Contacts of the helix formed by residues 64 - 78 (chain B) in PDB entry 3VAS
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 GLY 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 3.3 22.0 - - - -
16B LEU* 4.0 3.3 + - - +
63B GLY* 1.3 71.9 - - - -
65B ALA* 1.3 59.8 + - - -
66B THR 3.4 2.2 - - - -
67B LEU* 3.3 3.2 + - - -
68B ASN* 2.9 34.7 + - - -
401B ADN 2.8 27.4 + - - -
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Residues in contact with ALA 65 (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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64B GLY* 1.3 72.3 - - - +
66B THR* 1.3 64.0 + - - +
68B ASN* 3.3 3.6 + - - +
69B THR* 3.2 24.9 + - - -
165B TYR* 5.0 1.8 - - - +
167B ALA* 4.1 11.0 - - + -
169B PHE* 3.8 32.1 - - + -
197B SER* 5.4 0.2 - - - +
302B ASP* 3.7 27.8 - - - +
401B ADN 3.1 18.1 + - - +
402B CL 3.9 1.0 - - + +
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Residues in contact with THR 66 (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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12B MET 3.4 27.3 + - - +
13B GLY* 4.2 3.6 - - - -
65B ALA* 1.3 77.0 - - - +
67B LEU* 1.3 58.8 + - - +
69B THR* 3.3 2.3 + - - -
70B VAL* 2.9 33.3 + - + +
85B TYR* 4.0 5.2 - - + -
165B TYR* 3.4 39.0 - - + +
167B ALA* 3.0 24.6 + - - +
170B VAL* 4.1 0.2 - - - +
402B CL 3.1 19.9 - - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 4.6 3.8 - - + -
62B ALA* 5.1 4.5 - - + -
63B GLY* 3.5 27.8 - - - +
64B GLY* 3.3 3.2 + - - +
65B ALA 3.3 0.4 - - - -
66B THR* 1.3 78.8 - - - +
68B ASN* 1.3 58.1 + - - +
70B VAL* 4.6 0.4 - - + +
71B LYS* 2.8 46.5 + - + +
85B TYR* 3.7 42.6 + - + +
98B ILE* 3.9 28.3 - - + -
102B CYS* 3.8 13.5 - - - -
107B LEU* 3.8 28.0 - - + -
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Residues in contact with ASN 68 (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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62B ALA 3.9 1.6 - - - +
63B GLY* 3.6 16.6 - - - -
64B GLY 2.9 20.5 + - - +
65B ALA 3.4 5.4 - - - +
67B LEU* 1.3 76.0 - - - +
69B THR* 1.3 60.5 + - - +
71B LYS* 3.5 16.0 - - - +
72B MET* 3.1 18.2 + - - +
302B ASP* 3.3 21.6 + - + -
338B PHE* 3.2 51.0 - - + +
401B ADN 3.0 27.3 + - - -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 3.2 7.9 + - - -
66B THR 3.7 2.0 - - - -
68B ASN* 1.3 78.6 - - - +
70B VAL* 1.3 58.5 + - - +
72B MET 3.2 1.7 + - - -
73B ILE* 2.9 40.1 + - + +
165B TYR* 3.5 51.9 + - + -
302B ASP* 2.9 28.2 + - - +
305B ALA* 4.1 0.7 - - + -
306B ALA* 3.3 27.6 - - - +
309B ILE* 4.7 0.2 - - + -
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Residues in contact with VAL 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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9B VAL* 5.1 4.0 - - + -
10B PHE 4.7 0.9 - - - -
11B GLY* 3.7 27.4 - - - +
66B THR* 2.9 26.2 + - + +
67B LEU* 4.1 4.3 - - - +
69B THR* 1.3 75.4 - - - +
71B LYS* 1.3 63.6 + - - +
73B ILE* 3.3 12.0 + - + +
74B GLN* 3.0 21.8 + - - +
83B CYS* 3.6 24.8 - - + -
84B SER 3.8 15.7 - - - +
85B TYR* 4.6 6.3 - - + -
107B LEU* 3.9 9.6 - - + -
165B TYR* 4.4 16.2 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 5.0 1.8 - - - +
62B ALA* 3.1 30.3 + - - +
67B LEU* 2.8 36.9 + - + +
68B ASN* 3.5 13.0 + - - +
70B VAL* 1.3 74.5 - - - +
72B MET* 1.3 60.6 + - - +
74B GLN* 3.4 9.8 - - - +
75B TRP* 2.9 26.9 + - - +
101B ASP* 3.4 20.5 + - - +
102B CYS* 5.9 2.2 - - - -
105B LEU* 3.8 29.2 - - + +
107B LEU* 4.2 18.6 - - + +
338B PHE* 3.7 30.4 + - - -
340B LEU* 4.0 10.5 - - + +
