Contacts of the strand formed by residues 695 - 702 (chain B) in PDB entry 5IJ7
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 CYS 695 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B ILE* 3.5 31.6 - - - -
693B PRO* 3.3 23.1 - - - +
694B ASN* 1.3 85.8 - - - +
696B TYR* 1.3 66.2 + - - +
710B ILE* 4.0 16.4 - - + -
711B PHE 3.2 7.6 - - - +
713B LYS* 3.9 2.5 - - - +
716B ILE* 4.0 1.1 - - - -
722B LEU* 3.8 31.0 - - - -
723B PHE 3.1 15.1 + - - +
724B PHE* 3.4 9.0 - - + +
725B ASP 4.3 0.3 + - - -
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Residues in contact with TYR 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B TYR* 5.6 1.7 + - - -
635B ASN* 2.9 30.3 + - - +
693B PRO* 6.0 0.4 - - + -
695B CYS* 1.3 73.9 - - - +
697B ALA* 1.3 68.0 + - - +
698B LYS* 4.4 21.7 + - + -
709B GLY 3.7 0.5 - - - +
710B ILE* 3.4 5.3 - - - +
711B PHE* 2.8 67.4 + + + +
712B ALA 3.2 22.0 - - - -
713B LYS* 3.7 28.3 - - + -
724B PHE* 4.3 7.0 - - - -
725B ASP 5.6 0.7 - - - +
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Residues in contact with ALA 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B TYR* 1.3 77.7 - - - +
698B LYS* 1.3 61.8 - - - +
699B VAL* 4.2 0.9 - - + -
708B ILE* 3.9 11.0 - - + -
709B GLY 3.2 5.2 - - - -
710B ILE* 3.6 21.1 - - + -
724B PHE* 4.1 13.4 - - + -
725B ASP 5.9 0.7 - - - +
728B TYR* 6.1 1.2 - - - +
729B SER* 3.8 22.0 - - - +
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Residues in contact with LYS 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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574B TYR* 3.7 36.0 + - - -
577B VAL* 4.1 22.9 - - + +
696B TYR* 4.2 22.1 + - + -
697B ALA* 1.3 74.3 - - - +
699B VAL* 1.3 64.0 + - - +
700B MET* 3.5 31.8 + - + +
707B ARG 3.5 0.2 - - - +
708B ILE* 4.4 0.9 - - - -
709B GLY* 2.8 36.9 + - - -
711B PHE* 3.7 27.6 - - + -
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Residues in contact with VAL 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B VAL* 6.1 1.6 - - + -
577B VAL* 3.5 19.2 - - - +
668B ASN 4.3 9.9 - - - +
669B LEU* 3.5 28.7 - - + +
697B ALA* 4.2 1.3 + - + -
698B LYS* 1.3 70.9 - - - +
700B MET* 1.3 60.6 + - - +
706B HIS* 3.8 29.2 - - + +
707B ARG 3.4 7.4 - - - +
708B ILE* 3.6 26.2 - - + -
729B SER* 6.0 2.2 - - - +
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Residues in contact with MET 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B TYR* 6.3 1.1 - - - -
577B VAL* 3.4 20.0 - - + +
578B ARG 4.6 1.3 - - - +
579B GLU* 3.6 24.5 - - + +
603B ASN* 4.5 10.8 - - - +
606B ILE* 3.6 22.7 - - + -
698B LYS* 3.6 37.5 - - - +
699B VAL* 1.3 80.3 - - - +
701B MET* 1.3 62.3 + - - +
702B VAL* 3.5 14.3 + - + +
705B ASP 3.5 0.3 - - - +
706B HIS* 3.3 6.3 - - - -
707B ARG 2.8 31.7 + - - +
711B PHE* 3.6 22.2 - - + -
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Residues in contact with MET 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B TYR* 4.1 15.5 - - + -
541B ASN* 4.4 12.6 - - - +
544B GLU* 4.1 8.5 - - - +
576B ALA 5.8 0.2 - - - +
577B VAL 3.1 9.1 + - - +
578B ARG* 3.3 39.3 - - + +
579B GLU 3.1 23.6 + - - +
700B MET* 1.3 70.8 - - - +
702B VAL* 1.3 56.3 + - - +
703B ASN 4.1 2.2 + - - +
704B GLY* 3.6 38.6 - - - +
705B ASP 3.6 6.7 - - - +
706B HIS* 3.4 34.7 + - + +
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Residues in contact with VAL 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLU* 3.6 40.6 - - + +
606B ILE* 4.0 7.4 - - + -
607B GLN* 3.6 24.2 - - + +
700B MET* 3.8 17.9 - - + +
701B MET* 1.3 74.0 - - - +
703B ASN* 1.3 71.1 + - - +
705B ASP* 2.7 29.5 + - - +
707B ARG* 3.9 37.3 + - + +
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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