Contacts of the helix formed by residues 635 - 646 (chain B) in PDB entry 6WG4
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 SER 635 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B CYS* 3.4 0.9 - - - +
634B ARG* 1.3 81.2 - - - +
636B MET* 1.3 60.5 + - - +
637B GLU* 3.1 15.4 - - - +
638B VAL* 3.0 27.4 + - - +
639B SER* 2.6 34.1 + - - -
652B THR* 3.6 8.3 - - - +
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Residues in contact with MET 636 (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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634B ARG 5.5 0.2 - - - +
635B SER* 1.3 78.3 - - - +
637B GLU* 1.3 62.2 + - - +
638B VAL 3.3 0.2 - - - -
639B SER* 3.6 10.2 - - - -
640B THR* 2.9 27.9 + - - -
652B THR* 3.7 9.2 - - + +
654B GLU* 3.1 28.3 - - + +
656B ASP* 3.2 41.3 - - + +
658B VAL* 4.6 4.5 - - + +
664B LEU* 6.2 3.8 - - + -
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Residues in contact with GLU 637 (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 SER* 3.1 12.1 - - - +
636B MET* 1.3 80.0 - - - +
638B VAL* 1.3 63.5 + - + +
639B SER 3.4 0.2 + - - -
640B THR* 3.5 10.7 + - - -
641B GLN* 3.7 17.7 + - + +
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Residues in contact with VAL 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ASP* 3.3 39.0 - - + +
633B CYS* 3.6 14.4 - - + -
634B ARG* 3.8 8.5 - - + +
635B SER* 3.0 41.1 + - - +
637B GLU* 1.3 78.1 - - + +
639B SER* 1.3 59.1 + - - +
641B GLN* 3.5 7.4 + - + +
642B LEU* 3.0 36.7 + - + +
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Residues in contact with SER 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B CYS* 3.5 11.7 - - - +
635B SER 2.6 24.9 + - - -
636B MET* 3.6 4.9 - - - -
637B GLU 3.3 0.6 - - - -
638B VAL* 1.3 78.7 - - - +
640B THR* 1.3 56.9 + - - +
643B ALA* 2.9 33.1 + - - +
650B CYS* 3.6 29.2 - - - +
651B ILE* 4.6 0.7 + - - -
652B THR* 3.5 16.1 - - - +
656B ASP 5.4 0.4 - - - -
658B VAL* 3.9 17.3 - - - -
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Residues in contact with THR 640 (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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636B MET 2.9 17.0 + - - -
637B GLU* 3.5 6.2 + - - -
638B VAL 3.3 0.2 - - - -
639B SER* 1.3 76.4 - - - +
641B GLN* 1.3 70.1 + - - +
643B ALA* 3.6 1.2 + - - +
644B ARG* 3.3 27.3 + - + +
658B VAL* 3.5 28.2 - - + +
664B LEU* 5.8 1.0 - - - +
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Residues in contact with GLN 641 (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 GLU* 3.7 17.0 + - + +
638B VAL* 3.5 12.0 + - + +
639B SER 3.3 0.4 - - - -
640B THR* 1.3 85.0 - - - +
642B LEU* 1.3 59.1 + - + +
644B ARG* 3.0 37.7 + - - +
645B ALA* 3.0 30.9 + - - +
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Residues in contact with LEU 642 (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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601B PRO* 4.5 3.8 - - + -
603B THR* 4.6 12.8 - - - +
605B ASP* 4.2 7.4 - - + -
606B ALA* 3.7 25.6 - - + -
631B LEU* 4.4 12.9 - - + +
633B CYS* 4.0 8.1 - - - -
638B VAL* 3.0 39.4 + - + +
639B SER 3.9 2.5 - - - +
641B GLN* 1.3 75.1 - - + +
643B ALA* 1.3 62.6 + - - +
645B ALA* 4.5 2.7 - - - +
646B PHE* 2.9 60.7 + - + +
650B CYS* 3.9 13.4 - - - -
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Residues in contact with ALA 643 (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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639B SER 2.9 19.1 + - - +
640B THR 4.0 1.3 - - - +
642B LEU* 1.3 77.3 - - - +
644B ARG* 1.3 57.2 + - - +
646B PHE 3.0 14.2 - - - +
647B THR* 3.4 15.2 - - - +
648B MET 3.4 20.5 + - - +
650B CYS* 3.7 4.2 - - - -
658B VAL* 3.7 13.7 - - + +
659B SER 3.3 26.7 - - - +
660B HIS 4.2 5.9 - - - +
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Residues in contact with ARG 644 (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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640B THR* 3.3 19.4 + - + +
641B GLN* 3.0 42.3 + - - +
643B ALA* 1.3 77.2 - - + +
645B ALA* 1.3 72.4 + - - +
647B THR* 5.3 3.7 + - - -
660B HIS 5.5 2.0 - - - -
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Residues in contact with ALA 645 (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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641B GLN 3.0 18.5 + - - +
642B LEU* 4.5 0.4 - - - -
644B ARG* 1.3 96.9 - - - +
646B PHE* 1.3 86.6 + - + +
647B THR* 4.0 2.9 + - - -
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Residues in contact with PHE 646 (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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601B PRO* 3.5 45.1 - - + -
602B GLU 5.2 4.9 - - - -
631B LEU* 5.5 0.9 - - + -
642B LEU* 2.9 43.9 + - + +
643B ALA 3.0 3.1 - - - +
645B ALA* 1.3 91.1 - - + +
647B THR* 1.3 55.3 + - - +
648B MET* 2.7 37.3 + - + +
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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