Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 3V62
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 LEU 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.2 32.3 - - + +
19B PHE* 3.7 28.0 - - + +
20B LYS* 4.1 14.5 - - + +
23B VAL* 3.4 32.8 - - + +
24B GLN* 2.7 23.7 + - - +
26B VAL* 3.5 27.4 - - + +
70B MET* 4.8 2.0 - - + +
71B ASP* 1.3 72.0 + - - +
73B THR* 1.3 60.3 + - - +
75B LEU* 3.9 11.4 - - + +
76B SER* 2.9 29.8 + - - -
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Residues in contact with THR 73 (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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20B LYS* 5.0 4.3 - - - +
24B GLN* 4.4 3.2 + - - +
71B ASP* 2.7 19.2 + - - -
72B LEU* 1.3 67.0 - - - +
74B SER* 1.3 69.5 + - - +
76B SER* 2.8 17.5 + - - -
77B LYS* 2.9 29.0 + - - +
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Residues in contact with SER 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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71B ASP* 3.2 22.0 + - - +
73B THR* 1.3 78.2 - - - +
75B LEU* 1.3 64.3 + - - +
77B LYS* 2.9 24.9 + - - +
78B ILE* 3.0 15.4 + - - +
116B LEU* 3.4 27.5 - - - +
117B LYS* 6.0 1.6 - - - -
302B NEQ 5.5 0.4 - - - +
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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
----------------------------------------------------------
12B PHE* 3.8 10.3 - - + -
16B ILE* 3.3 34.8 - - + -
28B PHE* 4.7 1.8 - - + -
70B MET* 3.8 24.2 - - + -
71B ASP 3.1 12.7 + - - +
72B LEU* 3.9 14.6 - - + +
74B SER* 1.3 78.9 - - - +
76B SER* 1.3 63.2 + - - +
78B ILE* 3.3 8.2 + - + +
79B LEU* 3.1 35.9 + - + +
99B ILE* 6.0 0.7 - - + -
101B LEU* 4.0 25.6 - - + -
116B LEU* 3.6 27.8 - - + +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 5.5 5.4 - - - +
16B ILE* 3.6 9.7 - - - +
17B ASP* 4.9 0.9 + - - -
20B LYS* 3.2 30.7 - - - +
72B LEU 2.9 17.7 + - - -
73B THR* 2.8 10.3 + - - -
75B LEU* 1.3 68.9 - - - +
77B LYS* 1.3 67.7 + - - +
79B LEU* 3.1 19.8 + - - +
80B ARG* 3.0 34.1 + - - +
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Residues in contact with LYS 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 THR* 2.9 29.1 + - - +
74B SER* 3.0 18.5 - - - +
76B SER* 1.3 77.5 - - - +
78B ILE* 1.3 60.5 + - - +
80B ARG* 3.2 29.7 + - - +
81B CYS 3.9 2.8 + - - -
302B NEQ 3.3 49.1 - - + +
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Residues in contact with ILE 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 SER 3.0 12.0 + - - +
75B LEU* 3.5 7.2 - - - +
77B LYS* 1.3 75.5 - - - +
79B LEU* 1.3 62.0 + - - +
80B ARG 3.4 0.5 + - - -
81B CYS* 3.5 14.4 + - - +
101B LEU* 3.7 31.9 - - + -
103B PHE* 3.8 21.7 - - + -
114B TYR* 4.0 21.1 - - + -
115B SER 3.5 24.9 - - - +
116B LEU* 3.7 30.7 - - + -
302B NEQ 4.2 26.0 - - + +
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Residues in contact with LEU 79 (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 ALA* 4.1 16.4 - - + +
12B PHE* 3.7 37.9 - - + -
13B LYS* 4.3 28.2 + - + +
16B ILE* 4.1 14.6 - - + -
75B LEU* 3.1 32.6 + - + +
76B SER* 3.1 12.0 + - - +
78B ILE* 1.3 74.8 - - - +
80B ARG* 1.3 64.5 + - - +
82B GLY* 3.2 19.6 + - - +
84B ASN* 5.4 2.3 - - - +
88B LEU* 4.3 3.1 - - + -
101B LEU* 5.0 4.0 - - + -
103B PHE* 4.1 21.3 - - + -
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Residues in contact with ARG 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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13B LYS* 5.3 18.1 - - - +
20B LYS* 5.0 9.5 - - - +
76B SER* 3.0 44.0 + - - -
77B LYS* 3.2 19.5 + - - +
79B LEU* 1.3 71.8 - - - +
81B CYS* 1.3 55.2 + - - +
82B GLY 2.7 25.1 + - - +
302B NEQ 5.5 2.7 - - + -
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Residues in contact with CYS 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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77B LYS 4.1 1.8 - - - -
78B ILE 3.5 8.7 + - - +
80B ARG* 1.3 74.9 - - - +
82B GLY* 1.3 54.3 + - - +
103B PHE* 4.7 0.2 - - - -
110B ARG* 5.8 2.3 + - - -
112B ALA* 4.9 4.0 - - - +
114B TYR* 3.2 39.2 + - + +
302B NEQ 1.7 56.3 - - - +
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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