Contacts of the helix formed by residues 45 - 71 (chain B) in PDB entry 2WLJ
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 SER 45 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 1.3 75.4 - - - +
46B TRP* 1.3 61.0 + - - +
47B PRO* 3.8 11.3 - - - +
48B VAL* 3.3 27.9 + - - +
49B PHE* 2.8 26.9 + - - +
134B ARG* 3.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 6.2 2.2 - - + -
45B SER* 1.3 70.1 - - - +
47B PRO* 1.4 61.4 - - + +
49B PHE* 2.8 31.3 + + - +
50B ILE* 2.7 53.5 + - + +
131B ILE* 4.1 16.2 - - + -
134B ARG* 3.2 54.7 + - + +
135B PHE* 3.2 42.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 3.5 12.8 - - - +
46B TRP* 1.4 95.1 - - + +
48B VAL* 1.3 58.2 + - + +
50B ILE* 3.4 10.4 + - + +
51B THR* 2.8 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.8 25.1 - - + -
45B SER* 3.1 22.2 + - - +
47B PRO* 1.3 78.9 - - + +
49B PHE* 1.3 66.9 + - - +
51B THR* 3.1 9.1 + - - -
52B LEU* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 6.1 1.3 - - + -
41B LEU* 3.4 31.0 - - + -
44B VAL* 4.1 6.7 - - + +
45B SER 2.8 16.3 + - - +
46B TRP* 2.8 29.1 + + - +
48B VAL* 1.3 71.5 - - - +
50B ILE* 1.3 68.2 + - + +
52B LEU* 3.2 6.7 + - - +
53B ILE* 3.0 57.0 + - + +
127B ALA* 4.7 2.2 - - - -
130B LEU* 3.9 31.2 - - + -
131B ILE* 3.8 28.3 - - + -
134B ARG* 3.7 26.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
122A LEU* 4.6 22.4 - - + -
46B TRP* 2.7 38.0 + - + +
47B PRO* 3.8 8.5 - - + +
49B PHE* 1.3 83.3 - - + +
51B THR* 1.3 57.2 + - - +
53B ILE* 3.5 5.4 + - + +
54B THR* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO 2.8 19.2 + - - -
48B VAL* 3.1 11.8 + - - -
50B ILE* 1.3 78.0 - - - +
52B LEU* 1.3 55.7 + - + +
54B THR* 3.3 6.0 + - - -
55B GLY* 2.7 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 6.2 1.8 - - + -
41B LEU* 4.5 24.2 - - + +
44B VAL* 4.7 9.4 - - + -
48B VAL* 3.0 36.9 + - + +
49B PHE* 3.2 8.9 + - - +
51B THR* 1.3 76.8 - - + +
53B ILE* 1.3 60.0 + - - +
55B GLY* 3.8 0.8 - - - -
56B LEU* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.8 11.2 - - + -
122A LEU* 4.4 24.0 - - + -
41B LEU* 5.0 7.0 - - + -
49B PHE* 3.0 54.0 + - + +
50B ILE* 3.8 7.2 - - + +
52B LEU* 1.3 74.1 - - - +
54B THR* 1.3 64.5 + - - +
56B LEU* 3.2 15.9 + - + +
57B TYR* 3.0 24.8 + - + +
126B VAL* 6.3 0.7 - - + -
127B ALA* 4.8 17.5 - - + -
130B LEU* 4.6 12.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
115A LEU* 6.1 4.0 - - + -
118A LEU* 3.2 31.1 - - + +
50B ILE* 2.8 33.2 + - - +
51B THR* 3.6 6.7 - - - +
53B ILE* 1.3 78.4 - - - +
55B GLY* 1.3 57.5 + - - +
57B TYR* 3.0 4.6 + - - +
58B LEU* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR 2.7 19.9 + - - -
52B LEU* 3.8 1.6 - - - -
54B THR* 1.3 69.2 - - - +
56B LEU* 1.3 65.9 - - - +
57B TYR 3.0 2.2 + - - -
58B LEU* 3.3 8.4 + - - +
59B VAL* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 2.8 18.3 + - - +
53B ILE* 3.7 13.2 - - + +
55B GLY* 1.3 78.0 - - - +
57B TYR* 1.3 55.8 + - - +
59B VAL* 4.1 8.5 - - + +
60B THR* 2.6 47.8 + - - +
126B VAL* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.2 45.4 + - + +
115A LEU* 5.8 0.2 - - - -
117A ALA* 3.7 12.8 - - - +
118A LEU* 3.9 39.0 - - + -
121A MET* 5.1 8.7 - - - -
53B ILE* 3.0 16.5 + - + +
54B THR* 3.3 5.8 - - - +
55B GLY 3.0 0.4 - - - -
56B LEU* 1.3 77.2 - - - +
58B LEU* 1.3 75.9 + - + +
60B THR* 3.6 3.7 + - - -
61B ASN* 3.2 39.7 + - - -
91B VAL* 4.0 10.0 - - + +
94B MET* 3.0 38.6 - - + -
95B ALA* 5.0 3.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
114A THR* 4.4 9.0 - - + -
54B THR* 2.9 32.5 + - + +
55B GLY* 3.8 7.2 - - - +
57B TYR* 1.3 95.4 - - + +
59B VAL* 1.3 60.2 + - + +
61B ASN* 3.1 4.9 + - - +
