Contacts of the strand formed by residues 641 - 648 (chain B) in PDB entry 3QCA
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 GLN 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B LYS* 3.7 24.7 - - + +
639B PHE 4.5 3.4 - - - +
640B PRO* 1.3 93.8 - - + +
642B GLU* 1.3 74.1 + - - +
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Residues in contact with GLU 642 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B LYS 3.1 10.1 + - - -
576B LEU* 3.1 25.7 - - + +
577B ARG* 2.9 23.1 + - - -
617B SER* 4.4 7.4 + - - +
618B THR* 4.0 15.3 + - - +
622B ARG* 5.3 1.2 + - - -
637B LYS 3.4 20.4 - - - +
638B LEU* 3.4 28.1 - - + +
639B PHE 4.9 1.2 + - - +
640B PRO 4.3 0.2 - - - -
641B GLN* 1.3 83.4 - - - +
643B THR* 1.3 66.3 + - - +
644B LEU* 3.7 11.3 + - + +
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Residues in contact with THR 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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577B ARG* 3.3 29.9 + - + +
585B PHE* 5.0 10.8 - - + -
618B THR* 3.2 29.6 + - + +
642B GLU* 1.3 74.4 + - - +
644B LEU* 1.3 75.3 + - - +
645B PHE* 3.8 24.4 - - + -
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Residues in contact with LEU 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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576B LEU* 4.2 24.7 - - + -
577B ARG 2.7 16.2 + - - +
578B ILE* 3.6 27.6 - - + -
579B ARG 3.1 12.9 + - - -
599B VAL* 4.8 0.9 - - + -
615B LEU* 3.4 30.5 - - + -
616B LEU 3.1 7.2 - - - +
617B SER* 3.6 27.6 - - - +
624B VAL* 4.6 4.9 - - + -
638B LEU* 3.7 27.8 - - + -
642B GLU* 4.1 7.4 - - + +
643B THR* 1.3 82.3 - - - +
645B PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 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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579B ARG* 3.7 25.4 - - + -
585B PHE* 5.4 3.4 - + - -
614B LYS 3.4 1.2 - - - +
615B LEU* 4.4 0.9 - - - -
616B LEU* 2.7 56.0 + - + +
617B SER 5.4 0.2 - - - -
618B THR* 3.7 29.4 - - + -
643B THR* 3.8 22.4 - - + -
644B LEU* 1.3 77.9 - - - +
646B LEU* 1.3 68.1 + - - +
647B GLU* 5.0 6.5 - - - +
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Residues in contact with LEU 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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578B ILE* 3.4 23.5 - - + +
579B ARG 2.8 21.4 + - - +
580B THR* 4.4 8.9 - - + +
581B PRO* 4.5 12.6 - - + +
586B LEU* 4.3 7.0 - - + -
603B VAL* 4.2 14.1 - - + -
608B PHE* 3.6 40.4 - - + +
613B TYR* 3.8 23.6 - - + +
614B LYS 3.4 13.0 - - - +
615B LEU* 4.2 18.4 - - + -
645B PHE* 1.3 75.9 - - - +
647B GLU* 1.3 71.0 + - - +
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Residues in contact with GLU 647 (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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581B PRO* 4.9 7.6 - - + -
613B TYR* 3.4 14.1 - - - -
614B LYS* 3.0 38.4 + - + +
616B LEU* 4.8 9.0 - - + +
621B ARG* 3.4 25.0 + - - -
645B PHE* 4.8 8.3 - - - +
646B LEU* 1.3 80.7 - - - +
648B ALA* 1.3 66.6 + - - +
649B LYS 3.3 0.7 + - - -
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Residues in contact with ALA 648 (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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581B PRO* 5.2 3.9 - - + +
612B GLU 4.3 4.9 - - - -
613B TYR* 4.2 10.3 - - + -
614B LYS* 5.7 0.8 - - - +
647B GLU* 1.3 75.8 - - - +
649B LYS* 1.3 58.7 + - - +
650B GLU* 3.0 31.8 + - + +
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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