Contacts of the strand formed by residues 145 - 152 (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 CYS 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.5 16.4 - - - +
67A ALA* 3.7 42.2 - - - -
68A CYS* 3.9 11.2 - - - -
71A ALA* 4.0 10.1 - - - -
98A VAL 3.2 11.7 - - - +
99A LEU* 4.0 14.8 - - + -
139A MSE 3.7 5.4 - - - -
143A SER* 2.6 26.3 + - - -
144A LEU* 1.3 83.9 - - + +
146A LEU* 1.3 64.8 + - - +
147A VAL* 5.0 1.6 - - + -
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Residues in contact with LEU 146 (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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40A GLY* 3.8 13.0 - - - -
41A GLN 3.5 13.2 - - - +
42A PHE* 3.4 44.0 - - + -
96A GLU 4.1 0.3 - - - +
97A GLY* 3.4 3.5 - - - -
98A VAL* 2.9 37.6 + - + +
139A MSE 4.0 13.5 - - + -
140A PRO* 4.1 24.5 - - + -
145A CYS* 1.3 76.1 - - - +
147A VAL* 1.3 63.3 + - - +
148A TYR* 3.7 29.4 - - + +
133B ILE* 4.4 12.1 - - + +
155B ACT 4.8 2.7 - - + -
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Residues in contact with VAL 147 (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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40A GLY* 3.7 1.4 - - - -
41A GLN* 2.8 37.4 + - - +
68A CYS* 4.2 10.5 - - + +
71A ALA* 3.7 27.1 - - + +
72A THR* 3.7 26.2 - - - +
75A ALA* 4.4 3.6 - - + -
95A LEU* 3.6 22.7 - - + -
96A GLU 3.7 3.1 - - - -
97A GLY* 4.9 0.2 - - - -
112A LEU* 4.7 8.3 - - + -
115A ALA* 4.5 8.1 - - + -
145A CYS* 5.0 1.6 - - - -
146A LEU* 1.3 79.9 - - - +
148A TYR* 1.3 65.4 + - - +
149A LEU* 4.1 13.9 - - + -
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Residues in contact with TYR 148 (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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38A THR* 3.6 15.0 - - - +
39A SER 3.6 13.2 - - - -
40A GLY* 3.2 26.6 + - - -
41A GLN* 5.3 0.2 - - - -
94A ARG 4.2 0.2 - - - +
95A LEU* 3.6 4.3 - - - +
96A GLU* 2.8 44.2 + - + +
98A VAL* 4.4 10.5 - - + -
146A LEU* 3.7 30.4 - - + +
147A VAL* 1.3 76.1 - - - +
149A LEU* 1.3 64.4 + - - +
150A PHE* 4.3 12.3 - - + -
94B ARG* 3.9 0.9 - - - -
131B ARG 3.5 15.4 + - - -
132B MSE 3.4 41.3 - - + -
133B ILE* 3.3 26.3 + - - +
155B ACT 5.0 2.3 + - - +
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Residues in contact with LEU 149 (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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36A LEU* 3.9 0.5 - - - +
37A MSE 3.4 3.1 - - - -
38A THR* 3.0 42.9 + - + +
72A THR* 4.5 3.1 - - + -
75A ALA* 3.4 33.2 - - + -
76A ILE* 4.4 4.9 - - + +
79A LEU* 3.9 27.8 - - + -
92A ILE* 4.2 9.4 - - + -
94A ARG 3.7 4.0 - - - +
95A LEU* 3.7 21.3 - - + -
119A LEU* 4.0 35.9 - - + -
147A VAL* 4.1 4.0 - - + -
148A TYR* 1.3 79.8 - - - +
150A PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 150 (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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36A LEU 3.3 4.9 - - - -
37A MSE 3.5 37.2 - - + -
92A ILE* 3.4 7.1 - - - +
93A TYR* 3.1 55.8 + + + +
94A ARG* 3.1 29.9 + - + +
96A GLU* 3.5 39.0 - - + -
148A TYR* 4.3 10.8 - - + -
149A LEU* 1.3 79.2 - - - +
151A ALA* 1.3 60.6 + - - +
94B ARG* 3.4 25.8 - - - -
96B GLU* 5.4 1.6 - - - -
132B MSE 4.8 0.9 - - - -
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Residues in contact with ALA 151 (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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34A SER 3.5 0.5 - - - +
35A GLN* 3.5 4.3 - - - -
36A LEU* 2.9 42.8 + - + +
79A LEU* 4.4 17.0 - - + -
89A ILE* 3.9 20.4 - - + -
91A GLN 3.2 10.3 - - - +
92A ILE* 3.9 11.2 - - + -
93A TYR* 3.5 5.7 - - - -
150A PHE* 1.3 73.9 - - - +
152A GLU* 1.3 59.8 + - - +
153A LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 152 (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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34A SER* 3.2 15.1 + - - +
89A ILE* 3.7 5.7 - - - +
90A LYS* 2.9 52.1 + - + +
91A GLN* 2.6 53.4 + - + +
93A TYR* 3.7 3.0 - - + -
151A ALA* 1.3 72.9 - - - +
153A LEU* 1.3 66.2 + - - +
32C VAL* 3.6 26.6 - - + +
33C GLY* 4.4 8.5 + - - -
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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