62B ALA* 2.8 28.7 + - - +
87B PHE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY* 2.9 23.0 + - - +
56B LEU* 4.1 9.2 - - + +
58B LEU* 1.3 77.1 - - + +
60B THR* 1.3 60.2 + - - +
62B ALA* 3.2 10.1 + - + +
63B LEU* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 2.6 38.1 + - - +
57B TYR* 4.1 5.2 - - - -
58B LEU 3.2 0.4 - - - -
59B VAL* 1.3 78.3 - - - +
61B ASN* 1.3 58.4 + - - +
63B LEU* 3.4 10.3 + - + +
64B PHE* 3.1 53.4 + - + -
94B MET* 4.6 15.0 - - - -
119B CYS* 5.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.2 29.6 + - - +
58B LEU* 3.1 4.5 + - - +
60B THR* 1.3 74.6 - - - +
62B ALA* 1.3 59.2 + - - +
64B PHE 3.2 0.3 + - - -
65B ALA* 2.8 32.1 + - - +
87B PHE* 3.6 25.3 - - + -
90B SER* 2.4 31.3 + - - +
91B VAL* 3.1 29.0 + - + +
94B MET* 3.5 28.2 - - - +
116B GLU* 3.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU 2.8 17.1 + - - +
59B VAL* 3.3 15.3 - - + +
61B ASN* 1.3 70.5 - - - +
63B LEU* 1.3 63.9 + - + +
65B ALA* 3.3 2.3 + - - +
66B LEU* 3.2 29.6 + - + +
83B PHE* 3.8 24.6 - - + -
87B PHE* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 2.9 30.6 + - + +
60B THR* 3.7 13.0 - - + +
61B ASN 3.1 0.4 - - - -
62B ALA* 1.3 78.6 - - + +
64B PHE* 1.3 64.0 + - + +
66B LEU* 3.3 18.8 + - + +
67B ALA* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.1 43.7 + - + +
61B ASN 3.2 0.2 + - - -
63B LEU* 1.3 77.3 - - + +
65B ALA* 1.3 64.0 + - - +
67B ALA* 3.0 6.8 + - + +
68B TYR* 2.9 35.3 + + + -
90B SER* 3.3 19.5 - - - +
94B MET* 5.6 1.1 - - - -
112B LEU* 3.9 27.8 - - + -
115B LEU* 4.2 15.3 - - + -
116B GLU* 3.5 53.6 - - + +
119B CYS* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN 2.8 20.4 + - - +
62B ALA 3.6 4.5 - - - +
63B LEU 3.2 0.4 - - - -
64B PHE* 1.3 72.6 - - - +
66B LEU* 1.3 63.5 + - - +
68B TYR* 3.3 5.5 + - - +
69B LEU* 3.0 26.5 + - - +
83B PHE* 3.8 16.4 - - + -
86B ALA* 3.5 16.5 - - + +
87B PHE* 3.5 31.2 - - + +
90B SER* 4.4 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.2 15.9 + - + +
63B LEU* 3.4 21.5 - - + +
65B ALA* 1.3 74.2 - - - +
67B ALA* 1.3 66.3 + - - +
69B LEU* 2.9 13.0 + - + +
70B ALA* 2.7 24.1 + - - +
83B PHE* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 3.0 13.6 + - - +
64B PHE* 3.0 14.6 + - + +
66B LEU* 1.3 74.9 - - - +
68B TYR* 1.3 65.3 + - - +
70B ALA* 3.0 25.6 + - - +
71B CYS* 3.2 9.9 - - - -
112B LEU* 4.0 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 2.9 35.2 + + + -
65B ALA* 3.6 9.9 - - - +
67B ALA* 1.3 75.9 - - - +
69B LEU* 1.3 63.0 + - - +
71B CYS* 3.1 12.9 + - - -
72B GLY 3.6 5.4 + - - +
74B VAL* 3.5 19.1 - - + +
75B ILE* 3.9 22.2 - - + -
86B ALA* 4.3 4.5 - - + -
89B PHE* 3.7 30.4 - + - -
90B SER* 4.4 3.1 - - - -
109B ALA* 3.7 25.1 - - + -
112B LEU* 3.5 30.2 - - + -
113B VAL* 3.2 27.9 + - - +
116B GLU* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 3.0 15.7 + - - +
66B LEU* 2.9 17.8 + - + +
68B TYR* 1.3 68.5 - - + +
70B ALA* 1.3 67.4 + - - +
71B CYS 3.0 1.8 - - - -
72B GLY* 2.8 29.0 + - - +
75B ILE* 5.6 2.7 - - + -
81B GLY* 3.7 39.0 - - - +
82B SER 3.9 12.6 - - - +
83B PHE* 4.0 19.7 - - + -
86B ALA* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU 2.7 14.4 + - - +
67B ALA* 3.1 18.2 - - - +
69B LEU* 1.3 73.2 - - - +
71B CYS* 1.3 60.5 + - - +
72B GLY 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA 3.2 16.6 - - - -
68B TYR* 3.1 3.6 + - - -
69B LEU 3.0 1.2 - - - -
70B ALA* 1.3 77.2 - - - +
72B GLY* 1.3 59.3 + - - +
73B ASP 4.0 0.3 + - - -
74B VAL* 3.5 31.3 - - + +
108B LEU* 4.0 33.1 - - + +
112B LEU* 3.9 21.3 - - - -
----------------------------------------------------------
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