Contacts of the strand formed by residues 653 - 656 (chain B) in PDB entry 1OH7
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 653 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B ILE* 3.6 25.8 - - + +
268B ILE 3.0 13.8 + - - +
269B MET* 4.0 15.2 - - + -
270B ASP* 4.1 2.6 - - - +
273B THR* 3.2 25.8 + - + +
277B LEU* 4.5 4.7 - - + -
628B ALA* 4.2 20.6 - - + +
631B ALA* 4.4 18.6 - - + -
632B LEU* 4.7 9.0 - - + +
650B ILE* 3.8 11.9 - - + -
652B ARG* 1.3 79.0 - - - +
654B PHE* 1.3 60.8 + - - +
655B THR* 3.9 20.4 - - + -
689B LEU* 3.5 20.2 - - + +
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Residues in contact with PHE 654 (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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270B ASP* 3.4 18.6 - - - -
273B THR* 3.5 2.9 - - - -
652B ARG* 3.6 33.9 - - + -
653B ILE* 1.3 73.1 - - - +
655B THR* 1.3 65.9 + - - +
656B ARG 4.1 0.4 - - - -
679B ASN* 3.7 22.2 - - - -
680B ILE* 3.5 35.9 - - + -
683B ASN* 3.7 26.9 - - + -
684B ALA* 3.7 16.2 - - + -
688B SER* 3.8 5.6 - - - -
689B LEU 2.8 13.8 + - - +
690B VAL* 3.6 22.8 - - + -
691B LEU* 2.9 25.7 + - - +
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Residues in contact with THR 655 (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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272B ALA* 4.5 2.1 - - - +
273B THR* 2.9 43.7 + - + +
276B ASN* 3.1 22.6 + - - +
277B LEU* 4.0 17.7 - - + -
625B ARG* 5.8 0.2 - - - -
628B ALA* 4.2 0.2 - - + -
653B ILE* 3.9 11.4 - - + -
654B PHE* 1.3 79.7 - - - +
656B ARG* 1.3 57.5 + - - +
657B VAL* 3.2 16.6 - - - -
676B GLU* 4.9 1.2 - - - +
680B ILE* 5.2 1.0 - - - +
691B LEU* 3.4 25.4 - - + -
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Residues in contact with ARG 656 (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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276B ASN* 5.2 1.6 - - - +
654B PHE 4.1 0.8 - - - -
655B THR* 1.3 68.3 - - - +
657B VAL* 1.3 59.3 + - - +
658B GLY* 2.9 43.6 - - - +
672B VAL* 6.2 0.4 - - - +
673B GLU* 3.4 42.4 + - - +
676B GLU* 3.1 41.4 + - + +
677B THR* 4.3 12.8 - - - +
680B ILE* 3.7 24.2 - - + +
691B LEU 2.8 12.3 + - - +
692B MET* 4.5 4.5 - - - -
693B ASP* 3.1 26.9 + - - +
695B ILE* 4.3 11.7 - - + -
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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