Contacts of the strand formed by residues 660 - 668 (chain A) in PDB entry 1GGT
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 LEU 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A PHE* 3.6 24.2 - - + -
654A ASN* 3.0 46.9 - - + +
656A LEU* 4.6 7.6 - - + -
658A GLU* 3.5 2.2 + - + +
659A THR* 1.3 69.3 - - - +
661A ARG* 1.3 51.9 + - - +
663A VAL* 3.6 19.3 - - + -
682A GLU* 2.7 34.9 - - - +
683A ILE* 2.7 15.9 + - + -
709A MET* 4.6 4.5 - - + -
711A SER* 3.7 20.0 - - - +
713A SER* 4.0 20.9 - - - -
714A LEU* 4.3 12.8 - - + -
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Residues in contact with ARG 661 (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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658A GLU* 2.9 32.4 + - - +
659A THR* 3.0 27.4 + - - +
660A LEU* 1.3 78.1 - - - +
662A ASN* 1.3 75.1 + - - +
663A VAL 3.2 3.0 + - - -
681A ARG 3.0 8.1 - - - +
682A GLU* 3.7 31.3 + - - -
711A SER* 3.6 8.1 - - - -
712A ASP* 2.9 30.9 + - - +
713A SER* 4.6 3.0 + - - +
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Residues in contact with ASN 662 (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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661A ARG* 1.3 76.1 - - - +
663A VAL* 1.3 60.2 + - - +
664A TRP* 3.7 9.4 + - - +
679A MET* 3.3 32.8 - - + +
680A PHE 3.4 4.3 - - - -
681A ARG* 2.6 29.6 + - - +
711A SER* 3.8 10.0 - - - -
712A ASP* 4.2 12.3 + - - +
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A PHE* 4.8 3.8 - - + -
660A LEU* 3.6 32.1 - - + +
661A ARG 3.8 7.0 - - - +
662A ASN* 1.3 73.0 - - - +
664A TRP* 1.3 64.2 + - - +
665A VAL* 4.7 2.9 - - + -
678A LYS 3.5 0.6 - - - +
679A MET* 2.9 7.6 - - - +
680A PHE* 2.7 58.4 + - + +
683A ILE* 3.7 24.9 - - + -
709A MET* 3.8 30.7 - - + -
710A SER 3.7 3.8 - - - -
711A SER* 4.2 3.6 - - - -
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Residues in contact with TRP 664 (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 ASN* 3.7 9.1 + - - +
663A VAL* 1.3 73.7 - - - +
665A VAL* 1.3 62.5 + - - +
666A HIS* 4.0 17.8 - + - +
677A LYS* 4.0 24.7 - - + -
678A LYS 3.1 25.6 - - - -
679A MET* 3.0 51.4 - - + +
708A SER 3.6 0.2 - - - +
709A MET* 3.2 7.3 - - - +
710A SER* 2.9 39.5 + - - +
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Residues in contact with VAL 665 (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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632A ILE* 4.7 3.6 - - + -
650A VAL* 3.5 33.4 - - + -
652A PHE* 5.5 4.3 - - + -
663A VAL* 4.7 6.7 - - + -
664A TRP* 1.3 79.3 - - - +
666A HIS* 1.3 68.6 + - - +
677A LYS* 3.0 5.2 - - - +
678A LYS 2.6 37.3 + - - +
680A PHE* 3.6 32.1 - - + -
689A VAL* 5.3 4.7 - - + -
691A TRP* 3.7 22.2 - - + -
708A SER 3.1 10.5 - - - +
709A MET* 5.0 5.8 - - + -
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Residues in contact with HIS 666 (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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287A VAL* 5.1 7.4 - - + -
291A ALA* 3.9 29.9 + - + +
292A TRP* 5.2 3.9 - + - -
293A THR* 3.7 19.0 + - + +
297A ASP* 5.0 3.2 + - - -
664A TRP* 4.0 24.1 - + + +
665A VAL* 1.3 82.1 - - - +
667A LEU* 1.3 54.1 + - - +
676A MET 3.2 5.1 + - - +
677A LYS* 3.7 34.2 - - + +
691A TRP* 4.4 2.7 - - - -
707A ALA* 2.8 38.4 - - - +
708A SER* 2.7 37.3 + - - +
709A MET* 5.0 0.4 - - - -
710A SER* 5.3 1.3 - - - -
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Residues in contact with LEU 667 (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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293A THR* 5.0 0.4 + - - -
634A ILE* 5.0 1.3 - - + -
648A VAL* 4.2 25.1 - - + -
650A VAL* 4.3 21.3 - - + -
666A HIS* 1.3 73.4 - - - +
668A ASP* 1.3 69.5 + - - +
673A THR* 4.7 4.7 - - + -
674A ARG 4.1 0.9 - - - +
675A PRO* 3.1 4.2 - - - +
676A MET* 2.6 56.3 + - + +
691A TRP* 4.1 13.2 - - + -
693A GLU* 4.4 21.8 - - + -
695A CYS* 4.5 9.6 - - - -
705A LEU* 4.4 17.3 - - + -
706A ILE 3.4 17.3 - - - +
707A ALA* 4.7 0.9 - - + -
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Residues in contact with ASP 668 (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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226A SER* 3.2 32.5 + - - -
293A THR* 3.3 28.7 + - - +
294A GLY* 4.6 3.6 + - - -
296A VAL* 5.5 3.8 - - - +
297A ASP* 5.4 1.4 + - - +
667A LEU* 1.3 74.8 - - - +
669A GLY* 1.3 69.4 + - - +
670A PRO* 3.8 4.5 - - - +
673A THR* 3.8 11.2 - - - +
675A PRO* 2.9 34.3 - - - +
705A LEU* 3.4 9.5 - - - +
706A ILE* 2.9 35.8 + - + +
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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