Contacts of the helix formed by residues 96 - 105 (chain B) in PDB entry 2OV2
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 LYS 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 5.2 2.2 - - - +
60B GLY 5.0 1.2 + - - -
62B GLU* 3.7 20.6 + - - +
65B ASP* 2.8 34.9 + - - -
68B ARG* 3.8 6.3 - - - +
92B ASN* 2.9 26.0 + - + +
94B ARG 3.3 0.6 - - - -
95B ALA* 1.3 80.0 - - + +
97B TRP* 1.3 94.9 + - + +
98B TYR 3.5 1.6 - - - -
99B PRO* 3.4 4.6 - - - +
100B GLU* 3.0 40.7 + - + +
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Residues in contact with TRP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.0 15.9 - - + -
10B GLY* 3.3 41.3 - - - -
11B ASP* 2.8 35.7 + - - +
59B ALA 4.4 1.8 - - - -
60B GLY 4.4 5.8 - - - -
68B ARG* 3.6 52.3 - - - -
72B TYR* 5.0 1.1 - - - -
80B ILE* 3.8 25.8 - - + -
81B CYS 5.1 0.7 - - - -
89B SER 4.9 2.7 - - - -
92B ASN* 3.0 30.8 + - + +
93B VAL* 4.1 4.9 - - + +
96B LYS* 1.3 97.5 - - + +
98B TYR* 1.3 68.8 + - - +
100B GLU* 3.9 8.4 - - + +
101B VAL* 3.0 29.9 + - + +
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Residues in contact with TYR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.8 12.4 - - + +
93B VAL 2.9 17.9 + - - +
94B ARG* 4.5 8.3 - - + -
97B TRP* 1.3 77.2 - - - +
99B PRO* 1.3 70.7 - - + +
101B VAL* 3.9 1.3 - - - +
102B ARG* 3.0 62.7 + - + +
110B ILE* 4.3 9.2 - - + -
148B GLU* 4.7 4.9 + - + -
149B ILE* 3.1 60.0 + - + -
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Residues in contact with PRO 99 (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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94B ARG 3.3 24.2 - - - +
95B ALA 3.8 13.0 - - - +
96B LYS* 3.4 10.1 - - - +
98B TYR* 1.3 101.7 - - + +
100B GLU* 1.3 59.7 + - - +
102B ARG* 3.8 3.7 - - + +
103B HIS* 2.9 31.7 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 4.7 4.5 - - - +
68B ARG* 3.0 36.8 + - - +
69B PRO* 4.6 6.4 - - - +
72B TYR* 2.6 35.2 + - + +
96B LYS* 3.0 32.6 + - + +
97B TRP* 3.9 9.6 - - + +
98B TYR 3.4 0.2 - - - -
99B PRO* 1.3 77.4 - - - +
101B VAL* 1.3 65.6 + - + +
103B HIS* 3.3 7.8 + - - +
104B HIS* 3.1 30.5 + - + +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.1 18.2 - - + -
72B TYR* 4.4 15.7 - - - +
78B PHE* 3.8 51.8 - - + -
80B ILE* 4.6 4.0 - - + -
97B TRP* 3.0 21.2 + - + +
98B TYR 3.9 1.8 - - - +
100B GLU* 1.3 77.5 - - + +
102B ARG* 1.3 58.2 + - - +
104B HIS* 3.2 4.0 + - - +
105B CYS* 2.8 34.0 + - - +
110B ILE* 3.9 23.8 - - + -
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Residues in contact with ARG 102 (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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98B TYR* 3.0 49.0 + - + +
99B PRO* 4.2 4.3 - - + +
101B VAL* 1.3 78.8 - - - +
103B HIS* 1.3 66.9 + - - +
104B HIS 3.4 0.5 + - - -
105B CYS 3.0 22.5 + - - -
106B PRO* 3.2 46.7 + - - +
107B HIS* 4.7 2.6 + - - +
108B THR 2.8 32.5 + - - +
109B PRO* 4.6 1.4 - - - +
110B ILE* 3.8 26.6 - - + +
149B ILE 5.0 2.0 + - - -
150B GLY 4.4 14.5 + - - -
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Residues in contact with HIS 103 (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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99B PRO 2.9 19.2 + - - +
100B GLU* 3.5 7.9 - - - +
101B VAL 3.3 0.2 - - - -
102B ARG* 1.3 79.4 - - - +
104B HIS* 1.3 84.8 + + - +
106B PRO* 4.9 4.0 - - - +
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Residues in contact with HIS 104 (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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69B PRO* 3.6 37.6 - - + +
72B TYR* 3.5 34.7 - + + -
100B GLU* 3.1 26.2 + - + -
101B VAL 3.2 2.9 + - - +
103B HIS* 1.3 99.3 + + - +
105B CYS* 1.3 64.5 + - - +
106B PRO* 3.6 8.1 - - - +
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Residues in contact with CYS 105 (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 TYR* 3.5 35.0 - - - -
73B PRO* 5.3 1.1 - - - -
74B GLN 5.7 0.7 - - - -
75B THR* 4.7 2.2 - - - -
78B PHE* 3.8 27.1 - - + -
101B VAL 2.8 19.7 + - - +
102B ARG* 3.0 19.3 + - - -
104B HIS* 1.3 81.1 - - - +
106B PRO* 1.3 67.4 - - - +
107B HIS 3.1 3.3 + - - -
108B THR* 3.4 19.0 + - - +
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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