 24.8 + - - -
69B ALA 3.1 6.0 + - - +
71B THR* 1.3 73.9 - - - +
73B THR* 1.3 66.8 + - - +
75B HIS* 3.3 5.8 + - - +
76B ALA* 3.1 22.9 + - - +
85B ASP* 3.6 32.8 - - - +
88B TYR* 3.6 27.3 + + + -
89B ALA* 3.8 14.1 - - - -
92B ARG* 3.3 25.2 - - - +
1273D GLU* 3.6 13.3 + - - -
1276D ARG* 5.7 0.7 - - - +
1277D LEU* 3.6 32.3 - - + -
1280D TYR* 4.0 26.6 + + + -
1281D ASN* 5.2 3.1 + - - -
1297D LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 4.5 9.0 - - + -
69B ALA 3.0 14.5 + - - -
70B VAL* 3.3 15.6 - - - -
72B TYR* 1.3 76.0 - - - +
74B GLU* 1.3 64.7 + - + +
76B ALA* 2.9 13.5 + - - +
77B LYS 3.2 7.8 + - - -
78B ARG* 3.2 41.4 + - - +
79B LYS 4.4 2.7 - - - -
80B THR 3.6 26.5 - - - +
81B VAL* 3.8 12.3 - - - +
85B ASP* 3.1 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE* 4.3 8.8 - - - +
479A LYS* 3.5 46.9 + - + +
70B VAL* 2.9 34.5 + - + +
71B THR* 4.0 8.3 + - - +
73B THR* 1.3 73.2 - - - +
75B HIS* 1.3 64.6 + - - +
77B LYS* 2.8 14.5 + - - +
78B ARG 4.7 0.7 - - - -
1289D ARG* 3.3 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 3.1 18.9 + - - +
72B TYR* 3.6 8.1 - - - +
73B THR 3.2 0.2 - - - -
74B GLU* 1.3 76.6 - - - +
76B ALA* 1.3 58.1 + - - +
77B LYS* 3.3 2.3 + - - +
1277D LEU* 3.8 14.3 + - + +
1281D ASN* 3.3 31.6 + - - +
1283D ARG* 6.0 0.8 - - - +
1289D ARG* 2.9 60.5 + - + +
1290D GLU* 2.8 38.7 + - - -
1293D THR* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR 3.1 11.5 + - - +
73B THR 2.9 9.1 + - - +
75B HIS* 1.3 74.8 - - - +
77B LYS* 1.3 71.9 + - - +
78B ARG* 3.3 33.6 + - - +
1281D ASN* 3.0 28.0 - - - +
1283D ARG* 5.9 4.1 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il