Contacts of the helix formed by residues 67 - 81 (chain B) in PDB entry 3VOD
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 ASP 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 5.7 0.8 - - + +
70A ALA* 4.1 28.1 - - + +
61B LYS* 4.9 3.1 - - - +
66B VAL* 1.3 74.9 - - - +
68B LEU* 1.3 59.8 + - - +
69B GLY* 3.1 22.3 + - - -
70B ALA* 3.5 18.3 + - + +
71B LEU* 3.0 30.7 + - - +
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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
----------------------------------------------------------
57B PRO* 4.1 32.3 - - + +
58B VAL* 4.6 7.6 - - + +
61B LYS* 3.8 35.5 - - + +
66B VAL 3.5 2.2 + - - -
67B ASP* 1.3 73.4 + - - +
69B GLY* 1.3 58.5 + - - +
71B LEU* 3.5 7.2 + - + +
72B THR* 2.6 50.3 + - - +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 3.1 10.3 + - - -
68B LEU* 1.3 78.5 - - - +
70B ALA* 1.3 63.6 + - - +
72B THR* 3.2 7.7 + - - -
73B ARG* 3.1 30.4 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 4.2 28.6 + - + -
66B VAL* 6.3 1.1 - - + -
67B ASP* 3.5 19.5 + - + +
68B LEU 3.5 0.2 - - - -
69B GLY* 1.3 74.2 - - - +
71B LEU* 1.3 57.8 + - - +
73B ARG* 3.4 12.5 + - - +
74B MET* 3.0 30.7 + - + +
77B ARG* 5.5 0.3 + - - -
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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
----------------------------------------------------------
45B VAL* 4.1 26.7 - - + -
57B PRO* 3.7 24.9 - - + +
60B LEU* 4.1 17.3 - - + +
61B LYS* 3.8 25.4 - - + +
64B LEU* 4.1 10.3 - - + -
66B VAL* 4.4 13.0 - - + -
67B ASP 3.0 18.8 + - - +
68B LEU* 3.7 9.0 - - + +
69B GLY 3.2 0.2 - - - -
70B ALA* 1.3 78.5 - - - +
72B THR* 1.3 51.5 + - - +
74B MET* 3.4 7.6 + - + +
75B LEU* 2.8 43.9 + - + +
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 5.3 5.0 - - + +
68B LEU* 2.6 39.4 + - - +
69B GLY* 3.2 7.8 + - - -
71B LEU* 1.3 73.8 - - - +
73B ARG* 1.3 66.2 + - + +
75B LEU* 3.6 10.5 + - + +
76B ASP* 3.3 27.3 + - - +
86B ARG* 4.0 14.3 + - - +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 4.6 19.1 + - - -
69A GLY* 6.3 0.2 - - - -
69B GLY 3.1 19.4 + - - +
70B ALA* 3.7 10.1 - - - +
72B THR* 1.3 73.6 - - - +
74B MET* 1.3 61.6 + - - +
76B ASP* 3.1 10.1 + - - +
77B ARG* 3.0 49.4 + - - +
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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
----------------------------------------------------------
39B THR* 5.0 0.9 - - - +
41B ALA* 4.1 19.1 - - + +
42B GLN* 4.0 34.1 - - + +
45B VAL* 3.8 25.8 - - + -
70B ALA* 3.0 19.8 + - + +
71B LEU* 3.5 9.9 - - + +
73B ARG* 1.3 73.2 - - - +
75B LEU* 1.3 66.5 + - - +
77B ARG* 3.0 32.8 + - - +
78B LEU* 3.0 28.1 + - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.4 8.3 - - + -
49B ILE* 4.2 14.1 - - + -
57B PRO* 3.9 37.0 - - + -
60B LEU* 4.0 20.6 - - + -
71B LEU* 2.8 33.5 + - + +
72B THR* 3.7 7.9 - - + +
73B ARG 3.3 0.2 - - - -
74B MET* 1.3 73.4 - - - +
76B ASP* 1.3 57.1 + - - +
78B LEU* 3.6 7.4 + - + +
79B VAL* 2.9 32.6 + - + +
84B VAL* 4.6 5.2 - - + +
86B ARG* 3.5 19.5 - - - +
98B VAL* 4.1 22.2 - - + -
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.3 13.5 + - - +
73B ARG* 3.1 11.7 + - - +
74B MET 3.1 0.4 - - - -
75B LEU* 1.3 77.8 - - - +
77B ARG* 1.3 64.2 + - - +
79B VAL* 3.5 9.3 + - - +
80B SER* 3.2 25.5 + - - -
86B ARG* 2.9 28.5 + - - -
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Residues in contact with ARG 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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42B GLN* 4.3 23.6 - - - +
73B ARG* 3.0 32.6 + - - +
74B MET* 3.0 31.9 + - - +
76B ASP* 1.3 73.5 - - - +
78B LEU* 1.3 59.1 + - + +
80B SER* 3.1 23.6 + - - -
81B LYS* 3.1 22.8 + - + +
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Residues in contact with LEU 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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42B GLN* 4.3 24.9 - - + +
45B VAL* 3.7 32.5 - - + -
46B LEU* 4.3 10.8 - - + -
74B MET* 3.0 35.5 + - + +
75B LEU* 3.9 6.7 - - + +
77B ARG* 1.3 76.1 - - + +
79B VAL* 1.3 58.5 + - - +
80B SER 3.5 0.2 - - - -
81B LYS* 3.6 6.1 + - + -
82B GLY 3.4 2.6 + - - -
83B TRP* 2.9 59.8 + - + +
84B VAL* 3.2 24.4 + - + -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 2.9 26.8 + - + +
76B ASP* 3.7 16.4 - - - +
77B ARG 3.2 0.4 - - - -
78B LEU* 1.3 76.1 - - - +
80B SER* 1.3 64.4 + - - +
82B GLY* 3.1 13.7 + - - -
84B VAL* 3.2 31.5 - - + +
85B GLU* 4.9 5.4 - - - +
86B ARG* 4.5 15.5 - - + +
98B VAL* 6.2 0.2 - - + -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASP 3.2 12.4 + - - -
77B ARG* 3.1 11.8 + - - -
79B VAL* 1.3 77.0 - - - +
81B LYS* 1.3 62.0 + - - +
82B GLY* 3.1 1.3 + - - -
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Residues in contact with LYS 81 (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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37B ASP* 3.1 30.1 + - - +
42B GLN* 4.2 18.6 + - - +
77B ARG* 3.1 21.3 + - - +
78B LEU* 3.7 5.2 - - - +
79B VAL 3.3 0.2 - - - -
80B SER* 1.3 74.8 - - - +
82B GLY* 1.3 60.3 + - - +
83B TRP* 3.5 58.4 + - + -
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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