Contacts of the strand formed by residues 159 - 164 (chain B) in PDB entry 3OX4
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 5.1 3.1 - - - +
153B THR* 4.4 3.2 - - - +
154B ASP* 2.7 38.8 + - - +
157B ARG* 3.1 49.8 - - + +
158B HIS* 1.3 73.5 - - - +
160B LYS* 1.3 73.3 + - - +
161B MET* 3.5 12.7 + - + +
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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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71B ASN* 3.5 29.5 - - - +
72B PRO* 5.8 0.6 - - - +
121B GLU* 3.9 4.7 - - - +
151B ILE* 4.0 23.5 + - + +
152B ILE 3.7 3.1 - - - -
153B THR* 3.6 23.6 + - + +
159B VAL* 1.3 81.9 - - - +
161B MET* 1.3 60.0 + - - +
162B ALA 4.2 0.2 + - - -
267B HIS* 3.4 47.8 - - + +
268B GLN* 5.7 2.0 - - - +
270B GLY* 5.1 0.7 - - - -
271B GLY* 4.2 15.0 - - - +
277B HIS* 6.3 0.2 - - - -
360B ASP* 5.6 2.7 - - - +
1385B NAD 3.7 15.4 + - - -
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Residues in contact with MET 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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74B VAL* 5.1 5.2 - - - -
117B VAL* 4.8 10.8 - - + +
118B LYS* 3.2 39.3 - - + +
121B GLU* 3.0 39.9 - - + +
150B CYS 3.5 2.1 - - - +
151B ILE* 3.3 5.3 - - - -
152B ILE* 2.7 43.0 + - + +
154B ASP* 4.5 13.2 - - - +
157B ARG* 3.1 29.4 - - - +
159B VAL* 3.7 16.4 - - + +
160B LYS* 1.3 77.9 - - - +
162B ALA* 1.3 60.6 + - - +
163B ILE* 4.0 3.5 - - + +
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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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121B GLU* 3.7 9.1 + - - +
122B GLY* 3.1 23.0 + - - +
151B ILE* 3.4 24.7 - - + -
160B LYS 4.2 1.0 + - - -
161B MET* 1.3 72.3 - - - +
163B ILE* 1.3 62.0 - - - +
164B VAL* 3.8 11.3 + - + +
361B ALA* 4.8 19.1 - - + -
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Residues in contact with ILE 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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106B ALA* 5.3 2.9 - - + -
109B LEU* 4.3 13.0 - - + -
117B VAL* 3.9 35.0 - - + +
120B TYR* 3.5 35.0 - - + +
121B GLU* 4.1 3.6 - - + +
148B ARG 3.5 1.6 - - - +
149B PHE* 3.4 5.2 - - - +
150B CYS* 2.8 66.8 + - + +
151B ILE* 5.3 0.2 - - - +
152B ILE* 4.4 2.2 - - + -
161B MET* 4.9 4.0 - - + +
162B ALA* 1.3 75.6 - - - +
164B VAL* 1.3 58.9 + - - +
165B ASP* 4.0 19.7 - - + -
168B VAL* 4.3 8.7 - - + -
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Residues in contact with VAL 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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122B GLY* 2.9 17.0 + - - +
123B ILE* 3.3 23.2 - - + +
124B ASP* 2.8 25.7 + - - +
148B ARG* 3.4 36.6 - - - +
149B PHE* 4.1 20.9 - - + -
162B ALA* 4.5 14.8 - - + +
163B ILE* 1.3 73.7 - - - +
165B ASP* 1.3 60.0 + - - +
361B ALA* 5.6 7.6 - - + -
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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