Contacts of the strand formed by residues 96 - 102 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 5.1 2.0 - - - +
59C ALA* 4.0 24.7 - - + +
60C ASP* 3.9 26.0 - - - +
63C ALA* 4.3 1.1 - - + -
69C ALA* 3.4 6.1 - - + +
71C LEU* 4.3 5.6 - - + -
86C ILE* 4.2 18.9 - - + +
89C SER* 3.7 25.1 - - - +
94C VAL* 2.9 15.6 + - + +
95C PRO* 1.3 76.3 - - - +
97C LEU* 1.3 72.0 + - - +
98C HIS 3.7 0.3 + - - -
156C MET* 4.3 1.6 - - - -
162C PRO* 3.1 9.6 - - + +
163C GLY 3.1 20.9 + - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.4 0.7 - - + -
15C LEU* 3.5 31.9 - - + -
68C PHE* 4.1 5.8 - - + -
69C ALA 2.8 16.3 + - - +
70C ALA* 3.3 3.5 - - + +
71C LEU* 2.7 34.3 + - - +
95C PRO 4.1 0.4 - - - -
96C VAL* 1.3 73.6 - - - +
98C HIS* 1.3 64.8 + - - +
99C ILE* 3.9 19.1 - - + -
153C LEU* 3.9 14.4 - - + -
156C MET* 3.2 29.6 - - + -
163C GLY 3.7 11.0 - - - +
165C LEU* 4.0 30.3 - - + -
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Residues in contact with HIS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.6 20.2 - - + +
73C THR* 2.8 31.0 + - - +
79C GLU* 3.7 35.1 - - + +
82C ALA* 4.2 10.5 - - + -
83C MET* 6.1 2.0 - - + +
86C ILE* 3.8 29.2 - - + +
96C VAL 3.7 0.2 + - - -
97C LEU* 1.3 73.6 - - - +
99C ILE* 1.3 70.0 + - - +
100C VAL* 3.9 1.4 + - + +
130C SER* 5.0 2.6 + - - -
134C THR* 6.0 0.4 - - + -
163C GLY 2.9 16.3 + - - +
164C TYR* 3.5 23.2 - + + -
165C LEU 3.0 27.0 + - - +
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.8 34.8 - - + -
15C LEU* 4.4 8.7 - - + -
23C LEU* 4.4 22.4 - - + -
34C PHE* 4.5 12.1 - - + -
70C ALA* 4.8 0.9 - - + -
71C LEU 2.7 13.6 + - - +
72C LEU* 3.3 17.7 - - + +
73C THR 2.9 24.9 + - - -
97C LEU* 3.9 26.9 - - + +
98C HIS* 1.3 78.0 - - - +
100C VAL* 1.3 63.7 + - - +
101C GLY 5.0 0.2 - - - +
165C LEU* 3.5 12.6 - - + +
167C LEU* 4.4 18.2 - - + -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C THR* 3.3 13.2 - - - +
74C THR 4.0 2.9 - - - +
75C PHE* 3.6 27.1 - - + +
79C GLU* 3.7 15.3 - - + +
98C HIS* 4.6 2.0 - - - +
99C ILE* 1.3 78.1 - - - +
101C GLY* 1.3 74.8 + - - +
102C ALA* 3.5 1.9 + - + -
164C TYR* 3.3 40.6 - - + +
165C LEU 3.0 13.2 + - - +
166C MET* 3.7 5.3 - - + +
167C LEU 2.8 27.3 + - - -
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 3.6 23.5 - - - +
31C ASN* 4.2 11.2 - - - -
72C LEU* 4.4 4.0 - - - +
73C THR 3.0 13.3 + - - -
74C THR* 5.0 0.2 - - - -
75C PHE* 2.9 27.7 + - - +
99C ILE* 4.2 1.0 - - - -
100C VAL* 1.3 70.9 - - - +
102C ALA* 1.3 58.0 + - - -
167C LEU* 3.5 9.9 - - - -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 3.8 8.2 + - - +
75C PHE* 3.8 11.9 - - + -
100C VAL 4.3 0.2 - - - +
101C GLY* 1.3 75.9 - - - +
103C PRO* 1.3 74.6 - - + +
108C GLN* 3.8 10.3 - - - +
166C MET* 3.8 29.2 - - + -
167C LEU 3.0 11.1 + - - +
168C PRO* 4.3 1.3 - - + -
169C ALA* 2.9 30.0 + - - +
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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