Contacts of the strand formed by residues 684 - 689 (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 ARG 684 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B LYS 3.3 2.6 + - - +
569B THR* 3.6 21.7 - - + +
570B GLY* 2.9 25.1 + - - -
654B THR* 5.3 7.4 - - - +
682B LEU* 3.8 8.7 - - - +
683B GLU* 1.3 89.4 - - + +
685B ALA* 1.3 61.4 + - - +
686B ILE* 4.2 9.2 - - + +
719B MET* 4.6 0.9 - - - -
720B LYS* 3.5 23.9 + - + +
722B SER* 3.2 28.9 + - - -
888B HIS* 3.9 14.6 + - - -
889B ILE* 3.8 41.0 + - - +
892B ASN* 5.1 9.5 + - - +
893B GLU 5.0 2.6 + - - -
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Residues in contact with ALA 685 (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 3.5 4.5 - - - -
677B MET* 3.6 22.7 - - + -
684B ARG* 1.3 76.2 + - - +
686B ILE* 1.3 64.8 + - - +
719B MET* 3.9 13.9 - - + -
720B LYS 2.9 9.4 + - - +
721B TRP* 3.3 34.3 - - + -
722B SER* 3.2 23.0 + - - -
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Residues in contact with ILE 686 (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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569B THR* 4.2 9.4 - - + -
570B GLY 2.9 12.7 + - - +
571B ILE* 3.5 26.9 - - + -
572B LEU* 2.8 29.0 + - - +
677B MET* 4.7 0.2 - - - +
684B ARG* 4.2 8.7 - - - +
685B ALA* 1.3 77.8 - - - +
687B ALA* 1.3 63.4 + - - +
688B PHE* 3.1 9.0 + - + +
721B TRP* 4.3 2.5 - - - -
722B SER* 3.5 15.9 - - - +
724B ILE* 4.0 22.0 - - + +
885B VAL* 4.0 4.5 - - + -
888B HIS* 3.9 23.3 - - + +
889B ILE* 3.9 30.3 - - + -
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Residues in contact with ALA 687 (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* 3.9 5.6 - - - -
574B LEU* 3.9 9.9 - - + -
686B ILE* 1.3 68.9 - - - +
688B PHE* 1.3 59.2 + - - +
689B THR 3.7 1.2 + - - -
703B LEU* 3.9 3.1 - - + -
706B ILE* 3.6 31.2 - - + -
721B TRP* 4.0 9.6 - - + -
722B SER 2.9 14.8 + - - +
723B THR* 2.8 36.8 + - - +
724B ILE 2.9 12.9 + - - +
918B PHE* 4.2 2.7 - - + -
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Residues in contact with PHE 688 (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* 3.8 21.1 - - + -
572B LEU 2.8 15.6 + - - +
573B MET* 3.4 0.8 - - + -
574B LEU* 3.0 20.8 + - - -
643B MET* 4.1 5.2 - - - -
686B ILE* 3.1 7.0 + - + +
687B ALA* 1.3 69.6 - - - +
689B THR* 1.3 72.8 + - - +
690B GLN* 3.1 14.7 + - - +
724B ILE* 3.7 26.5 - - + -
727B TRP* 3.5 24.0 - + - -
881B LEU* 3.6 39.9 - - + -
884B LEU* 3.7 21.3 - - + -
885B VAL* 3.6 28.5 - - + -
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Residues in contact with THR 689 (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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574B LEU* 3.9 17.7 + - - +
687B ALA 3.7 2.6 + - - -
688B PHE* 1.3 79.8 - - - +
690B GLN* 1.3 61.4 + - - +
691B TYR* 3.3 27.6 + - - +
699B THR* 2.7 32.7 + - - +
703B LEU* 6.0 0.2 - - - -
723B THR* 5.9 0.4 - - - -
724B ILE 3.2 19.4 + - - +
725B ASP 3.4 24.2 - - - +
727B TRP* 3.0 28.0 + - - +
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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