Contacts of the strand formed by residues 677 - 682 (chain A) in PDB entry 1JV2
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 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646A SER* 3.9 4.3 - - - -
647A ILE* 3.8 31.9 + - + +
648A PRO 3.2 22.4 + - - -
649A LEU* 3.5 36.4 + - - +
652A ASP* 3.1 35.6 + - - +
670A PHE* 4.1 21.4 - - + -
671A LYS 3.8 4.9 - - - -
672A THR* 4.1 14.1 - - + +
676A THR* 1.3 80.1 + - - +
678A GLN* 1.3 66.4 + - - +
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Residues in contact with GLN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ILE* 3.6 24.9 - - + +
645A VAL 3.0 16.6 - - - +
646A SER* 4.2 7.1 + - - +
647A ILE* 4.6 2.2 - - - +
670A PHE* 4.4 5.4 - - - -
671A LYS* 3.0 54.0 + - + +
673A GLU* 5.2 2.6 + - - +
674A ASN 5.6 0.2 + - - -
676A THR* 3.3 40.4 + - - +
677A ARG* 1.3 73.7 - - - +
679A VAL* 1.3 64.5 + - - +
680A VAL* 3.7 15.9 + - + -
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Residues in contact with VAL 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU 3.5 1.7 - - - +
644A ILE* 3.6 2.4 - - - -
645A VAL* 2.6 47.4 + - + +
647A ILE* 4.0 13.7 - - + -
653A PHE* 3.9 35.7 - - + -
668A CYS* 4.4 4.9 - - + -
669A ALA 4.2 7.2 - - - +
670A PHE* 4.3 5.8 - - + +
678A GLN* 1.3 74.9 - - - +
680A VAL* 1.3 63.7 + - - +
681A CYS* 4.1 20.0 - - - -
697A LEU* 5.0 4.3 - - + -
699A PHE* 3.9 28.0 - - + -
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A GLU* 4.2 17.7 - - + +
643A LEU 3.3 3.8 - - - +
644A ILE* 3.4 28.0 - - + -
667A SER 4.5 1.0 - - - +
668A CYS* 3.3 0.9 - - - -
669A ALA* 2.8 38.6 + - + +
671A LYS* 4.6 21.8 - - + +
678A GLN* 3.7 15.0 + - + +
679A VAL* 1.3 75.3 - - - +
681A CYS* 1.3 67.6 + - - +
682A ASP* 4.9 5.6 - - - +
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Residues in contact with CYS 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A GLU* 3.0 10.9 - - - +
643A LEU* 2.9 54.6 + - + -
666A LEU* 3.9 4.0 - - + -
668A CYS* 2.0 51.6 - - - +
679A VAL* 4.1 11.9 - - - -
680A VAL* 1.3 77.8 - - - +
682A ASP* 1.3 63.2 + - - +
683A LEU* 3.3 16.1 + - + -
697A LEU* 4.4 2.7 - - - -
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Residues in contact with ASP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A ALA 4.2 5.4 - - - +
642A GLU* 4.7 2.0 - - - +
666A LEU* 4.0 12.8 - - - +
667A SER* 3.5 43.3 + - - +
680A VAL* 4.9 5.9 - - - +
681A CYS* 1.3 72.1 - - - +
683A LEU* 1.3 62.3 + - - +
684A GLY 3.2 9.8 + - - +
685A ASN 6.0 0.7 - - - +
532B LYS* 4.5 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