Contacts of the strand formed by residues 184 - 188 (chain B) 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 SER 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLN* 2.8 28.8 + - - -
84B GLN* 3.5 23.0 + - - -
121B TYR* 2.5 40.1 + - - -
125B LEU* 5.5 1.2 - - - +
132B TYR* 4.0 10.8 - - - -
182B LYS 3.3 6.1 + - - -
183B THR* 1.3 72.4 - - - +
185B PHE* 1.3 62.5 + - - +
186B ALA 4.2 0.2 - - - -
244B LEU* 4.5 10.8 - - - +
278B GLY 3.4 6.1 - - - -
279B PHE* 4.3 0.4 - - - +
11D THR* 4.5 2.6 - - - +
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Residues in contact with PHE 185 (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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132B TYR* 4.9 2.9 - + + -
183B THR 5.6 0.2 - - - -
184B SER* 1.3 75.7 - - - +
186B ALA* 1.3 64.7 + - - +
188B HIS* 4.1 10.3 - + + -
206B LYS* 4.0 16.2 - - + -
207B SER 3.9 4.3 - - - -
208B TRP* 3.8 37.0 - + - -
244B LEU* 4.2 5.7 - - - +
276B HIS* 4.1 3.8 - + - -
277B ALA* 3.3 27.7 - - - +
278B GLY* 3.0 62.5 + - - +
279B PHE* 3.7 6.3 - - - -
280B ASN* 5.6 1.1 - - - -
500B OGA 3.4 47.3 - - - +
11D THR* 5.3 9.6 - - + +
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Residues in contact with ALA 186 (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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84B GLN* 4.6 5.5 - - - +
184B SER 4.2 0.6 + - - -
185B PHE* 1.3 76.4 - - - +
187B TRP* 1.3 56.8 + - - +
188B HIS* 2.7 31.8 + - - -
241B LYS* 3.3 40.0 + - + +
242B MET 4.0 0.9 - - - -
243B THR 3.4 17.3 - - - +
244B LEU* 3.4 18.5 - - + +
276B HIS 3.2 3.3 - - - +
277B ALA* 3.9 1.1 - - - -
11D THR 5.2 3.4 + - - -
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Residues in contact with TRP 187 (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 TRP* 5.6 0.4 - - - -
186B ALA* 1.3 75.3 - - - +
188B HIS* 1.3 60.8 + - - +
209B TYR* 3.6 35.4 - + + -
210B SER 4.2 1.3 - - - -
211B VAL* 3.9 16.6 - - + -
219B LEU* 3.9 15.5 - - + -
238B LEU* 3.5 31.0 - - + +
241B LYS* 4.6 0.2 - - - -
243B THR* 3.1 17.5 + - - +
244B LEU* 4.2 1.1 - - - -
245B ILE* 3.0 55.1 + - + +
247B PRO* 6.2 0.4 - - + -
250B LEU* 3.5 31.9 - - + -
257B PHE* 5.2 0.2 - - + -
275B TYR* 3.6 33.4 - - + -
276B HIS* 3.3 31.0 - - - -
277B ALA* 3.5 13.2 - - + +
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Residues in contact with HIS 188 (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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185B PHE* 4.1 10.3 - + + -
186B ALA 2.7 23.5 + - - -
187B TRP* 1.3 75.3 - - - +
189B THR* 1.3 78.8 + - - +
190B GLU* 3.5 2.9 - - - -
238B LEU* 4.3 7.4 - - - +
239B ARG* 5.4 1.8 - - - -
241B LYS* 3.8 39.4 + - + +
275B TYR* 3.3 17.4 - - - -
276B HIS* 3.0 44.4 + + - -
500B OGA 3.2 8.3 - - - -
501B NI 2.2 44.8 - - + +
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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