Contacts of the strand formed by residues 671 - 676 (chain O) in PDB entry 2O93
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 GLN 671 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580O VAL* 3.2 47.1 + - + +
581O GLU* 5.6 0.8 - - - +
583O GLN* 3.2 16.2 - - - +
657O ASN* 3.1 31.0 + - - -
658O PHE* 2.8 51.4 + - + +
659O TYR* 5.0 0.7 - - - -
669O GLN* 3.4 17.1 - - - +
670O PRO* 1.3 82.0 - - - +
672O HIS* 1.3 65.5 + - - +
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Residues in contact with HIS 672 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583O GLN* 3.2 27.4 - - - +
586O ASP* 4.3 5.5 - - - +
655O LYS* 4.9 14.5 - - + +
656O VAL 3.9 2.0 - - - +
657O ASN* 3.1 24.1 + - - -
658O PHE* 3.7 1.8 - - - -
670O PRO* 4.0 18.2 + - + -
671O GLN* 1.3 77.8 - - - +
673O PHE* 1.3 62.0 + - - +
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Residues in contact with PHE 673 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585O THR* 3.7 19.3 - - + -
586O ASP* 3.2 15.5 - - - -
587O SER* 3.6 26.5 - - - -
588O CYS* 3.8 11.4 - - - -
596O MET* 4.3 10.1 - - - -
611O PHE* 3.7 27.8 - + + -
642O ILE* 3.2 37.9 - - + -
655O LYS* 3.5 3.0 - - - +
656O VAL* 2.8 38.7 + - + +
658O PHE* 4.0 7.4 - + + -
672O HIS* 1.3 76.5 - - - +
674O THR* 1.3 78.3 + - - +
675O TYR* 3.7 28.7 - + - -
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Residues in contact with THR 674 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586O ASP 3.0 8.5 + - - -
587O SER* 2.7 37.7 - - - -
588O CYS 3.4 1.9 + - - -
653O PRO* 3.7 26.7 - - + -
654O VAL 3.5 12.3 - - - +
655O LYS* 2.7 43.2 + - + +
673O PHE* 1.3 74.8 - - - +
675O TYR* 1.3 65.0 + - - +
676O HIS* 3.8 10.0 + - + -
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Residues in contact with TYR 675 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588O CYS* 3.3 17.3 - - - -
589O LEU 4.0 11.2 - - - -
590O VAL* 4.2 9.9 - - + -
592O GLY* 4.9 0.2 - - - -
611O PHE* 4.0 3.4 - + - -
622O TRP* 3.5 26.1 - + - -
642O ILE* 3.3 28.6 - - + +
643O PRO* 2.6 40.7 + - - +
645O TYR* 3.5 35.9 - + + -
650O ILE* 3.9 6.3 - - + +
653O PRO* 3.3 7.8 - - - +
654O VAL* 2.9 34.3 + - + +
656O VAL* 3.9 22.0 - - + +
673O PHE* 3.7 11.2 - + - -
674O THR* 1.3 73.1 - - - +
676O HIS* 1.3 60.6 + - - +
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Residues in contact with HIS 676 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587O SER* 3.4 32.1 + - - -
588O CYS* 2.8 19.7 + - - +
589O LEU* 3.2 16.0 - - + +
590O VAL* 2.8 27.6 + - - +
653O PRO* 3.4 30.2 - - + +
674O THR* 4.2 9.0 - - + -
675O TYR* 1.3 72.1 - - - +
677O PRO* 1.3 72.8 - - + +
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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