Contacts of the strand formed by residues 121 - 125 (chain B) in PDB entry 1OX6
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 GLU 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.9 6.4 - - + -
119B VAL* 4.2 0.2 - - - +
120B PRO* 1.3 72.6 - - - +
122B ILE* 1.3 60.2 + - - +
123B GLY 4.7 0.2 - - - +
125B ASN* 2.9 30.9 + - - -
145B PHE* 3.2 17.8 - - + +
146B VAL* 3.2 6.1 - - - -
147B HIS* 2.5 65.2 + - - +
173B TYR* 3.4 43.3 - - + +
178B PHE* 3.5 10.8 - - - -
236B LEU* 3.6 16.2 - - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.4 23.0 + - + +
121B GLU* 1.3 79.2 - - - +
123B GLY* 1.3 56.5 + - - +
144B TYR* 3.5 25.6 - - + +
145B PHE 3.5 2.2 - - - -
146B VAL* 4.6 7.9 - - + -
173B TYR* 5.1 0.4 + - - -
236B LEU* 3.8 14.9 - - - +
239B ARG* 3.5 38.5 + - - +
360B LYS* 4.2 5.2 - - + +
397B GLN* 4.6 15.3 - - + +
464B GLY 3.9 22.7 - - - +
465B GLU* 3.9 22.0 - - + +
495B PRO* 4.3 8.3 - - + +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU* 4.0 0.8 - - - +
122B ILE* 1.3 78.4 - - - +
124B TRP* 1.3 71.5 + - - -
125B ASN 3.7 1.5 + - - -
143B TYR 3.6 0.7 - - - +
144B TYR* 3.5 9.3 - - - -
145B PHE* 2.7 42.1 + - - +
236B LEU* 4.0 12.9 - - - +
239B ARG* 4.4 6.7 - - - -
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Residues in contact with TRP 124 (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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123B GLY* 1.3 77.0 - - - -
125B ASN* 1.3 61.3 + - - +
142B ARG* 2.9 45.4 + - + -
143B TYR 3.2 19.7 - - - +
144B TYR* 3.7 25.4 - + + -
196B LYS 3.2 24.5 - - - -
197B SER* 3.5 23.6 - - - -
236B LEU* 3.6 7.2 - - - +
237B THR* 3.2 31.4 + - + +
239B ARG* 4.5 10.7 - - + +
292B ASP* 3.6 41.6 + - + +
325B VAL* 4.2 5.6 - - + -
326B PRO* 4.3 0.9 - - + -
548B ARG* 3.4 42.8 - - + -
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Residues in contact with ASN 125 (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* 2.9 22.1 + - - +
123B GLY 3.7 1.8 + - - -
124B TRP* 1.3 75.2 - - - +
126B SER* 1.3 82.4 + - - +
142B ARG* 3.7 4.5 - - - -
143B TYR* 3.1 29.6 + - - +
145B PHE* 3.6 25.7 - - + -
171B ALA* 4.7 3.6 - - - -
172B LYS 3.0 31.5 + - - +
173B TYR* 4.0 3.6 - - - +
178B PHE* 4.3 3.6 - - - -
229B ASN* 3.4 6.6 + - - -
231B TYR* 4.6 0.9 - - - -
235B GLY 3.3 19.1 + - - +
236B LEU* 3.8 10.6 - - + +
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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