Contacts of the strand formed by residues 596 - 601 (chain B) in PDB entry 2OBF
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 ASP 596 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573B ARG* 2.9 20.0 + - + +
574B THR* 3.3 10.8 - - + +
575B LEU* 2.8 27.0 + - - +
594B PHE* 4.3 0.6 - - - +
595B GLU* 1.3 79.7 - - + +
597B ILE* 1.3 64.6 + - - +
598B THR* 3.9 1.7 + - - -
650B ARG 3.8 1.6 - - - -
652B LYS* 3.5 16.2 - - + +
653B ARG* 2.8 43.2 + - - -
672B PRO* 3.7 15.8 - - - +
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Residues in contact with ILE 597 (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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575B LEU* 3.4 20.2 - - + -
587B LEU* 3.8 30.3 - - + -
590B ALA* 4.9 1.3 - - + -
591B CYS* 3.8 37.0 - - + +
594B PHE* 3.9 21.3 - - + +
596B ASP* 1.3 80.1 + - - +
598B THR* 1.3 69.5 + - - +
599B MET* 4.1 1.1 + - + -
647B LEU* 4.0 12.6 - - + -
650B ARG* 2.8 24.7 + - + +
651B VAL* 3.4 10.2 - - + -
652B LYS* 2.9 26.0 + - - -
653B ARG 3.9 1.7 + - - -
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Residues in contact with THR 598 (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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575B LEU 2.9 14.0 + - - -
576B ILE* 4.0 13.9 - - + +
577B ASP* 2.9 29.3 + - - +
596B ASP* 3.9 1.9 + - - -
597B ILE* 1.3 74.6 - - - +
599B MET* 1.3 72.9 + - - +
600B THR* 3.8 9.6 - - + -
653B ARG* 2.6 44.2 + - + +
655B LEU* 3.8 16.8 - - + -
665B LEU* 5.3 0.2 - - + -
671B ALA* 3.7 13.5 - - + +
672B PRO* 4.1 2.4 - - - +
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Residues in contact with MET 599 (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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577B ASP* 4.0 2.7 - - - +
580B SER* 3.7 21.1 - - - +
583B THR 3.4 25.6 - - - +
584B VAL* 4.2 10.8 - - + -
586B GLN* 4.4 0.4 - - - +
587B LEU* 3.5 34.5 - - + -
597B ILE* 4.1 0.9 + - + -
598B THR* 1.3 75.1 - - - +
600B THR* 1.3 68.8 + - - +
610B LEU* 4.0 23.3 - - + -
613B TRP* 6.4 0.4 - - - -
614B LEU* 5.7 4.0 - - - -
647B LEU* 6.2 0.4 - - - -
651B VAL* 3.9 29.8 - - + -
653B ARG 2.9 12.3 + - - +
654B VAL* 3.3 13.8 - - + -
655B LEU 2.8 23.2 + - - -
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Residues in contact with THR 600 (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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576B ILE* 4.3 6.1 - - + -
577B ASP 2.7 21.5 + - - +
578B ILE* 3.6 2.4 - - - -
579B GLY 3.1 13.0 + - - -
580B SER* 2.7 41.0 + - - -
598B THR* 3.8 17.3 - - + -
599B MET* 1.3 84.1 - - - +
601B ASP* 1.3 63.0 + - - +
607B ARG* 5.2 2.0 - - - -
610B LEU* 5.5 0.9 - - - -
654B VAL* 5.1 2.0 - - - -
655B LEU* 3.0 15.0 - - + +
657B ILE* 3.4 15.2 - - + +
665B LEU* 3.8 20.4 - - + -
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Residues in contact with ASP 601 (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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579B GLY* 3.6 8.6 - - - -
581B GLY* 2.8 28.9 + - - +
600B THR* 1.3 75.8 - - - +
602B PHE* 1.3 58.0 + - - +
603B LEU 3.0 19.5 + - - +
606B ASN* 3.0 17.6 + - + +
607B ARG* 2.6 37.0 + - + +
610B LEU* 5.6 0.9 - - + -
655B LEU 2.9 6.7 + - - -
656B PRO* 3.1 9.7 - - - +
657B ILE* 3.4 12.0 - - - +
3002B SAH 2.8 39.1 + - - -
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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