Contacts of the strand formed by residues 695 - 705 (chain B) in PDB entry 4QUN
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 TYR 695 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664B PHE 4.3 1.1 - - - -
665B ALA* 3.3 27.4 - - - +
670B ASN* 3.3 49.4 - - + +
673B LYS* 4.0 30.4 + - + +
674B ASN* 2.6 29.2 + - - -
681B PRO* 3.1 35.2 - - + +
686B ARG* 3.8 20.0 - - - +
689B LEU* 3.4 11.8 - - - +
693B GLU 3.3 4.4 + - - -
694B ASP* 1.3 83.9 - - - +
696B ILE* 1.3 70.9 + - - +
697B ASN* 3.6 12.3 + - - -
727B GLN* 4.4 5.5 + - - -
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Residues in contact with ILE 696 (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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673B LYS* 5.7 1.8 - - - -
681B PRO* 4.3 1.7 - - - +
686B ARG* 4.8 1.6 - - - +
687B VAL* 3.4 28.2 + - + +
689B LEU* 4.0 17.0 - - + -
694B ASP 3.8 0.4 + - - -
695B TYR* 1.3 90.6 - - - +
697B ASN* 1.3 69.7 + - - +
698B ALA* 2.9 29.1 + - + +
717B THR* 4.6 6.5 - - - +
718B GLN* 6.1 2.0 - - + +
724B THR* 5.1 7.2 - - - +
727B GLN* 3.9 12.1 - - + +
728B PHE* 3.8 38.8 - - + +
731B VAL* 4.1 11.2 - - + -
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Residues in contact with ASN 697 (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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673B LYS 4.1 3.7 + - - +
674B ASN* 2.9 28.3 + - - +
679B VAL 2.8 26.5 + - - +
681B PRO* 3.5 15.1 - - - +
695B TYR* 3.8 7.9 - - - -
696B ILE* 1.3 72.7 - - - +
698B ALA* 1.3 53.8 + - - +
717B THR* 2.5 25.9 + - - -
718B GLN* 3.4 41.0 + - - +
881B ARG* 3.0 29.9 + - - -
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Residues in contact with ALA 698 (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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681B PRO* 4.0 2.5 - - - +
686B ARG* 3.3 9.5 - - - +
687B VAL* 2.9 38.9 + - + -
696B ILE* 2.9 23.5 + - + +
697B ASN* 1.3 77.5 + - - +
699B SER* 1.3 63.5 + - - +
715B ILE* 4.1 6.1 - - + -
716B ALA 3.3 8.3 - - - +
717B THR* 3.4 16.6 - - - +
731B VAL* 5.7 1.6 - - + -
881B ARG* 4.1 1.7 - - - +
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Residues in contact with SER 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B PRO* 3.7 13.2 - - - +
685B THR* 3.3 9.6 + - - -
687B VAL* 4.1 5.6 - - - -
698B ALA* 1.3 73.6 - - - +
700B TYR* 1.3 64.0 + - - +
701B VAL* 3.5 1.6 + - - +
715B ILE* 3.4 2.9 - - - -
716B ALA* 2.8 33.2 + - - -
880B GLN 3.7 19.7 + - - -
881B ARG* 3.0 41.1 + - - +
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Residues in contact with TYR 700 (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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685B THR* 2.8 41.7 + - + +
686B ARG 3.7 16.6 - - - -
687B VAL* 3.8 23.0 - - + +
688B LEU* 4.5 5.0 + - + -
699B SER* 1.3 72.7 - - - +
701B VAL* 1.3 62.6 + - - +
702B ASN* 4.2 15.9 - - - +
714B TYR 3.7 4.7 - - - +
715B ILE* 4.0 15.7 - - + -
735B GLN* 3.0 37.1 + - - -
837B PRO* 5.8 3.6 - - + -
880B GLN* 3.6 16.0 - - - +
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Residues in contact with VAL 701 (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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699B SER* 3.9 8.3 - - - +
700B TYR* 1.3 79.9 - - - +
702B ASN* 1.3 62.3 + - - +
703B MET* 4.2 17.5 - - + -
714B TYR* 2.8 51.8 + - + -
716B ALA* 4.0 18.6 - - + -
853B VAL* 4.8 3.4 - - + -
877B MET* 4.6 5.6 - - + -
880B GLN* 3.5 22.7 - - + +
881B ARG* 4.1 21.1 - - + -
884B MET* 4.1 16.6 - - + -
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Residues in contact with ASN 702 (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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700B TYR* 4.6 15.2 - - - +
701B VAL* 1.3 76.4 - - - +
703B MET* 1.3 62.4 + - - +
704B GLU* 3.9 11.5 + - + +
711B VAL* 3.9 15.7 - - + -
712B ASN 3.5 2.9 - - - -
713B LYS* 3.3 39.6 - - - +
714B TYR 3.8 3.8 + - - +
880B GLN* 2.8 31.9 + - - +
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Residues in contact with MET 703 (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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701B VAL* 4.2 4.5 - - + -
702B ASN* 1.3 78.8 - - - +
704B GLU* 1.3 63.1 + - - +
705B ILE* 4.0 3.6 + - - +
711B VAL* 3.5 1.5 - - - -
712B ASN* 2.7 46.8 + - + +
714B TYR* 3.9 11.4 - - + -
853B VAL* 3.6 21.3 - - + -
857B THR* 3.8 24.7 - - + +
873B ILE* 3.7 39.9 - - + +
876B LYS* 4.1 12.8 - - + -
877B MET* 3.8 20.6 - - + -
880B GLN* 4.0 12.6 - - - -
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Residues in contact with GLU 704 (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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702B ASN* 4.3 10.9 - - + +
703B MET* 1.3 76.2 - - - +
705B ILE* 1.3 66.2 + - - +
706B PRO* 3.4 21.1 - - + +
710B LEU 3.6 6.7 - - - +
711B VAL* 4.2 20.8 - - + +
857B THR* 5.3 3.5 - - - +
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Residues in contact with ILE 705 (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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703B MET 4.6 5.4 - - - +
704B GLU* 1.3 75.2 - - - +
706B PRO* 1.3 66.6 - - + +
707B ALA 3.2 0.7 - - - +
708B ALA* 2.9 29.5 + - + -
709B ASN 3.4 7.6 + - - -
710B LEU* 2.8 39.4 + - + +
712B ASN* 5.0 4.3 - - - +
857B THR* 4.1 17.3 - - + +
860B CYS* 3.8 23.3 - - + -
861B LEU* 3.7 27.6 - - + -
864B ARG* 4.5 5.2 - - - -
866B LEU* 3.8 22.9 - - + -
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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