Contacts of the strand formed by residues 91 - 99 (chain A) in PDB entry 2OTM
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 GLN 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE* 3.4 8.9 - - - +
90A LYS* 1.3 81.2 - - - +
92A ILE* 1.3 59.7 + - - +
93A TYR* 3.6 20.7 + - + +
126A ALA* 3.3 14.4 - - - +
128A ARG 4.7 6.8 - - - +
151A ALA* 3.2 3.6 - - - -
152A GLU* 2.6 65.5 + - + +
30C SER* 5.0 2.3 - - - -
31C ILE 2.8 32.7 + - - +
32C VAL* 3.8 6.1 - - - +
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Residues in contact with ILE 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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79A LEU* 3.5 31.9 - - + -
89A ILE* 3.8 20.0 - - + -
91A GLN* 1.3 68.9 - - - +
93A TYR* 1.3 57.8 + - - +
94A ARG 4.0 11.4 - - - +
119A LEU* 3.8 30.7 - - + -
123A PHE* 4.2 27.6 - - + -
126A ALA 2.9 15.7 + - - +
127A GLY* 4.1 6.5 - - - +
128A ARG 3.3 10.4 - - - +
129A HIS* 3.2 17.7 - - - +
149A LEU* 4.2 9.9 - - + -
150A PHE 3.4 11.4 - - - +
151A ALA* 3.9 6.5 - - + -
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Residues in contact with TYR 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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35A GLN* 3.3 28.5 + - + +
36A LEU 4.9 0.7 + - - -
37A MSE 5.0 1.2 - - - +
91A GLN* 3.6 25.6 - - - +
92A ILE* 1.3 72.5 - - - +
94A ARG* 1.3 66.2 + - + +
128A ARG 4.3 4.0 - - - -
129A HIS* 3.8 2.9 - - - -
130A SER* 3.0 13.2 + - - -
150A PHE* 3.1 33.6 + + + +
151A ALA 3.5 26.0 + - - -
152A GLU* 3.7 14.4 - - + -
30C SER* 2.7 31.3 + - - +
31C ILE 4.7 2.0 - - - +
32C VAL* 3.8 38.4 - - + -
37C MSE 3.9 21.5 - - + -
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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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92A ILE* 3.4 6.8 - - - +
93A TYR* 1.3 97.2 - - + +
95A LEU* 1.3 63.6 + - - +
96A GLU* 2.9 23.0 + - + +
129A HIS* 4.1 2.9 - - - -
130A SER* 3.0 38.8 + - - -
131A ARG 4.3 2.2 - - - +
132A MSE 3.0 37.5 - - - +
149A LEU* 3.7 2.3 - - - -
150A PHE* 3.1 45.4 + - + +
37C MSE 3.7 20.1 - - - +
38C THR 2.8 27.9 + - - -
39C SER* 4.5 0.2 - - - +
148C TYR* 4.0 3.4 - - - -
150C PHE* 3.4 22.0 - - - -
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Residues in contact with LEU 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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94A ARG* 1.3 72.9 - - - +
96A GLU* 1.3 77.6 + - - +
97A GLY 4.7 0.7 - - - +
112A LEU* 4.2 14.4 - - + -
115A ALA* 3.6 27.4 - - + -
116A SER* 3.5 27.6 - - - +
119A LEU* 4.1 8.7 - - + -
129A HIS* 3.7 17.7 - - + +
130A SER 3.0 5.5 + - - -
131A ARG* 3.1 11.4 - - + +
132A MSE 3.0 21.7 + - - -
147A VAL* 3.6 33.0 - - + -
148A TYR 3.6 2.0 - - - +
149A LEU* 3.7 10.8 - - + -
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Residues in contact with GLU 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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94A ARG* 2.9 26.0 + - + +
95A LEU* 1.3 82.2 - - - +
97A GLY* 1.3 58.2 - - - +
132A MSE 3.1 33.2 - - + +
134A TRP* 3.7 19.3 - - + -
147A VAL* 3.7 0.3 - - - -
148A TYR* 2.8 42.5 + - + +
150A PHE* 3.5 27.0 - - + -
154A CA 4.2 7.8 - - - -
132B MSE 3.5 27.6 - - + +
150C PHE* 5.2 0.5 - - - -
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Residues in contact with GLY 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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95A LEU* 4.2 0.6 - - - +
96A GLU* 1.3 74.3 - - - +
98A VAL* 1.3 62.6 + - - -
99A LEU* 5.4 0.4 - - - -
112A LEU* 4.0 26.5 - - - +
132A MSE 3.1 9.1 + - - -
133A ILE* 3.4 8.0 - - - +
134A TRP* 3.0 27.6 + - - +
146A LEU 3.4 8.7 - - - -
147A VAL* 4.5 2.0 - - - -
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Residues in contact with VAL 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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97A GLY* 1.3 75.9 - - - -
99A LEU* 1.3 63.3 + - - +
134A TRP* 3.4 27.4 - - + +
136A ASN* 3.4 38.4 - - + +
139A MSE 3.4 22.6 - - + +
145A CYS* 3.2 7.4 - - - +
146A LEU* 2.9 43.9 + - + +
148A TYR* 4.4 16.2 - - + -
133B ILE 5.0 1.8 - - - +
134B TRP* 4.0 13.2 - - + +
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Residues in contact with LEU 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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55A LEU* 4.5 9.9 - - + -
64A GLY 5.0 1.8 - - - +
68A CYS* 3.9 22.4 - - - -
98A VAL* 1.3 77.9 - - - +
100A ASN* 1.3 59.6 + - - +
101A VAL* 3.6 15.0 - - + -
108A HIS* 3.8 29.8 - - + +
111A ALA* 4.1 13.9 - - + -
112A LEU* 4.4 18.8 - - + +
133A ILE* 4.4 11.4 - - + -
134A TRP 3.0 8.1 + - - +
135A THR* 3.1 9.5 - - - -
136A ASN 3.0 22.7 + - - -
139A MSE 4.4 4.7 - - - -
144A LEU* 3.4 24.9 - - + +
145A CYS* 4.0 5.2 - - + -
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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