Contacts of the strand formed by residues 131 - 137 (chain A) in PDB entry 2OX0
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 ILE 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 3.6 29.8 - - + -
71A ILE 3.3 8.1 - - - +
72A GLN* 3.4 43.1 - - + +
89A LYS* 4.3 9.4 - - + -
92A MET* 4.6 12.8 - - + -
97A PHE* 3.3 18.2 - - + -
100A ILE* 5.2 10.5 - - + -
106A TYR* 5.4 6.3 - - + +
129A PRO 4.8 0.4 - - - +
130A PRO* 1.3 75.5 - - + +
132A TYR* 1.3 62.0 + - - +
180A MET* 3.3 28.9 - - + +
183A THR* 3.3 12.6 - - - +
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Residues in contact with TYR 132 (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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71A ILE* 2.7 39.1 + - + +
73A GLN* 3.7 28.9 - - - +
97A PHE* 4.2 0.7 - - - -
130A PRO 4.2 0.2 - - - -
131A ILE* 1.3 72.6 - - - +
133A GLY* 1.3 58.7 + - - +
134A ALA* 3.0 27.2 + - + -
177A TYR* 3.7 20.0 - + + +
178A PHE 3.2 23.1 - - - -
179A GLY* 3.7 4.7 - - - -
183A THR* 3.7 19.7 - - + +
184A SER 4.0 13.2 - - - -
185A PHE* 4.9 0.2 - - - -
206A LYS* 3.2 10.6 + - - -
280A ASN* 3.2 27.8 + - - -
284A ASN* 5.4 0.2 - - - -
500A OGA 2.5 30.8 + - - -
11C THR* 4.3 7.6 - - + -
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Residues in contact with GLY 133 (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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67A ILE* 3.8 24.7 - - - -
70A PRO* 4.6 2.2 - - - -
97A PHE* 3.5 14.7 - - - -
132A TYR* 1.3 67.2 - - - +
134A ALA* 1.3 59.9 + - - -
136A VAL* 3.8 9.2 - - - +
177A TYR* 3.5 3.1 - - - -
178A PHE* 2.8 46.8 + - - +
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Residues in contact with ALA 134 (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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67A ILE* 4.8 1.1 - - - +
69A ALA 4.4 11.3 + - - +
70A PRO* 5.1 1.0 - - - +
71A ILE* 4.2 12.0 - - + +
132A TYR* 3.0 24.0 + - + -
133A GLY* 1.3 73.1 - - - +
135A ASP* 1.3 71.2 + - - +
136A VAL* 3.2 8.6 + - - +
177A TYR* 3.8 13.5 - - + +
11C THR* 3.2 31.4 - - - +
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Residues in contact with ASP 135 (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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71A ILE* 5.6 0.9 - - - +
134A ALA* 1.3 75.2 - - - +
136A VAL* 1.3 62.2 + - - +
137A ASN 3.6 0.3 + - - -
175A TYR* 3.6 31.0 - - + -
176A LEU 3.4 6.2 + - - -
177A TYR* 3.3 17.1 + - - -
8C ARG* 3.4 30.4 + - - +
9C MLY 4.4 0.2 - - - +
10C SER* 3.6 9.2 + - - -
11C THR* 2.8 49.2 + - - -
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Residues in contact with VAL 136 (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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65A LEU* 4.6 14.6 - - + -
66A VAL 3.9 18.6 - - - +
67A ILE* 3.7 32.5 - - + -
68A PRO* 4.3 11.9 - - + -
133A GLY 3.8 10.8 - - - +
134A ALA 3.7 11.7 - - - +
135A ASP* 1.3 76.2 - - - +
137A ASN* 1.3 72.9 + - - +
138A GLY 3.2 0.2 + - - -
175A TYR* 3.2 5.1 - - - -
176A LEU* 2.7 49.4 + - + +
178A PHE* 4.5 3.6 - - + -
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Residues in contact with ASN 137 (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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68A PRO* 5.8 1.4 - - - +
135A ASP 3.6 1.8 + - - -
136A VAL* 1.3 80.6 - - - +
138A GLY* 1.3 59.2 + - - +
169A GLU* 3.1 39.1 + - - +
173A THR* 4.4 4.2 + - - -
174A PRO 3.8 4.7 - - - +
175A TYR* 3.3 20.4 - - - -
8C ARG* 3.3 13.1 + - - +
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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