Contacts of the strand formed by residues 688 - 695 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651B GLU* 3.9 24.2 - - + +
652B PHE 3.7 4.0 - - - +
653B THR* 2.7 28.3 + - - +
686B ASN 4.9 0.7 + - - -
687B SER* 1.3 76.7 - - - +
689B VAL* 1.3 77.5 + - - +
690B GLN* 5.7 2.9 - - + +
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Residues in contact with VAL 689 (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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650B VAL 4.1 0.4 - - - +
651B GLU* 3.7 4.3 - - - -
652B PHE* 3.3 38.3 + - + +
665B VAL* 5.7 2.0 - - + -
680B PHE* 3.9 34.5 - - + -
682B GLU 4.7 3.6 - - - +
683B ILE* 3.6 41.5 - - + -
687B SER* 6.0 0.7 - - - -
688B THR* 1.3 84.0 - - - +
690B GLN* 1.3 64.1 + - - +
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Residues in contact with GLN 690 (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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635B LYS* 4.8 4.7 + - - -
649B THR* 3.5 26.5 - - + +
650B VAL 3.6 5.6 - - - +
651B GLU* 3.9 23.2 - - + +
678B LYS* 5.8 0.9 - - - -
680B PHE* 4.2 12.7 - - - -
688B THR* 5.7 2.5 - - + +
689B VAL* 1.3 80.2 - - - +
691B TRP* 1.3 60.5 + - - +
692B GLU* 4.1 17.7 + - + +
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Residues in contact with TRP 691 (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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648B VAL 3.3 1.9 - - - +
649B THR* 3.3 5.9 - - - -
650B VAL* 3.0 52.0 + - + +
665B VAL* 3.8 36.8 - - + -
666B HIS 4.3 0.4 - - - -
667B LEU* 3.9 22.4 - - + -
676B MET* 3.9 28.9 - - + -
677B LYS 4.1 14.8 - - - -
678B LYS* 3.9 37.1 - - + +
680B PHE* 4.4 11.7 - - + -
690B GLN* 1.3 74.6 - - - +
692B GLU* 1.3 71.7 + - - +
693B GLU* 2.7 40.6 + - + +
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Residues in contact with GLU 692 (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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637B ARG* 2.9 36.1 + - - -
647B THR* 3.4 13.0 - - + +
648B VAL 3.2 5.6 - - - -
649B THR* 2.9 30.5 + - + +
690B GLN* 4.1 15.2 + - + +
691B TRP* 1.3 84.6 + - - +
693B GLU* 1.3 63.7 + - - +
694B VAL* 6.0 0.7 - - - -
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Residues in contact with GLU 693 (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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647B THR* 4.5 0.9 - - - +
648B VAL* 2.8 43.8 + - - +
667B LEU* 4.3 15.7 - - + -
676B MET* 3.5 36.6 - - + +
691B TRP* 2.7 43.7 + - + +
692B GLU* 1.3 76.2 - - - +
694B VAL* 1.3 70.7 + - - +
695B CYS* 4.7 0.7 - - - -
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Residues in contact with VAL 694 (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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645B ASP* 3.3 39.5 - - + +
646B MET 3.1 16.2 - - - +
647B THR* 4.2 16.4 - - + +
676B MET* 5.0 3.3 - - - +
692B GLU 6.0 0.2 - - - -
693B GLU* 1.3 85.1 + - - +
695B CYS* 1.3 62.5 + - - +
696B ARG* 5.4 0.2 - - - +
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Residues in contact with CYS 695 (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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645B ASP* 3.6 1.2 - - - -
646B MET* 2.8 37.7 + - + +
648B VAL* 3.9 22.7 - - + -
667B LEU* 4.3 11.0 - - - -
672B VAL* 3.6 29.6 - - + +
673B THR* 3.7 30.3 - - - -
676B MET* 4.8 3.1 - - - -
693B GLU 3.8 3.8 + - - -
694B VAL* 1.3 80.1 - - - +
696B ARG* 1.3 61.1 + - - +
697B PRO* 3.4 2.6 - - + +
705B LEU* 5.2 1.3 - - - -
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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