Contacts of the helix formed by residues 62 - 80 (chain B) in PDB entry 2VGL
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LYS* 4.0 22.2 - - + +
28B GLU* 4.5 2.0 + - - -
31B LYS* 3.4 27.2 - - - +
60B THR* 2.8 31.6 + - - +
61B ASP* 1.3 94.9 + - - +
63B LEU* 1.3 73.8 + - - +
64B GLU* 3.2 6.4 + - - +
65B LEU* 3.1 25.0 + - + -
66B LYS* 3.5 9.2 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASP 3.6 4.4 + - - +
62B ASN* 1.3 74.8 + - - +
64B GLU* 1.3 69.7 + - - +
65B LEU 3.0 1.5 + - - -
66B LYS* 3.1 2.7 + - + +
67B LYS* 2.9 28.5 + - + +
99B ASN* 3.6 23.3 - - + +
101B LEU* 3.8 25.4 - - + -
102B ILE* 3.0 42.8 - - + -
134M THR* 5.5 9.2 - - + +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 2.7 39.7 + - + +
35B LYS* 3.8 15.2 + - - -
62B ASN* 3.2 8.6 + - - +
63B LEU* 1.3 78.5 - - - +
65B LEU* 1.3 58.1 + - - +
67B LYS* 3.5 2.1 + - - +
68B LEU* 3.0 28.5 + - + +
134M THR* 3.5 36.6 - - + +
135M GLN* 3.0 37.5 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.2 16.2 - - + -
30B ARG* 3.6 32.1 - - + +
31B LYS* 4.2 33.6 - - + +
34B VAL* 4.7 5.2 - - + -
57B CYS* 3.5 35.2 - - + +
60B THR* 3.8 12.3 - - + +
62B ASN* 3.1 22.6 + - + +
63B LEU 3.0 0.6 - - - -
64B GLU* 1.3 74.6 - - - +
66B LYS* 1.3 65.4 + - - +
68B LEU* 3.5 4.9 + - + +
69B VAL* 3.2 22.2 + - + +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MET* 3.4 37.1 + - + +
60B THR* 4.0 20.3 + - + +
61B ASP 5.4 1.1 - - - +
62B ASN 3.5 13.0 + - - +
63B LEU* 3.1 4.6 + - + +
65B LEU* 1.3 77.1 - - - +
67B LYS* 1.3 59.5 + - - +
69B VAL* 3.2 8.1 + - - +
70B TYR* 3.0 41.2 + - + -
94B ASP* 3.3 27.5 + - - -
97B ASP* 3.3 24.2 + - - -
102B ILE* 4.3 24.3 - - + +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 2.9 20.1 + - + +
64B GLU 3.5 5.2 - - - +
66B LYS* 1.3 77.1 - - - +
68B LEU* 1.3 56.0 + - + +
70B TYR* 3.3 3.6 + - - +
71B LEU* 3.0 40.9 + - + +
102B ILE* 5.5 0.6 - - + +
105B LEU* 2.9 44.8 - - + +
108B ARG* 3.5 16.6 - - - +
110M GLU* 2.9 46.9 + - - +
113M ASP* 5.3 0.2 - - - +
114M GLU* 4.6 2.8 + - - -
132M PHE* 3.9 15.2 + - - +
134M THR* 3.6 13.0 - - - +
135M GLN* 6.0 1.3 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 3.5 38.6 - - + +
34B VAL* 3.9 12.7 - - + +
35B LYS* 4.0 13.2 - - + +
38B ILE* 3.9 14.2 - - + +
64B GLU* 3.0 25.7 + - + +
65B LEU* 3.6 6.3 - - + +
66B LYS 3.3 0.4 - - - -
67B LYS* 1.3 72.9 - - + +
69B VAL* 1.3 67.1 + - - +
71B LEU* 3.2 18.0 + - + +
72B TYR* 3.2 12.3 + - - +
106M VAL* 3.4 33.7 - - + -
135M GLN* 3.4 23.8 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 4.4 5.8 - - + -
54B VAL* 3.5 38.1 - - + +
55B VAL* 4.5 1.6 - - - -
57B CYS* 3.8 17.9 - - + -
58B MET* 3.6 28.9 - - + +
65B LEU* 3.2 17.3 + - + +
66B LYS 3.6 5.4 - - - +
68B LEU* 1.3 76.6 - - - +
70B TYR* 1.3 64.2 + - - +
72B TYR* 3.2 8.7 + - - +
73B LEU* 3.0 38.4 + - + +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B MET* 3.0 33.5 - - + +
66B LYS* 3.0 33.6 + - + +
67B LYS 3.4 9.4 - - - +
68B LEU 3.1 0.2 - - - -
69B VAL* 1.3 76.9 - - - +
71B LEU* 1.3 64.8 + - + +
73B LEU* 2.9 6.6 + - + +
74B MET* 2.9 28.0 + - + +
91B PHE* 3.3 31.5 - + - -
94B ASP* 3.6 13.4 - - - +
102B ILE* 5.4 2.2 - - + -
105B LEU* 3.4 48.2 - - + -
106B ALA* 3.2 24.8 - - + +
109B THR* 3.5 19.5 - - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.2 10.1 - - + -
67B LYS* 3.0 43.0 + - + +
68B LEU* 3.2 11.6 + - + +
70B TYR* 1.3 75.8 - - + +
72B TYR* 1.3 61.1 + - - +
74B MET* 3.6 6.4 - - - +
75B ASN* 3.2 29.6 + - - +
105B LEU* 5.4 1.3 - - + -
