Contacts of the helix formed by residues 53 - 72 (chain D) in PDB entry 6O81
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 ASN 53 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TRP* 3.5 16.1 - - - -
52D SER* 1.3 83.1 + - - +
54D ALA* 1.3 73.3 + - - +
55D GLY* 3.2 12.3 - - - +
56D GLU* 3.4 21.3 + - + +
57D LEU 3.7 1.0 + - - -
93D TYR* 3.7 27.9 + - - -
125D HIS* 5.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TRP* 4.7 4.5 - - - +
53D ASN* 1.3 76.1 + - - +
55D GLY* 1.3 59.4 + - - +
56D GLU 3.2 0.2 - - - -
57D LEU* 3.3 9.2 + - - +
58D MET* 2.9 35.9 + - + +
89D ILE* 4.3 14.3 - - + +
93D TYR* 3.7 41.2 - - + -
125D HIS* 6.1 1.8 - - - -
129D LEU* 5.2 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASN* 3.2 12.8 - - - +
54D ALA* 1.3 77.2 - - - +
56D GLU* 1.3 58.8 + - - +
58D MET* 3.3 16.0 + - - +
59D GLU* 2.9 29.1 + - - +
93D TYR* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ARG 4.4 6.8 - - - +
51D TRP* 3.9 13.4 - - + -
52D SER* 3.6 27.0 + - - -
53D ASN* 3.4 16.1 + - + +
54D ALA 3.2 0.4 - - - -
55D GLY* 1.3 75.1 - - - +
57D LEU* 1.3 59.8 + - - +
59D GLU* 3.4 6.1 + - - +
60D LEU* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 5.5 0.4 - - + -
46D ILE* 4.2 21.5 - - + -
49D HIS* 5.9 2.7 - - + -
51D TRP* 3.9 53.9 - - + +
53D ASN 3.7 2.4 + - - -
54D ALA* 3.3 12.6 + - - +
56D GLU* 1.3 75.8 - - - +
58D MET* 1.3 59.6 + - - +
60D LEU* 4.3 16.2 - - + -
61D ILE* 2.9 51.0 + - + +
89D ILE* 4.3 29.6 - - + -
133D ILE* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ALA* 2.9 25.0 + - + +
55D GLY* 3.4 16.8 - - - +
56D GLU 3.2 0.2 - - - -
57D LEU* 1.3 77.4 - - - +
59D GLU* 1.3 58.3 + - - +
61D ILE 3.5 0.5 + - - -
62D ARG* 2.9 41.3 + - - +
86D LEU* 3.8 25.3 - - + +
89D ILE* 3.9 19.3 - - + +
90D ARG* 3.8 55.4 - - + +
93D TYR* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLY 2.9 16.3 + - - +
56D GLU* 3.9 6.8 - - - +
57D LEU 3.3 0.2 - - - -
58D MET* 1.3 73.0 - - - +
60D LEU* 1.3 61.5 + - - +
62D ARG* 3.6 12.5 - - + +
63D ARG* 2.8 74.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 3.9 28.0 - - + -
49D HIS* 4.0 28.9 - - + +
50D ARG 6.2 0.4 - - - +
56D GLU* 2.9 20.8 + - + +
57D LEU* 3.7 15.0 - - + +
59D GLU* 1.3 81.3 + - - +
61D ILE* 1.3 65.9 + - + +
63D ARG* 3.3 13.1 + - - +
64D GLU* 3.0 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.7 28.3 - - + -
45D ILE* 4.3 15.7 - - + -
46D ILE* 4.9 6.3 - - + -
57D LEU* 2.9 34.5 + - + +
60D LEU* 1.3 88.3 - - + +
62D ARG* 1.3 58.4 + - - +
64D GLU* 4.0 5.6 - - + +
65D GLY* 2.8 27.0 + - - -
68D MET* 5.2 0.6 - - + +
82D VAL* 3.7 27.2 - - + +
85D VAL* 5.1 9.0 - - + -
86D LEU* 3.8 24.7 - - + -
89D ILE* 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D MET* 2.9 29.9 + - - +
59D GLU* 3.6 11.7 - - + +
60D LEU 3.2 0.2 - - - -
61D ILE* 1.3 77.2 - - - +
63D ARG* 1.3 56.4 + - - +
65D GLY 3.3 0.7 + - - -
66D ARG* 2.9 39.6 + - - +
86D LEU* 4.1 13.9 - - + +
90D ARG* 4.0 6.5 - - - +
347D ASP* 2.8 24.7 + - - +
348D ASP* 2.4 34.5 + - - +
350D VAL* 4.2 7.9 - - - +
351D LEU* 3.4 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU* 2.8 63.8 + - - +
