Contacts of the strand formed by residues 640 - 644 (chain B) in PDB entry 2QY0
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 VAL 640 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B TRP* 3.8 25.8 - - + +
461B GLN* 5.4 3.8 + - - +
472B GLY 5.0 0.2 + - - -
473B ALA* 3.2 31.8 - - + +
481B LEU* 4.4 12.1 - - + -
559B ILE* 4.1 12.6 - - + -
575B TYR 3.9 0.7 - - - +
576B VAL* 3.9 22.3 - - - +
577B SER* 4.4 5.3 + - - +
638B GLY 4.9 1.3 - - - +
639B GLY* 1.3 77.0 - - - -
641B PHE* 1.3 62.9 + - - +
642B ALA* 4.2 7.6 - - + -
653B ALA* 3.8 18.4 - - + -
655B GLY 3.1 12.8 - - - +
656B ILE* 4.9 3.6 - - + -
657B VAL* 4.7 2.2 - - - -
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Residues in contact with PHE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLY* 3.6 21.8 - - - -
575B TYR 3.6 3.1 - - - -
576B VAL* 3.5 19.5 - - + -
595B LEU* 3.5 35.4 - - + -
597B VAL* 4.0 20.2 - - + -
621B PHE* 4.0 8.1 - + + -
623B ALA* 3.5 27.4 - - + -
639B GLY 4.1 0.2 + - - -
640B VAL* 1.3 71.8 - - - +
642B ALA* 1.3 60.6 + - - +
643B VAL* 3.8 12.1 - - + -
653B ALA* 3.6 4.0 - - - -
654B THR* 3.1 46.3 + - - +
655B GLY* 2.8 15.3 + - - +
656B ILE* 4.3 0.6 - - - +
670B TYR* 3.7 27.0 - + + -
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Residues in contact with ALA 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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458B PHE* 5.5 1.6 - - + -
460B TRP* 4.1 16.4 - - + +
559B ILE* 3.9 22.7 - - + -
574B GLY* 3.2 1.6 - - - -
575B TYR* 2.7 51.9 + - + +
640B VAL* 3.8 7.4 - - + +
641B PHE* 1.3 73.3 - - - +
643B VAL* 1.3 61.5 + - - +
644B ARG 4.2 0.2 - - - -
651B TRP* 4.2 9.6 - - + -
652B VAL 3.2 5.2 - - - -
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Residues in contact with VAL 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 4.4 11.7 - - + +
572B LEU* 3.9 36.1 - - + -
573B MET 4.1 7.4 - - - +
574B GLY* 4.2 6.7 - - - -
597B VAL* 5.5 0.2 - - + -
641B PHE* 3.8 16.8 - - + -
642B ALA* 1.3 77.0 - - - +
644B ARG* 1.3 76.1 + - - +
645B ASP* 3.4 4.6 + - - +
646B PRO* 5.4 0.9 - - + -
651B TRP* 4.3 2.7 - - - -
652B VAL* 2.9 32.6 + - - +
654B THR* 3.5 34.3 - - + +
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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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442A GLU* 3.3 52.0 + - - +
443A GLN* 4.8 6.5 - - - -
444A ARG* 4.4 11.4 - - - +
572B LEU* 5.5 1.2 - - - +
573B MET 5.0 2.4 + - - +
575B TYR* 5.5 2.2 - - + -
643B VAL* 1.3 76.8 - - - +
645B ASP* 1.3 82.9 + - - +
646B PRO* 3.1 26.1 + - - +
649B ASP* 3.0 33.1 + - - +
650B ARG 3.5 7.4 - - - +
651B TRP* 3.7 41.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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