Contacts of the helix formed by residues 96 - 105 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G ASP* 5.1 2.2 - - - +
60G GLY 5.0 1.4 + - - -
62G GLU* 3.5 20.4 + - - +
65G ASP* 2.9 36.9 + - - -
68G ARG* 4.3 0.6 - - - +
92G ASN* 2.8 26.6 + - + +
94G ARG 3.5 0.4 - - - -
95G ALA* 1.3 75.2 - - + +
97G TRP* 1.3 97.1 + - + +
99G PRO* 3.5 4.7 - - - +
100G GLU* 3.0 45.5 + - + +
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Residues in contact with TRP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.9 15.3 - - + -
10G GLY* 3.3 37.9 - - - -
11G ASP* 2.8 33.5 + - - +
59G ALA 4.5 0.4 - - - -
60G GLY 4.4 6.7 - - - -
68G ARG* 3.6 51.6 - - - -
72G TYR* 4.9 1.1 - - - -
80G ILE* 3.5 29.4 - - + -
81G CYS 5.0 1.3 - - - -
89G SER 4.9 2.0 - - - -
92G ASN* 3.0 33.9 + - + +
93G VAL* 3.9 7.4 - - + +
96G LYS* 1.3 96.7 - - + +
98G TYR* 1.3 60.9 + - - +
100G GLU* 3.8 8.5 - - + +
101G VAL* 2.9 35.6 + - + +
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Residues in contact with TYR 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY 4.9 1.4 + - - -
31C GLU* 3.0 45.0 + - + +
33C ILE* 5.2 3.1 - - - +
80G ILE* 4.1 11.1 - - + +
93G VAL 2.9 22.1 + - - +
94G ARG* 4.6 5.8 - - + +
97G TRP* 1.3 69.8 - - - +
99G PRO* 1.3 79.7 - - + +
101G VAL* 5.0 0.7 - - - -
102G ARG* 3.0 57.9 + - + +
110G ILE* 4.6 4.9 - - + -
148G GLU 4.8 3.7 + - - -
149G ILE* 3.4 55.6 - - + -
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Residues in contact with PRO 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ARG 3.2 27.4 - - - +
95G ALA 3.8 13.5 - - - +
96G LYS 3.5 12.8 - - - +
98G TYR* 1.3 100.6 - - + +
100G GLU* 1.3 61.6 + - - +
102G ARG* 3.8 3.2 - - + +
103G HIS* 2.9 25.9 + - - +
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ASP* 4.6 3.2 - - - +
68G ARG* 3.1 33.5 + - - +
69G PRO* 4.3 8.0 - - - +
72G TYR* 2.7 34.5 + - + +
96G LYS* 3.0 34.7 + - + +
97G TRP* 3.8 10.3 - - + +
98G TYR 3.2 0.2 - - - -
99G PRO* 1.3 79.2 - - - +
101G VAL* 1.3 63.4 + - - +
103G HIS* 3.4 7.4 + - - +
104G HIS* 3.1 30.2 + - + +
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 4.0 20.2 - - + -
72G TYR* 4.4 16.2 - - - +
78G PHE* 3.6 53.6 - - + -
80G ILE* 4.5 8.3 - - + -
97G TRP* 2.9 23.3 + - + +
98G TYR 4.3 1.1 - - - +
100G GLU* 1.3 71.9 - - + +
102G ARG* 1.3 57.4 + - - +
104G HIS* 3.0 5.2 + - - +
105G CYS* 2.7 33.4 + - - +
110G ILE* 4.2 17.9 - - + -
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Residues in contact with ARG 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA* 6.0 0.8 - - - +
98G TYR* 3.0 52.2 + - + +
99G PRO* 4.1 3.4 - - + +
101G VAL* 1.3 78.3 - - - +
103G HIS* 1.3 63.0 + - - +
104G HIS 3.3 0.5 + - - -
105G CYS 2.9 18.4 + - - -
106G PRO* 3.1 48.2 + - + +
107G HIS* 3.5 9.2 + - - +
108G THR* 2.7 37.2 + - - +
109G PRO* 4.8 0.6 - - - +
110G ILE* 3.4 31.0 - - + +
149G ILE 4.7 1.4 + - - -
150G GLY* 4.1 16.2 + - - -
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Residues in contact with HIS 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PRO 2.9 18.1 + - - +
100G GLU* 3.5 8.1 - - - +
102G ARG* 1.3 76.4 - - - +
104G HIS* 1.3 84.1 + + + +
106G PRO* 5.1 3.1 - - - +
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Residues in contact with HIS 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G PRO* 3.7 35.6 - - + +
72G TYR* 3.6 31.5 - + + -
73G PRO* 6.4 0.4 - - + -
100G GLU* 3.1 24.8 + - + -
101G VAL 3.0 4.0 + - - +
103G HIS* 1.3 101.7 - + - +
105G CYS* 1.3 65.8 + - - +
106G PRO* 3.6 8.5 - - - +
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Residues in contact with CYS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G TYR* 3.7 27.6 - - - -
73G PRO* 5.4 1.1 - - - -
74G GLN 5.6 1.1 - - - -
75G THR* 4.8 2.5 - - - -
78G PHE* 3.6 33.9 - - + -
101G VAL* 2.7 18.3 + - + +
102G ARG* 2.9 25.1 + - - -
104G HIS* 1.3 80.8 - - - +
106G PRO* 1.3 60.8 - - - +
107G HIS 3.3 3.1 - - - -
108G THR* 3.4 21.8 - - - +
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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