Contacts of the strand formed by residues 640 - 644 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D TRP* 3.9 29.8 - - + +
461D GLN* 5.3 4.1 + - - +
472D GLY 5.1 1.0 + - - +
473D ALA* 3.4 28.3 - - + +
481D LEU* 4.9 5.8 - - + +
559D ILE* 4.3 5.2 - - + -
575D TYR 3.5 8.1 - - - +
576D VAL* 3.8 14.9 - - - +
577D SER* 4.5 6.0 + - - +
638D GLY 4.6 2.5 - - - +
639D GLY* 1.3 78.6 - - - +
641D PHE* 1.3 60.6 + - - +
642D ALA* 4.2 13.4 - - + +
653D ALA* 3.9 19.3 - - + -
655D GLY 3.1 12.3 - - - +
656D ILE* 4.8 7.4 - - + -
657D VAL* 4.9 2.2 - - - -
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Residues in contact with PHE 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D GLY* 3.5 31.4 - - - -
575D TYR 3.5 2.2 - - - -
576D VAL* 3.5 20.6 - - + -
595D LEU* 3.6 24.0 - - + -
597D VAL* 4.1 24.0 - - + -
621D PHE* 4.1 8.5 - + - -
623D ALA* 3.8 20.9 - - + -
639D GLY 4.2 0.2 + - - -
640D VAL* 1.3 72.3 - - - +
642D ALA* 1.3 57.9 + - - +
643D VAL* 3.7 13.9 - - + -
653D ALA* 3.8 2.3 - - - -
654D THR* 3.0 48.7 + - - -
655D GLY* 2.8 16.3 + - - +
656D ILE* 4.7 0.2 - - - +
670D TYR* 3.7 29.1 - + + -
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Residues in contact with ALA 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D PHE* 5.5 1.8 - - + -
460D TRP* 4.0 16.8 - - + +
559D ILE* 3.9 23.6 - - + -
574D GLY* 3.5 1.4 - - - -
575D TYR* 2.6 51.5 + - + +
640D VAL* 4.2 8.1 - - + +
641D PHE* 1.3 73.8 - - - +
643D VAL* 1.3 61.3 + - - +
651D TRP* 4.2 8.9 - - + -
652D VAL 3.4 4.7 - - - -
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Residues in contact with VAL 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D PHE* 3.9 20.4 - - + +
572D LEU* 4.0 29.2 - - + -
573D MET 4.4 5.8 - - - +
574D GLY* 4.3 7.2 - - - -
641D PHE* 3.7 26.2 - - + -
642D ALA* 1.3 72.7 - - - +
644D ARG* 1.3 74.4 + - - +
645D ASP* 3.4 3.4 + - - -
646D PRO* 5.2 1.3 - - + -
651D TRP* 4.4 2.2 - - - -
652D VAL* 2.9 34.0 + - - +
654D THR* 3.6 26.9 - - + -
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Residues in contact with ARG 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C GLU* 3.2 55.5 + - - +
443C GLN* 4.5 6.8 - - - -
444C ARG* 4.0 13.5 - - - +
572D LEU* 5.7 0.5 - - - +
573D MET 5.2 2.0 + - - -
575D TYR* 5.5 2.2 - - + -
642D ALA 4.1 1.2 + - - -
643D VAL* 1.3 74.9 - - - +
645D ASP* 1.3 79.2 + - - +
646D PRO* 3.0 26.6 + - - +
649D ASP* 2.8 44.3 + - - +
650D ARG 3.8 3.4 - - - -
651D TRP* 3.8 37.1 - - + +
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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