Contacts of the strand formed by residues 657 - 663 (chain B) in PDB entry 2HRC
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 HIS 657 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B PRO* 5.4 0.4 - - - -
569B THR* 3.3 29.4 - - + +
571B ILE* 5.1 3.8 - - + -
644B VAL* 3.2 26.9 - - + +
647B LEU* 3.3 49.9 - - + +
648B ASP* 2.8 30.8 + - - +
651B SER* 3.2 28.6 - - - -
654B THR* 2.6 23.3 + - - -
655B ALA* 3.5 11.2 - - + -
656B PRO* 1.3 77.3 - - - +
658B LYS* 1.3 63.2 + - - +
889B ILE* 4.5 6.0 - - + +
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Residues in contact with LYS 658 (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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567B PRO* 4.0 23.0 - - + +
569B THR 2.9 7.0 + - - +
570B GLY* 3.3 4.2 - - - -
571B ILE* 2.8 25.7 + - - +
644B VAL* 4.1 5.6 - - - -
657B HIS* 1.3 76.2 - - - +
659B TYR* 1.3 68.7 + - - +
660B TYR* 3.3 27.8 - - + +
676B GLU* 3.3 21.2 + - - -
680B ASP* 2.9 26.9 + - - +
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Residues in contact with TYR 659 (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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571B ILE* 3.3 10.8 - - - +
573B MET* 4.1 15.5 - - - -
636B THR 4.8 0.2 - - - -
637B SER* 3.6 31.9 + - - -
640B GLY* 3.5 17.5 - - - -
641B GLU* 3.6 30.2 + - + +
643B MET* 3.9 14.4 - - + -
644B VAL* 3.7 16.8 - - + +
658B LYS* 1.3 85.2 - - + +
660B TYR* 1.3 69.3 + - - +
661B ILE* 3.9 26.7 - - + -
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Residues in contact with TYR 660 (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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570B GLY* 3.8 2.5 - - - -
571B ILE 2.9 7.8 + - - +
572B LEU* 3.4 17.7 - - + -
573B MET* 2.8 27.5 + - - +
658B LYS* 3.3 37.8 - - + +
659B TYR* 1.3 80.3 - - - +
661B ILE* 1.3 63.9 + - - +
673B ALA* 4.1 9.9 - - + -
676B GLU* 3.3 34.8 - - - -
677B MET* 3.5 37.0 - - + -
680B ASP* 2.6 28.8 + - - +
682B LEU* 3.4 31.3 - - + +
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Residues in contact with ILE 661 (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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572B LEU* 4.1 1.3 - - - -
573B MET* 3.8 6.1 - - + +
633B LYS* 4.1 19.3 - - + -
636B THR* 3.7 28.9 - - + -
637B SER* 3.5 26.0 - - - +
659B TYR* 3.9 18.8 - - + -
660B TYR* 1.3 73.2 - - - +
662B GLY* 1.3 62.5 + - - +
663B PHE* 3.5 41.7 - - + -
668B PRO* 3.3 26.2 - - + +
673B ALA* 3.4 13.7 - - - +
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Residues in contact with GLY 662 (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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572B LEU* 3.8 15.1 - - - +
573B MET 2.9 13.8 + - - -
574B LEU* 3.5 13.9 - - - +
575B ASN 3.4 19.6 + - - +
660B TYR 3.7 1.6 + - - -
661B ILE* 1.3 73.6 - - - +
663B PHE* 1.3 65.7 + - - -
664B ARG 3.9 0.2 + - - -
668B PRO 3.8 2.0 - - - -
670B THR* 3.9 17.8 + - - -
673B ALA* 4.2 0.2 - - - -
702B SER* 5.0 0.9 + - - -
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Residues in contact with PHE 663 (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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573B MET 5.5 0.2 - - - -
575B ASN* 3.2 21.5 - - + -
576B MET 3.9 1.1 - - - +
577B GLY* 3.6 11.2 - - - -
578B GLY 5.4 2.2 - - - -
632B ILE* 3.8 31.6 - - + -
633B LYS* 3.8 33.0 - - + -
636B THR* 4.1 7.0 - - + -
661B ILE* 3.5 28.7 - - + -
662B GLY* 1.3 74.0 - - - +
664B ARG* 1.3 64.1 + - - +
666B VAL* 3.2 40.7 - - + +
667B HIS 3.8 14.1 - - - -
668B PRO* 2.8 10.5 + - + +
669B LEU* 3.2 7.1 - - - -
670B THR* 2.9 20.5 + - - -
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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