Contacts of the helix formed by residues 154 - 164 (chain B) in PDB entry 2OX6
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 SER 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 3.3 5.1 + - - -
152B SER* 3.3 8.1 + - - -
153B GLU* 1.3 82.4 + - - +
155B ARG* 1.3 59.4 + - - +
156B GLU* 3.4 10.1 + - - +
157B SER* 2.9 28.5 + - - -
158B ARG* 3.0 32.7 + - - +
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Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 5.5 0.3 - - - +
90B TYR* 3.5 7.8 + - - +
99B TYR 3.6 7.5 + - - -
100B ASN* 2.7 30.9 + - - -
102B GLU* 2.7 40.1 + - - -
103B PHE* 3.3 14.9 - - - -
113B TYR* 3.8 18.2 + - - -
154B SER* 1.3 69.9 - - - +
156B GLU* 1.3 67.1 + - + +
158B ARG* 3.3 29.8 + - + +
159B ALA* 3.0 24.4 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.2 8.7 + - - +
155B ARG* 1.3 79.3 - - + +
157B SER* 1.3 56.1 + - - +
159B ALA* 3.2 8.2 + - - +
160B LYS* 2.9 48.4 + - - +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.5 18.0 - - - -
145B TYR* 4.4 3.5 - - - -
146B ARG* 4.6 0.7 - - - -
151B LEU* 3.6 26.3 - - - +
152B SER* 2.7 30.2 + - - -
154B SER* 2.9 18.1 + - - -
156B GLU* 1.3 74.1 - - - +
158B ARG* 1.3 64.4 + - - +
160B LYS* 3.4 9.5 + - - +
161B TRP* 3.0 19.2 + - - +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.6 15.9 - - + +
90B TYR* 2.8 36.3 + - - -
99B TYR* 2.9 42.0 + - - +
137B LEU* 4.2 10.3 - - + -
142B TYR* 3.4 30.3 - - + +
153B GLU* 2.8 32.7 + - - -
154B SER* 3.0 12.3 + - - +
155B ARG* 3.4 39.4 - - + +
156B GLU 3.3 0.4 - - - -
157B SER* 1.3 75.5 - - - +
159B ALA* 1.3 58.8 + - - +
161B TRP* 3.3 6.6 + - - +
162B ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 159 (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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86B ALA* 4.9 9.8 - - - +
88B VAL* 3.9 12.5 - - + +
155B ARG 3.0 13.2 + - - +
156B GLU* 3.2 11.6 + - - +
158B ARG* 1.3 74.2 - - - +
160B LYS* 1.3 65.1 + - - +
162B ALA* 3.2 3.9 + - - +
163B ALA* 3.0 23.0 + - - +
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Residues in contact with LYS 160 (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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145B TYR* 3.8 18.3 + - + +
151B LEU* 4.3 28.6 - - + +
156B GLU* 2.9 36.1 + - - +
157B SER* 3.7 7.4 + - - +
159B ALA* 1.3 75.0 - - + +
161B TRP* 1.3 63.9 + - - +
163B ALA* 3.4 16.3 + - - +
164B THR* 3.5 13.3 - - - +
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Residues in contact with TRP 161 (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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88B VAL* 5.5 0.7 - - + -
135B ILE* 3.8 13.2 - - + -
136B ASN 3.5 27.1 - - - -
137B LEU* 3.9 20.2 - - + -
138B ASN* 3.5 21.8 - - + -
141B ALA* 3.8 32.0 + - + +
142B TYR* 3.7 18.8 - - + -
145B TYR* 3.5 47.9 - + + -
157B SER 3.0 12.1 + - - +
158B ARG 3.5 7.6 - - - +
160B LYS* 1.3 76.5 - - - +
162B ALA* 1.3 76.1 + - + +
164B THR* 2.6 31.6 + - - -
165B GLN* 3.6 35.9 + - + +
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Residues in contact with ALA 162 (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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86B ALA* 3.7 22.0 - - + +
88B VAL* 3.6 20.4 - - + -
135B ILE* 4.0 16.6 - - + +
158B ARG 2.9 17.0 + - - +
159B ALA* 3.2 6.0 + - - +
161B TRP* 1.3 87.4 - - + +
163B ALA* 1.3 55.9 + - - +
165B GLN* 2.9 29.3 + - - +
166B LEU 3.8 2.1 + - - -
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Residues in contact with ALA 163 (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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83B ARG* 6.2 2.5 - - - +
86B ALA* 3.8 4.8 - - + +
159B ALA 3.0 12.9 + - - +
160B LYS* 3.6 12.8 - - - +
161B TRP 3.2 0.2 - - - -
162B ALA* 1.3 75.4 - - - +
164B THR* 1.3 61.6 + - + +
165B GLN 3.1 1.1 + - - -
166B LEU* 3.3 34.7 + - + +
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Residues in contact with THR 164 (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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145B TYR* 3.7 27.7 - - + +
160B LYS 3.5 15.9 - - - +
161B TRP* 2.6 24.1 + - - +
163B ALA* 1.3 77.3 - - + +
165B GLN* 1.3 74.5 + - - +
166B LEU 3.4 3.0 - - - +
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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