Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 1OVM
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 VAL 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A SER 5.2 2.0 - - - +
59A ALA* 3.9 27.1 - - + +
60A ASP* 3.9 22.4 - - - +
63A ALA* 4.3 1.3 - - + -
69A ALA* 3.4 6.5 - - + +
71A LEU* 4.3 5.6 - - + -
86A ILE* 4.2 19.7 - - + +
89A SER* 3.6 25.8 - - - +
94A VAL* 2.9 14.7 + - + +
95A PRO* 1.3 77.5 - - - +
97A LEU* 1.3 71.1 + - - +
98A HIS 3.7 0.5 + - - -
156A MET* 4.3 1.8 - - - -
162A PRO* 3.1 8.8 - - + +
163A GLY 3.0 21.6 + - - +
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Residues in contact with LEU 97 (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 LEU* 4.4 0.9 - - + -
15A LEU* 3.5 32.1 - - + -
68A PHE* 4.1 6.0 - - + -
69A ALA 2.8 16.3 + - - +
70A ALA* 3.3 2.6 - - + -
71A LEU* 2.7 34.8 + - - +
95A PRO 4.2 0.6 - - - -
96A VAL* 1.3 72.3 - - - +
98A HIS* 1.3 66.1 + - - +
99A ILE* 3.9 17.7 - - + -
152A VAL* 4.5 0.2 - - + -
153A LEU* 3.8 13.7 - - + -
156A MET* 3.2 30.9 - - + -
163A GLY 3.7 11.0 - - - +
165A LEU* 4.0 29.8 - - + -
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Residues in contact with HIS 98 (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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71A LEU* 3.6 19.3 - - + -
73A THR* 2.8 31.2 + - - +
79A GLU* 3.7 34.7 - - + +
82A ALA* 4.2 11.0 - - + -
83A MET* 6.1 2.2 - - + +
86A ILE* 3.8 29.0 - - + +
96A VAL 3.7 0.2 + - - -
97A LEU* 1.3 72.9 - - - +
99A ILE* 1.3 71.6 + - - +
100A VAL* 4.0 2.1 + - + +
130A SER* 5.0 2.6 + - - -
134A THR* 5.9 0.2 - - + -
163A GLY 2.9 17.1 + - - +
164A TYR* 3.5 24.3 - + + -
165A LEU 2.9 26.2 + - - +
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Residues in contact with ILE 99 (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 LEU* 4.0 31.2 - - + -
15A LEU* 4.4 10.8 - - + -
23A LEU* 4.3 23.3 - - + -
34A PHE* 4.5 11.9 - - + -
70A ALA* 4.7 1.1 - - + -
71A LEU 2.7 13.9 + - - +
72A LEU* 3.2 17.7 - - + +
73A THR 2.9 24.1 + - - -
97A LEU* 3.9 26.9 - - + -
98A HIS* 1.3 76.7 - - - +
100A VAL* 1.3 63.5 + - - +
165A LEU* 3.5 11.7 - - + +
167A LEU* 4.4 18.8 - - + -
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Residues in contact with VAL 100 (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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73A THR* 3.3 13.7 - - - +
74A THR 3.9 3.6 - - - +
75A PHE* 3.6 35.2 - - + +
79A GLU* 3.7 14.1 - - + +
98A HIS* 4.5 2.2 - - - +
99A ILE* 1.3 77.4 - - - +
101A GLY* 1.3 66.5 + - - +
102A ALA* 3.5 1.2 + - + -
164A TYR* 3.2 42.6 - - + +
165A LEU 3.0 11.4 + - - +
166A MET* 3.7 6.2 - - + +
167A LEU 2.9 25.9 + - - -
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Residues in contact with GLY 101 (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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30A TYR* 3.6 23.8 - - - +
31A ASN* 4.1 11.9 - - - -
72A LEU* 4.3 4.1 - - - +
73A THR 3.0 12.8 + - - -
74A THR 3.9 0.2 - - - -
75A PHE* 3.0 27.4 + - - +
99A ILE* 4.2 1.2 - - - -
100A VAL* 1.3 71.5 - - - +
102A ALA* 1.3 57.4 + - - -
167A LEU* 3.5 10.5 - - - -
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Residues in contact with ALA 102 (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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30A TYR* 3.8 8.4 + - - +
75A PHE* 3.9 9.6 - - + -
100A VAL* 4.3 0.4 - - + +
101A GLY* 1.3 74.3 - - - +
103A PRO* 1.3 73.7 - - + +
108A GLN* 3.8 10.5 - - - +
166A MET* 3.7 30.3 - - + -
167A LEU 3.0 11.0 + - - +
168A PRO* 4.2 1.8 - - + -
169A ALA* 2.9 29.8 + - - +
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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