Contacts of the strand formed by residues 646 - 653 (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 MET 646 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A VAL* 3.4 36.1 - - + -
637A ARG 3.6 12.6 - - - +
638A GLY* 5.0 0.7 - - - -
639A THR 4.0 8.5 - - - +
640A GLN* 4.2 19.7 - - + -
645A ASP* 1.3 77.2 - - - +
647A THR* 1.3 64.8 + - - +
648A VAL* 3.7 7.6 + - + -
672A VAL* 4.4 12.1 - - + -
694A VAL* 3.3 2.1 - - - -
695A CYS* 2.7 45.3 + - - +
697A PRO* 4.4 14.4 - - + -
705A LEU* 4.1 13.7 - - + -
723A VAL* 4.3 17.0 - - + -
725A ILE* 4.2 11.9 - - + -
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Residues in contact with THR 647 (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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636A VAL* 3.2 3.8 - - - -
637A ARG* 2.6 57.6 + - - +
638A GLY* 4.9 1.2 - - - -
645A ASP* 6.0 0.2 - - - +
646A MET* 1.3 70.9 - - - +
648A VAL* 1.3 67.6 + - - +
692A GLU* 4.0 30.7 - - + +
693A GLU 3.9 4.3 - - - +
694A VAL* 3.5 22.4 - - + +
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Residues in contact with VAL 648 (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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634A ILE* 3.8 16.2 - - + -
635A LYS 3.3 4.3 - - - +
636A VAL* 4.7 0.7 - - + -
646A MET* 4.1 14.6 - - + +
647A THR* 1.3 77.1 - - - +
649A THR* 1.3 68.9 + - - +
650A VAL* 5.0 1.6 - - + +
667A LEU* 4.2 20.6 - - + -
691A TRP 3.3 0.9 - - - +
692A GLU* 2.9 27.9 - - - +
693A GLU 2.8 23.7 + - - +
695A CYS* 3.9 22.0 - - + -
705A LEU* 3.7 33.0 - - + -
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Residues in contact with THR 649 (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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633A ILE 3.4 1.2 - - - +
634A ILE* 3.0 8.0 - - - +
635A LYS* 2.6 58.7 + - + +
637A ARG* 2.8 20.7 + - - +
648A VAL* 1.3 74.0 - - - +
650A VAL* 1.3 69.8 + - - +
651A GLU* 4.9 4.5 - - + +
690A GLN* 4.3 19.5 - - + +
691A TRP 3.2 7.2 - - - +
692A GLU* 2.6 32.0 + - + +
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Residues in contact with VAL 650 (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* 3.5 20.6 - - + -
633A ILE 3.3 2.9 - - - -
634A ILE* 4.3 9.6 - - + -
648A VAL* 5.2 0.9 - - + -
649A THR* 1.3 75.2 - - - +
651A GLU* 1.3 64.5 + - - +
652A PHE* 4.8 2.7 - - + +
665A VAL* 3.5 25.8 - - + -
667A LEU* 4.3 21.3 - - + -
689A VAL* 3.8 1.5 - - + +
690A GLN* 3.2 4.7 - - - +
691A TRP* 2.8 55.7 + - + +
707A ALA* 4.0 21.8 - - + -
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Residues in contact with GLU 651 (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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631A GLU 4.5 1.0 - - - +
632A ILE* 3.4 5.3 - - - +
633A ILE* 2.7 51.0 + - + +
635A LYS* 3.2 25.8 + - + +
649A THR* 5.0 7.0 - - + -
650A VAL* 1.3 74.1 - - - +
652A PHE* 1.3 61.0 + - - +
653A THR* 4.3 2.9 + - - +
688A THR* 3.9 24.7 - - + +
689A VAL 3.5 4.9 - - - +
690A GLN* 3.0 27.8 - - + +
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Residues in contact with PHE 652 (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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630A PRO 4.7 10.3 - - - -
631A GLU 5.2 1.1 - - - -
632A ILE* 4.3 29.2 - - + +
650A VAL* 4.1 4.6 - - + +
651A GLU* 1.3 74.1 - - - +
653A THR* 1.3 72.1 + - - +
654A ASN* 3.7 21.6 + - + -
655A PRO* 3.9 11.0 - - + -
660A LEU* 3.6 23.6 - - + -
663A VAL* 4.8 1.8 - - + -
665A VAL* 5.5 4.9 - - + -
683A ILE* 4.4 16.2 - - + +
688A THR* 3.6 1.7 - - - -
689A VAL* 2.8 49.6 + - + +
709A MET* 3.7 36.1 - - + -
714A LEU* 4.1 5.6 - - + -
717A VAL* 4.2 11.9 - - + -
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Residues in contact with THR 653 (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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630A PRO* 4.3 9.2 - - - +
631A GLU 5.5 3.4 + - - -
651A GLU* 4.4 3.0 + - - +
652A PHE* 1.3 82.6 - - - +
654A ASN* 1.3 57.4 + - - +
655A PRO* 2.8 28.0 - - + +
686A ASN* 3.6 12.6 - - - +
687A SER 3.3 17.3 - - - +
688A THR* 3.6 17.8 - - - +
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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