Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 2OMZ
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 MET 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A TRP* 4.1 18.4 - - + -
409A GLN* 3.6 39.5 - - - +
-2B PRO* 4.1 13.5 - - + +
-1B LEU* 4.1 8.5 - - + -
2B TRP* 3.8 27.1 - - + +
4B ILE* 3.5 20.2 - - + -
77B PHE* 3.3 5.3 - - - -
78B SER* 3.1 41.6 + - - +
90B ASP 3.4 1.8 + - - -
91B PRO* 1.3 70.9 - - - +
93B GLU* 1.3 80.7 + - - +
94B ILE* 3.5 6.9 + - + +
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Residues in contact with GLU 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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387A TRP* 5.7 2.4 - - - -
75B THR* 3.6 27.3 + - + +
76B LEU 3.5 5.4 - - - -
77B PHE* 3.7 28.6 - - + -
91B PRO 4.0 2.2 + - - -
92B MET* 1.3 90.0 - - - +
94B ILE* 1.3 64.3 + - - +
95B LEU* 4.4 9.2 + - + +
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Residues in contact with ILE 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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4B ILE* 4.7 13.9 - - + -
7B ILE* 3.4 28.0 - - + -
24B ILE* 3.9 19.7 - - + -
38B ILE* 5.7 2.2 - - + -
60B LEU* 5.0 3.8 - - + -
74B TYR 3.6 3.5 - - - +
75B THR* 3.8 1.2 - - - -
76B LEU* 3.1 41.2 + - + +
77B PHE 5.0 1.1 - - - -
78B SER* 3.7 34.3 - - - +
92B MET* 3.6 11.4 - - + +
93B GLU* 1.3 80.5 - - - +
95B LEU* 1.3 60.6 + - - +
96B ILE* 3.7 17.1 + - + -
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Residues in contact with LEU 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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7B ILE* 5.4 4.0 - - - +
73B THR* 4.6 19.7 - - + -
74B TYR 3.8 12.6 - - - +
75B THR* 3.9 17.5 - - + +
93B GLU* 4.2 10.6 - - + +
94B ILE* 1.3 72.5 - - - +
96B ILE* 1.3 65.1 + - - +
97B THR* 3.5 25.7 + - - +
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Residues in contact with ILE 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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7B ILE* 3.7 30.3 - - + +
9B CYS* 3.5 30.7 - - + -
21B LEU* 4.6 0.2 - - + -
51B PHE* 3.8 29.6 - - + -
60B LEU* 4.5 4.3 - - + -
73B THR* 3.5 7.4 - - - +
74B TYR* 3.1 42.0 + - + +
76B LEU* 3.6 31.9 - - + -
94B ILE* 3.7 14.8 + - + -
95B LEU* 1.3 73.1 - - - +
97B THR* 1.3 61.6 - - - +
98B VAL* 4.2 2.0 + - + +
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Residues in contact with THR 97 (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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7B ILE 5.1 5.8 + - - +
9B CYS* 3.9 15.2 + - - +
68B ARG* 6.1 1.8 - - - +
72B ALA* 3.8 8.3 - - + +
73B THR* 4.6 8.2 - - + +
95B LEU* 3.5 23.9 + - - +
96B ILE* 1.3 72.3 - - - +
98B VAL* 1.3 74.0 + - - +
99B THR* 3.4 19.5 + - + +
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Residues in contact with VAL 98 (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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9B CYS 3.4 12.3 - - - +
11B GLU* 3.9 7.9 - - + -
66B LEU* 3.8 28.0 - - + -
68B ARG* 2.5 71.7 + - + +
71B ILE 3.7 15.7 - - - +
72B ALA* 3.0 22.0 + - - +
74B TYR* 3.8 24.9 - - + -
96B ILE* 5.0 1.6 - - + -
97B THR* 1.3 76.8 - - - +
99B THR* 1.3 53.9 + - - +
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Residues in contact with THR 99 (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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8B SER* 4.7 6.5 + - - +
9B CYS 3.2 9.2 + - - +
10B PRO* 3.5 22.5 - - - +
11B GLU* 3.1 21.3 + - - +
68B ARG* 2.7 26.5 - - - +
97B THR* 3.8 21.8 - - + +
98B VAL* 1.3 71.2 - - - +
100B ASP* 1.3 58.9 + - - +
101B GLN 3.7 4.1 + - - -
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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