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Residues in contact with MET 72 (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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68B ASN 3.1 18.8 + - - +
69B THR 3.8 2.7 - - - +
71B LYS* 1.3 75.8 - - - +
73B ILE* 1.3 59.4 + - - +
75B TRP* 4.0 22.7 - - + -
76B ILE* 2.8 38.6 + - + +
303B ALA* 3.6 31.2 - - - +
306B ALA* 3.8 5.6 - - + -
328B ALA* 3.7 36.3 - - + +
331B TYR* 4.1 14.4 - - + -
332B ILE* 4.2 6.5 - - + -
338B PHE* 4.0 9.0 - - + -
340B LEU* 4.0 18.2 - - + -
346B TYR* 4.2 4.5 - - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.2 22.0 - - + -
69B THR* 2.9 34.8 + - + +
70B VAL* 3.5 12.6 - - + +
72B MET* 1.3 76.5 - - - +
74B GLN* 1.3 62.3 + - - +
76B ILE* 3.3 0.7 + - - +
77B ILE* 3.0 49.1 + - + +
83B CYS* 3.7 15.5 - - - -
165B TYR* 5.2 2.9 - - + -
306B ALA* 3.7 21.5 - - - +
309B ILE* 3.9 27.6 - - + -
310B ALA* 4.4 12.6 - - + -
313B ILE* 5.1 1.3 - - + -
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Residues in contact with GLN 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 VAL 3.0 13.4 + - - +
71B LYS* 3.4 12.3 - - - +
72B MET 3.2 0.2 - - - -
73B ILE* 1.3 78.6 - - - +
75B TRP* 1.3 62.0 + - - +
77B ILE* 3.5 3.3 + - - +
78B GLN* 3.1 22.9 + - - -
79B LYS 2.9 29.2 + - - -
80B PRO* 3.8 2.6 - - - +
81B PHE 3.7 0.4 - - - +
82B VAL* 3.2 8.9 + - - +
83B CYS* 2.9 42.6 + - + +
105B LEU* 3.2 25.6 + - + +
106B ASP* 3.4 21.6 + - - +
107B LEU* 4.4 6.3 - - + +
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Residues in contact with TRP 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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71B LYS 2.9 17.7 + - - +
72B MET* 3.2 14.3 + - + +
74B GLN* 1.3 80.7 - - - +
76B ILE* 1.3 69.8 + - + +
78B GLN* 3.7 8.2 + - - +
105B LEU* 4.0 24.7 - - + -
331B TYR* 3.7 24.9 - + - -
340B LEU* 3.8 28.6 - - + +
341B GLY 3.0 29.0 + - - -
342B SER 3.9 1.6 - - - -
343B ARG* 3.0 54.8 + - + +
346B TYR* 3.5 52.3 - + + -
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Residues in contact with ILE 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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72B MET* 2.8 36.9 + - + +
73B ILE 3.7 4.0 - - - +
75B TRP* 1.3 86.1 - - + +
77B ILE* 1.3 62.0 + - - +
78B GLN* 3.7 1.7 - - - +
306B ALA 4.2 1.8 - - - +
307B GLY* 3.9 30.7 - - - +
310B ALA* 3.8 13.7 - - + -
311B ASP* 5.2 2.5 - - - +
314B ARG* 3.7 24.9 + - - +
343B ARG* 2.7 38.0 + - - +
346B TYR* 4.0 26.2 - - + +
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Residues in contact with ILE 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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4B LEU* 3.6 31.9 - - + +
73B ILE* 3.0 34.3 + - + +
74B GLN* 4.2 3.1 - - - +
76B ILE* 1.3 73.9 - - - +
78B GLN* 1.3 65.9 + - - +
79B LYS* 3.0 18.3 + - + +
82B VAL* 4.4 25.4 - - + -
310B ALA* 4.1 18.6 - - + +
313B ILE* 4.3 8.5 - - + -
314B ARG* 4.1 27.0 + - - +
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Residues in contact with GLN 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 GLN* 3.1 17.1 + - - -
75B TRP* 3.7 3.8 + - - +
76B ILE 3.7 0.6 - - - +
77B ILE* 1.3 78.1 - - - +
79B LYS* 1.3 62.8 + - - +
80B PRO* 3.2 10.4 - - - +
106B ASP* 5.3 1.9 - - - +
343B ARG* 3.4 57.1 + - + +
344B ASP* 4.8 6.1 + - - -
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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
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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