Contacts of the strand formed by residues 670 - 675 (chain A) in PDB entry 6ZGI
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 ILE 670 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A PHE* 4.8 11.2 - - + -
645A THR* 4.1 33.2 - - + -
646A ARG 5.7 0.4 - - - +
650A LEU* 5.3 1.6 - - + -
655A HIS* 6.0 1.8 - - + -
665A PRO* 4.3 0.3 - - - +
666A ILE* 3.0 36.1 + - + -
667A GLY 2.9 21.1 + - - +
668A ALA* 4.1 8.7 - - + +
669A GLY* 1.3 79.7 - - - +
671A CYS* 1.3 71.3 + - - +
694A ALA* 4.5 14.6 - - + -
695A TYR 3.4 10.8 - - - +
696A THR* 3.7 23.8 - - + +
864B LEU* 5.9 0.7 - - - +
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Residues in contact with CYS 671 (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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662A CYS* 2.0 53.2 - - - -
663A ASP 4.4 0.4 - - - +
664A ILE 3.3 5.8 - - - +
665A PRO* 4.3 0.7 - - - -
666A ILE* 4.0 4.0 - - - -
669A GLY 5.0 0.2 - - - -
670A ILE* 1.3 78.5 - - - +
672A ALA* 1.3 61.5 + - - +
694A ALA* 3.4 3.6 - - - -
695A TYR* 2.9 53.0 + - + +
697A MET* 3.6 25.6 - - + -
864B LEU* 5.1 1.3 - - - -
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Residues in contact with ALA 672 (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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598A ILE* 4.6 15.0 - - + -
650A LEU* 5.8 2.7 - - + -
653A ALA* 6.0 0.2 - - + -
663A ASP* 3.3 5.2 - - - +
664A ILE* 2.9 37.3 + - + +
666A ILE* 3.9 22.7 - - + -
671A CYS* 1.3 77.3 - - - +
673A SER* 1.3 62.5 + - - +
692A ILE* 4.6 8.7 - - + -
693A ILE 3.2 11.7 - - - +
694A ALA* 4.7 4.7 - - + -
695A TYR* 4.0 2.9 + - - -
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Residues in contact with SER 673 (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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663A ASP* 3.1 21.7 + - - +
664A ILE* 4.7 6.5 - - - -
672A ALA* 1.3 76.6 - - - +
674A TYR* 1.3 61.2 + - - +
675A GLN* 2.7 33.4 + - - -
692A ILE* 3.3 9.2 - - - +
693A ILE* 2.9 33.5 + - - +
695A TYR* 3.8 22.4 - - - -
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Residues in contact with TYR 674 (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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600A PRO* 4.0 26.0 - - + -
604A THR* 3.7 29.3 + - + +
605A SER* 3.8 21.0 + - - -
607A GLN* 4.4 11.5 + - + -
663A ASP* 4.6 1.8 + - - -
664A ILE* 5.6 1.3 - - + +
673A SER* 1.3 76.7 + - - +
675A GLN* 1.3 71.9 + - - +
690A GLN* 3.2 38.9 + - + +
691A SER* 3.5 30.7 - - - -
692A ILE* 4.0 13.9 - - + -
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Residues in contact with GLN 675 (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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660A TYR* 5.9 2.2 - - + -
663A ASP* 5.0 0.2 - - - +
673A SER* 2.7 25.8 + - - +
674A TYR* 1.3 83.1 - - - +
676A THR* 1.3 65.5 + - - +
690A GLN* 3.1 14.2 + - - +
691A SER 2.9 32.1 + - - +
693A ILE* 3.7 35.7 - - + -
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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