60D LEU* 3.8 14.6 - - - +
62D ARG* 1.3 76.8 - - - +
64D GLU* 1.3 66.1 + - + +
66D ARG* 3.6 11.2 + - + +
67D ARG* 3.5 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 3.6 29.8 - - + +
45D ILE* 5.0 9.4 - - + -
49D HIS* 6.0 0.7 + - - -
60D LEU* 3.0 33.5 + - + +
61D ILE* 4.0 7.6 - - + +
63D ARG* 1.3 81.8 - - + +
65D GLY* 1.3 56.5 + - - +
67D ARG* 3.3 35.4 + - - +
68D MET* 3.0 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ILE 2.8 18.5 + - - -
62D ARG 3.8 1.1 - - - -
64D GLU* 1.3 73.7 - - - +
66D ARG* 1.3 61.0 + - - +
68D MET* 3.7 16.1 - - - +
69D THR* 2.9 35.7 + - - +
79D GLY* 6.5 0.2 - - - -
82D VAL* 4.4 6.3 - - - -
351D LEU* 3.7 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 2.9 25.6 + - - +
63D ARG* 3.7 10.8 - - - +
64D GLU 3.3 0.2 - - - -
65D GLY* 1.3 75.7 - - - +
67D ARG* 1.3 57.0 + - + +
69D THR* 3.2 8.4 + - - -
70D ALA* 2.9 29.9 + - - +
350D VAL* 4.4 17.2 + - - +
351D LEU* 3.2 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASP* 4.9 7.5 + - - -
15D ILE* 3.5 15.2 - - - +
16D GLU* 2.6 39.4 + - - -
19D VAL* 4.0 24.2 - - + +
63D ARG* 3.5 15.7 + - + +
64D GLU* 3.3 31.9 + - - +
66D ARG* 1.3 78.0 - - + +
68D MET* 1.3 57.2 + - - +
70D ALA* 3.3 6.6 + - - +
71D ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 6.3 1.8 - - + -
18D PHE* 3.8 35.0 - - + -
19D VAL* 4.8 10.3 - - + -
22D LEU* 4.2 5.0 - - + +
38D THR* 5.0 4.7 - - - -
41D LEU* 4.4 13.0 - - + -
42D LEU* 5.2 7.9 - - + -
45D ILE* 5.8 3.6 - - + -
61D ILE* 5.2 1.1 - - + +
64D GLU* 3.0 39.2 + - + +
65D GLY* 3.2 12.0 + - - +
67D ARG* 1.3 78.4 - - + +
69D THR* 1.3 61.0 + - + +
71D ALA* 3.7 15.9 + - - +
72D GLN 3.8 5.9 + - - +
78D VAL* 4.1 26.7 - - + +
82D VAL* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLY* 2.9 19.3 + - - +
66D ARG* 3.2 12.1 + - - -
68D MET* 1.3 76.4 - - + +
70D ALA* 1.3 64.2 + - - +
71D ALA 3.2 0.9 - - - -
72D GLN 4.3 5.2 - - - -
73D PRO* 3.3 31.2 - - - +
75D GLU 5.6 2.5 - - - +
76D THR* 6.3 0.9 - - - -
78D VAL* 5.4 1.6 - - + -
79D GLY* 4.1 21.3 - - - +
83D ARG* 5.6 1.8 - - - +
351D LEU* 3.8 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA 4.6 6.6 - - - +
23D LYS* 4.5 7.6 - - - -
66D ARG 2.9 18.8 + - - +
67D ARG* 3.3 8.0 + - - +
69D THR* 1.3 75.4 + - - +
71D ALA* 1.3 64.5 + - - +
73D PRO* 4.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA* 5.0 4.3 - - - +
19D VAL* 3.7 36.6 - - + +
22D LEU* 4.2 10.5 - - + -
23D LYS* 3.4 30.1 - - + +
67D ARG 2.9 16.0 + - - +
68D MET* 3.7 9.6 - - - +
69D THR 3.2 0.4 - - - -
70D ALA* 1.3 79.6 - - - +
72D GLN* 1.3 62.6 + - - +
73D PRO* 4.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 4.5 11.7 + - - -
22D LEU* 3.0 37.7 + - + +
23D LYS 4.2 9.7 + - - -
24D ARG 5.5 1.6 + - - -
25D GLY* 5.1 4.4 + - - -
68D MET 3.8 6.7 + - - +
69D THR* 3.5 7.4 + - - +
71D ALA* 1.3 80.3 + - - +
73D PRO* 1.3 76.6 - - - +
74D SER* 3.5 15.3 + - - +
75D GLU* 3.3 44.8 - - + +
78D VAL* 5.4 0.2 - - - +
287D LYS* 3.8 17.8 - - - +
----------------------------------------------------------
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