Contacts of the strand formed by residues 688 - 695 (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 THR 688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A GLU* 3.9 27.4 - - + +
652A PHE 3.6 4.9 - - - +
653A THR* 3.6 24.0 - - - +
683A ILE* 5.5 0.4 - - - -
686A ASN 4.3 2.3 + - - -
687A SER* 1.3 90.1 + - - +
689A VAL* 1.3 64.9 + - - +
690A GLN* 4.3 2.3 + - + +
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Residues in contact with VAL 689 (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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650A VAL* 3.8 1.4 - - + +
651A GLU* 3.5 3.7 - - - +
652A PHE* 2.8 48.6 + - + +
665A VAL* 5.3 1.6 - - + -
680A PHE* 3.5 47.8 - - + -
682A GLU 5.6 0.2 - - - +
683A ILE* 3.7 37.0 - - + +
687A SER 4.4 0.2 - - - -
688A THR* 1.3 75.9 - - - +
690A GLN* 1.3 63.3 + - - +
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Residues in contact with GLN 690 (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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649A THR* 4.3 14.1 - - + +
650A VAL 3.2 9.0 - - - +
651A GLU* 3.0 30.5 - - + +
678A LYS* 6.0 0.2 + - - -
680A PHE* 4.1 12.8 - - - -
688A THR* 5.6 1.8 - - + +
689A VAL* 1.3 79.3 - - - +
691A TRP* 1.3 63.6 + - - +
692A GLU* 5.5 7.9 - - + -
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Residues in contact with TRP 691 (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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648A VAL 3.3 0.9 - - - +
649A THR* 3.2 4.9 - - - -
650A VAL* 2.8 51.6 + - + +
665A VAL* 3.7 41.7 - - + -
667A LEU* 4.1 21.1 - - + -
676A MET* 3.9 30.5 - - + -
677A LYS 4.1 3.8 - - - -
678A LYS* 3.2 57.4 - - + +
680A PHE* 4.4 10.1 - - + -
690A GLN* 1.3 77.7 - - - +
692A GLU* 1.3 77.4 + - - +
693A GLU* 3.4 35.3 + - + +
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Residues in contact with GLU 692 (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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637A ARG* 2.6 36.8 + - - -
647A THR* 4.0 14.6 - - + +
648A VAL 2.9 6.5 - - - +
649A THR* 2.6 20.0 + - + +
690A GLN* 5.5 8.3 - - + -
691A TRP* 1.3 84.7 - - - +
693A GLU* 1.3 68.2 + - - +
694A VAL* 4.3 0.7 - - - -
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Residues in contact with GLU 693 (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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647A THR* 4.7 0.4 - - - -
648A VAL* 2.8 33.6 + - - +
667A LEU* 4.4 13.9 - - + -
676A MET* 3.6 34.8 - - + +
691A TRP* 3.4 42.5 + - + +
692A GLU* 1.3 75.2 - - - +
694A VAL* 1.3 75.1 + - - +
695A CYS* 4.5 0.7 - - - -
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Residues in contact with VAL 694 (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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645A ASP* 3.7 37.9 - - + +
646A MET 3.3 11.0 - - - +
647A THR* 3.5 23.6 - - + +
676A MET* 5.3 0.9 - - - +
692A GLU 5.9 0.4 - - - -
693A GLU* 1.3 85.1 + - - +
695A CYS* 1.3 68.1 + - - +
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Residues in contact with CYS 695 (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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645A ASP* 3.4 2.4 - - - -
646A MET* 2.7 48.2 + - + +
648A VAL* 3.9 22.9 - - + -
667A LEU* 4.5 10.1 - - - -
672A VAL* 3.8 22.2 - - + +
673A THR* 3.9 27.8 - - - -
676A MET* 4.8 4.7 - - - -
693A GLU 4.1 4.5 - - - -
694A VAL* 1.3 82.2 - - - +
696A ARG* 1.3 60.1 + - - +
697A PRO* 3.9 1.3 - - - -
705A LEU* 5.8 0.4 - - - -
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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