Contacts of the strand formed by residues 648 - 653 (chain B) in PDB entry 6QVC
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 648 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638B PRO* 3.7 23.1 - - + -
639B LEU 4.1 1.8 - - - +
640B VAL* 3.9 7.6 - - + -
646B MET 3.4 4.4 + - - -
647B ILE* 1.3 83.4 - - - +
649B LEU* 1.3 66.2 + - - +
650B GLY 3.7 20.9 - - - +
824B SER* 3.8 31.4 + - - +
826B PHE 5.1 4.0 - - - +
850B TYR* 3.7 42.2 - - + -
852B THR* 4.8 6.5 - - + -
855B GLY* 3.3 12.2 + - - +
857B LEU* 4.6 15.0 - - + +
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Residues in contact with LEU 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A VAL* 5.8 0.5 - - - +
639B LEU* 3.0 17.6 + - + +
640B VAL 3.6 3.8 - - - +
641B ASP* 3.4 37.2 - - + +
647B ILE* 3.7 23.6 - - + +
648B LEU* 1.3 84.1 - - - +
650B GLY* 1.3 60.4 + - - +
821B ILE* 5.8 2.9 - - + -
823B GLN* 3.0 28.3 + - - +
824B SER* 4.0 8.6 + - - -
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Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B PRO* 3.3 7.3 - - - +
639B LEU* 2.8 31.7 + - - +
648B LEU* 3.7 8.6 - - - +
649B LEU* 1.3 79.6 - - - +
651B SER* 1.3 62.0 + - - -
821B ILE* 5.1 3.8 - - - +
822B ASP 3.2 14.1 - - - -
823B GLN* 4.7 1.1 - - - -
824B SER* 4.1 11.7 - - - -
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Residues in contact with SER 651 (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 THR* 4.1 13.7 + - - +
637B LEU 3.0 14.4 - - - -
638B PRO* 4.7 0.9 - - - -
639B LEU* 4.3 1.5 - - - +
650B GLY* 1.3 75.7 - - - -
652B VAL* 1.3 67.5 + - - +
820B CYS 5.4 0.2 - - - +
821B ILE* 5.4 0.4 - - - +
822B ASP* 3.2 30.0 + - - +
823B GLN 5.1 5.0 + - - -
824B SER* 5.6 2.9 - - - -
850B TYR* 5.9 5.4 - - - -
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Residues in contact with VAL 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B THR* 2.9 3.9 + - - -
637B LEU* 2.8 43.8 + - + +
639B LEU* 4.5 16.2 - - + -
651B SER* 1.3 78.8 - - - +
653B GLU* 1.3 76.7 + - - +
656B GLU* 5.7 3.6 - - + -
657B LEU* 3.7 25.4 - - + -
819B CYS* 6.3 2.0 - - - -
820B CYS 4.3 9.9 - - - +
821B ILE* 4.0 28.5 - - + -
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Residues in contact with GLU 653 (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 3.7 10.5 - - - +
636B THR* 3.9 9.4 - - - +
652B VAL* 1.3 87.8 - - - +
654B ARG* 1.3 64.9 + - - +
655B SER* 4.0 12.9 + - - +
656B GLU* 3.7 21.5 + - + +
657B LEU* 3.5 13.2 + - - +
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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