Contacts of the helix formed by residues 86 - 96 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.8 0.2 - - - -
83A SER* 3.1 20.0 + - - +
84A LEU 3.6 0.2 - - - -
85A VAL* 1.3 79.6 - - - +
87A PRO* 1.3 64.8 - - - +
88A ALA* 3.1 7.0 + - - +
89A SER* 2.8 49.2 + - - -
90A PHE* 3.3 4.9 + - - +
129A LEU* 5.2 0.2 - - - -
137A ILE* 5.1 0.9 - - - -
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.7 8.3 - - - +
86A SER* 1.3 84.8 - - - +
88A ALA* 1.3 51.3 + - - +
90A PHE* 3.1 3.3 + - - +
91A GLU* 2.8 47.4 + - - +
129A LEU* 3.8 12.1 - - + -
134A LEU* 4.0 35.7 - - + -
135A ALA 3.5 24.5 - - - +
137A ILE* 4.2 18.4 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.2 1.3 - - - +
86A SER* 3.1 6.9 - - - +
87A PRO* 1.3 78.9 - - - +
89A SER* 1.3 57.7 + - - +
91A GLU* 3.4 8.3 + - - +
92A ASN* 3.0 37.7 + - - +
134A LEU* 6.0 0.2 - - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.4 20.4 + - - -
12A GLY 5.5 0.2 - - - -
14A VAL* 3.6 26.9 - - - -
81A CYS 5.0 0.7 - - - +
82A PHE* 3.6 9.6 - - - +
83A SER 2.9 23.3 + - - -
86A SER* 2.8 31.0 + - - -
88A ALA* 1.3 77.8 - - - +
90A PHE* 1.3 60.2 + - - +
92A ASN* 3.3 11.3 + - - +
93A VAL* 3.4 9.7 + - - +
97A TRP* 4.9 2.1 - - - -
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.4 50.0 - + + -
86A SER 3.9 4.5 - - - +
87A PRO 3.1 8.7 + - - +
89A SER* 1.3 76.8 + - - +
91A GLU* 1.3 82.4 + - - +
92A ASN 3.0 1.3 - - - -
93A VAL* 3.0 21.3 + - + +
94A ARG* 6.0 0.2 - - - -
137A ILE* 3.5 36.6 - - + -
141A GLN* 3.7 18.6 - - + -
142A GLY* 4.2 3.8 - - - -
145A MET* 3.5 51.0 - - + +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PRO* 2.8 38.0 + - - +
88A ALA* 3.7 8.5 - - - +
90A PHE* 1.3 91.0 - - - +
92A ASN* 1.3 59.9 + - - +
94A ARG* 3.3 33.9 + - - +
95A ALA* 3.1 24.3 + - + +
137A ILE* 5.2 1.0 - - - +
145A MET* 4.8 2.5 - - - -
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 2.7 39.7 + - - +
88A ALA* 3.0 20.0 + - - +
89A SER 3.6 5.2 - - - +
90A PHE 3.0 0.6 - - - -
91A GLU* 1.3 74.8 - - - +
93A VAL* 1.3 60.2 + - - +
94A ARG 3.3 0.2 - - - -
95A ALA* 3.8 16.5 - - - +
96A LYS* 2.9 31.2 + - + +
97A TRP* 3.0 16.4 + - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.0 20.0 - - + -
81A CYS 4.7 1.6 - - - +
82A PHE* 3.9 20.9 - - + -
89A SER 3.4 11.0 + - - +
90A PHE* 3.0 16.8 + - + +
92A ASN* 1.3 76.2 - - - +
94A ARG* 1.3 59.6 + - - +
97A TRP* 4.2 8.1 - - + -
98A TYR* 3.0 34.6 + - + +
112A LEU* 3.8 25.8 - - + -
145A MET* 3.9 18.6 - - + -
149A ILE* 4.0 17.5 - - + -
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 4.0 0.8 + - - -
91A GLU* 3.3 38.1 + - - +
92A ASN 3.3 0.2 - - - -
93A VAL* 1.3 81.0 - - - +
95A ALA* 1.3 64.8 + - - +
98A TYR* 4.9 5.6 - - - +
99A PRO* 3.3 21.2 - - - +
145A MET* 3.8 28.9 - - + +
148A GLU* 2.9 39.6 + - - +
149A ILE* 5.2 3.4 - - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU* 3.1 16.2 + - + +
92A ASN* 3.9 15.3 - - - +
94A ARG* 1.3 83.1 - - + +
96A LYS* 1.3 59.4 + - + +
99A PRO* 4.0 8.2 - - - +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 5.3 1.6 - - - +
60A GLY 5.2 0.6 + - - -
62A GLU* 4.1 21.6 + - - +
65A ASP* 2.8 38.6 + - - -
68A ARG* 4.3 1.4 - - - +
92A ASN* 2.9 21.3 + - + +
94A ARG 3.4 0.6 - - - -
95A ALA* 1.3 80.4 - - - +
97A TRP* 1.3 97.7 + - + +
99A PRO* 3.4 7.7 - - - +
100A GLU* 3.1 42.1 + - - +
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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