18M ARG* 4.4 2.2 + - - +
106M VAL* 3.5 41.3 - - + +
109M TYR* 4.4 10.9 - - + +
110M GLU* 3.8 30.1 - - + +
113M ASP* 4.0 18.6 - - + +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 4.8 1.8 - - + -
37B VAL* 3.4 32.3 - - + -
38B ILE* 4.3 10.5 - - + +
41B MET* 3.5 28.2 - - + +
47B VAL* 3.5 21.3 + - + -
51B PHE* 3.7 34.6 - + - +
54B VAL* 3.6 35.1 - - + +
55B VAL 5.7 0.2 - - - -
68B LEU 3.2 9.6 + - - +
69B VAL 3.2 8.5 + - - +
70B TYR 3.1 0.4 - - - -
71B LEU* 1.3 75.0 - - - +
73B LEU* 1.3 75.5 + - + +
75B ASN* 3.2 23.8 + - - +
76B TYR* 3.3 27.9 + + - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.5 37.5 - - + -
55B VAL* 4.3 7.6 - - + -
58B MET* 4.0 16.2 - - - -
69B VAL* 3.0 37.4 + - + +
70B TYR* 2.9 9.6 + - - +
72B TYR* 1.3 82.9 - - + +
74B MET* 1.3 58.9 + - - +
76B TYR* 2.9 24.1 + - - +
77B ALA* 3.1 8.5 + - - +
84B ALA* 4.0 15.9 - - + +
87B ALA* 4.3 12.8 - - + -
91B PHE* 4.2 27.1 - - + -
109B THR* 5.1 2.5 - - + -
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 2.9 16.1 + - + +
71B LEU* 3.6 6.7 - - - +
73B LEU* 1.3 74.2 - - - +
75B ASN* 1.3 60.6 + - - +
77B ALA* 3.1 51.3 + - + +
78B LYS 4.4 1.4 + - - -
108B ARG* 5.5 6.5 - - - -
109B THR* 3.6 41.6 - - + +
112B CYS* 3.3 33.7 - - + -
18M ARG* 3.4 21.4 + - - +
113M ASP* 3.4 29.6 - - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.7 24.0 - - - +
41B MET* 3.3 35.8 - - + +
71B LEU 3.2 17.3 + - - +
72B TYR* 3.2 8.6 + - - +
74B MET* 1.3 75.1 - - - +
76B TYR* 1.3 60.5 + - - +
77B ALA 3.2 0.9 + - - -
79B SER* 3.0 24.6 + - - -
18M ARG* 2.7 27.6 + - - +
109M TYR* 3.6 24.0 - - - -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET* 3.3 22.9 - - + -
46B ASP* 5.1 0.2 + - - -
47B VAL* 3.5 10.9 + - - +
48B SER* 3.1 31.0 + - - -
51B PHE* 3.7 21.1 - + - -
72B TYR* 3.3 31.1 + + - -
73B LEU* 2.9 11.5 + - - +
75B ASN* 1.3 81.2 - - - +
77B ALA* 1.3 63.7 + - - +
78B LYS 3.8 0.2 - - - -
79B SER* 3.9 6.3 - - - -
80B GLN* 2.9 61.0 + - + +
81B PRO* 3.8 1.4 - - - +
83B MET* 3.5 25.6 - - + -
84B ALA* 3.8 16.3 - - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU 3.1 5.0 + - - +
74B MET* 3.1 47.5 + - + +
75B ASN 3.2 0.2 - - - -
76B TYR* 1.3 80.2 - - - +
78B LYS* 1.3 63.1 + - + +
81B PRO* 3.4 20.4 - - - +
84B ALA* 4.1 8.7 - - + -
112B CYS* 3.8 21.1 - - + +
113B ILE* 4.7 8.8 - - + +
114B ARG 5.0 0.5 + - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET 4.4 2.0 + - - -
75B ASN 4.6 0.4 + - - -
77B ALA* 1.3 79.6 - - + +
79B SER* 1.3 69.2 + - - +
81B PRO* 3.4 11.9 - - - +
111B GLY 5.2 1.6 + - - -
112B CYS* 3.4 34.7 + - + +
113B ILE 4.9 0.6 + - - -
114B ARG* 4.2 10.9 - - + +
19M VAL* 3.1 44.9 - - + +
20M TYR* 4.0 22.0 + - - +
22M ASP* 3.1 41.0 + - - +
118M PHE* 5.6 4.2 - - - -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN 3.0 24.2 + - - -
76B TYR* 4.1 7.4 - - - -
77B ALA 3.3 1.2 - - - -
78B LYS* 1.3 82.7 - - - +
80B GLN* 1.3 73.6 + - - +
81B PRO* 3.5 2.8 - - - +
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 5.8 1.2 + - - -
48B SER* 5.4 5.5 - - - -
76B TYR* 2.9 40.5 + - + +
79B SER* 1.3 86.5 + - - +
81B PRO* 1.3 66.0 - - - +
82B ASP* 3.3 5.2 - - + +
83B MET* 3.0 39.5 + - + +
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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
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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) + - + + + + + -
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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