Contacts of the helix formed by residues 86 - 96 (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 SER 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B SER* 3.0 20.5 + - - +
84B LEU 3.5 0.2 - - - -
85B VAL* 1.3 77.9 - - - +
87B PRO* 1.3 61.0 - - - +
88B ALA* 3.8 9.4 + - - +
89B SER* 2.8 54.5 + - - -
90B PHE* 3.1 5.3 + - - +
137B ILE* 4.9 0.9 - - - -
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Residues in contact with PRO 87 (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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85B VAL* 3.7 8.5 - - - +
86B SER* 1.3 86.7 - - - +
88B ALA* 1.3 55.8 + - - +
90B PHE* 3.4 9.4 + - + +
91B GLU* 3.0 34.4 + - - +
129B LEU* 3.8 13.5 - - + -
134B LEU* 4.0 25.1 - - + -
135B ALA 3.7 22.0 - - - +
137B ILE* 4.0 11.2 - - + -
107C HIS* 3.7 28.3 + - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 4.2 2.7 - - - +
86B SER* 3.1 9.1 + - - +
87B PRO* 1.3 77.7 - - - +
89B SER* 1.3 57.4 + - - +
91B GLU* 3.4 13.7 + - - +
92B ASN* 3.1 34.4 + - - +
134B LEU* 5.8 0.4 - - - +
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.2 21.8 + - - +
12B GLY 5.4 0.9 - - - -
14B VAL* 3.6 25.1 - - - -
81B CYS 4.9 1.4 - - - +
82B PHE* 3.4 10.5 - - - +
83B SER 3.0 23.7 + - - -
86B SER* 2.8 30.5 + - - -
88B ALA* 1.3 78.8 - - - +
90B PHE* 1.3 59.9 + - - +
92B ASN* 3.5 4.2 + - - +
93B VAL* 3.5 14.9 + - - +
97B TRP* 4.9 1.4 - - - -
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Residues in contact with PHE 90 (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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82B PHE* 3.4 48.5 - + + -
86B SER 3.1 4.9 + - - +
87B PRO 3.4 8.3 - - - +
88B ALA 3.2 0.2 - - - -
89B SER* 1.3 79.6 + - - +
91B GLU* 1.3 65.9 + - - +
93B VAL* 3.0 22.6 + - + +
137B ILE* 3.5 33.2 - - + -
141B GLN* 3.5 26.2 - - + -
142B GLY* 4.1 4.0 - - - -
145B MET* 3.6 36.5 - - + +
106C PRO* 3.8 32.3 - - + -
107C HIS* 4.2 11.0 - + + -
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Residues in contact with GLU 91 (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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87B PRO 3.0 16.7 + - - +
88B ALA* 3.6 13.0 - - - +
90B PHE* 1.3 75.1 - - + +
92B ASN* 1.3 60.0 + - - +
94B ARG* 3.2 8.7 + - - +
95B ALA* 3.0 25.1 + - + +
145B MET* 4.9 6.3 - - - -
106C PRO* 5.1 12.6 - - + +
107C HIS* 2.6 35.6 + - + +
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Residues in contact with ASN 92 (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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11B ASP* 2.8 42.2 + - - +
88B ALA* 3.1 20.1 + - - +
89B SER 3.8 3.4 - - - +
90B PHE 3.2 0.8 - - - -
91B GLU* 1.3 74.0 - - - +
93B VAL* 1.3 64.9 + - - +
94B ARG 3.2 0.4 - - - -
95B ALA* 3.8 16.0 - - - +
96B LYS* 2.9 25.9 + - + +
97B TRP* 3.0 15.7 + - - +
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Residues in contact with VAL 93 (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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80B ILE* 4.0 13.7 - - + -
81B CYS 4.8 1.1 - - - +
82B PHE* 3.9 17.9 - - + -
89B SER 3.5 12.6 + - - +
90B PHE* 3.0 17.4 + - + +
92B ASN* 1.3 76.9 - - - +
94B ARG* 1.3 57.4 + - - +
97B TRP* 4.2 7.6 - - + -
98B TYR* 2.9 34.0 + - - +
112B LEU* 3.7 34.3 - - + -
145B MET* 4.1 15.0 - - + -
149B ILE* 3.8 20.6 - - + -
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Residues in contact with ARG 94 (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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90B PHE 4.1 0.4 + - - -
91B GLU 3.2 7.3 + - - +
92B ASN 3.2 0.2 - - - -
93B VAL* 1.3 80.9 - - - +
95B ALA* 1.3 65.7 + - - +
96B LYS 3.3 0.4 - - - -
98B TYR* 4.5 11.1 - - + +
99B PRO* 3.3 19.2 - - - +
145B MET* 4.0 19.4 - - + +
148B GLU* 3.4 43.6 + - + +
149B ILE* 4.8 4.7 - - + -
102C ARG 4.2 1.0 + - - -
103C HIS* 2.7 40.1 + - - +
104C HIS 4.6 2.6 + - - -
106C PRO* 3.6 21.8 - - - +
1203C CL 4.0 9.7 - - - +
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Residues in contact with ALA 95 (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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91B GLU* 3.0 16.7 + - + +
92B ASN* 3.9 14.1 - - - +
94B ARG* 1.3 81.8 - - - +
96B LYS* 1.3 59.8 + - + +
99B PRO* 3.8 9.3 - - - +
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Residues in contact with LYS 96 (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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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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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