Contacts of the strand formed by residues 469 - 475 (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 ARG 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B PHE* 3.5 35.0 - - + -
464B THR 3.5 4.3 - - - -
465B ASN* 4.0 4.6 + - - +
468B GLY* 1.3 72.9 - - - -
470B GLY* 1.3 63.9 + - - +
509B VAL* 4.1 20.8 - - - +
513B MET* 5.5 1.4 - - - +
579B PHE* 3.0 31.4 + - + +
580B GLY* 4.9 1.1 - - - -
586B ILE* 4.3 14.6 - - - +
587B ALA 2.9 27.9 + - - -
588B HIS* 5.2 3.8 + - - -
634B GLN 5.7 0.2 - - - -
635B GLY* 3.2 29.4 + - - +
637B SER* 6.0 0.7 - - - -
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Residues in contact with GLY 470 (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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463B PHE* 3.6 8.5 - - - -
464B THR* 2.8 41.6 + - - +
469B ARG* 1.3 78.2 - - - +
471B GLY* 1.3 58.3 + - - -
486B THR* 4.8 6.3 - - - -
579B PHE* 4.8 2.8 - - - -
635B GLY 3.4 15.3 - - - +
637B SER* 3.8 8.5 - - - -
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Residues in contact with GLY 471 (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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461B GLN* 4.0 7.9 - - - -
462B VAL 3.1 12.6 - - - -
464B THR* 4.4 9.6 + - - +
470B GLY* 1.3 74.5 - - - -
472B GLY* 1.3 51.6 + - - -
482B THR* 2.6 28.4 + - - -
486B THR* 5.1 0.7 + - - -
579B PHE* 5.7 0.9 - - - -
635B GLY 4.0 2.6 + - - -
636B ASP 4.6 2.0 - - - -
637B SER 2.9 11.4 + - - +
638B GLY* 3.0 12.0 - - - -
639B GLY* 4.0 4.9 - - - -
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Residues in contact with GLY 472 (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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460B TRP* 5.2 0.2 - - - -
461B GLN* 3.5 10.0 + - - -
462B VAL* 3.0 34.8 + - - +
464B THR* 5.5 0.4 - - - -
471B GLY* 1.3 74.1 - - - -
473B ALA* 1.3 60.4 + - - +
480B ILE* 4.3 4.0 - - - -
481B LEU 3.2 10.1 - - - -
482B THR* 4.1 2.9 - - - -
638B GLY 3.1 13.8 + - - -
639B GLY* 3.9 4.7 - - - -
640B VAL* 5.0 0.5 + - - +
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Residues in contact with ALA 473 (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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460B TRP* 3.1 25.8 - - + -
462B VAL* 3.8 4.4 - - - +
472B GLY* 1.3 73.2 - - - +
474B LEU* 1.3 63.2 + - - +
475B LEU* 3.6 0.7 + - - +
480B ILE* 3.4 1.4 - - - -
481B LEU* 2.9 35.4 + - + +
559B ILE* 4.1 10.5 - - + -
638B GLY 4.4 0.2 + - - -
640B VAL* 3.2 33.2 - - + -
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Residues in contact with LEU 474 (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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460B TRP* 2.8 21.9 + - - +
462B VAL* 3.6 7.7 - - + +
473B ALA* 1.3 72.9 - - - +
475B LEU* 1.3 65.9 - - - +
476B GLY 3.6 21.5 - - - +
477B ASP 4.4 5.6 - - - -
478B ARG* 4.9 1.3 - - - -
479B TRP 3.4 19.5 - - - +
480B ILE* 4.6 3.8 - - + -
504B LEU* 4.5 13.2 - - + -
546B LEU* 5.0 1.6 - - + -
550B VAL* 4.1 15.7 - - + -
552B LEU* 3.9 14.6 - - + -
556B LEU* 3.9 22.7 - - + -
557B LEU 3.9 5.6 - - - -
558B PRO* 3.3 17.0 - - + +
559B ILE* 3.2 24.4 + - - +
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Residues in contact with LEU 475 (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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473B ALA 3.6 2.0 + - - +
474B LEU* 1.3 78.9 - - - +
476B GLY* 1.3 69.3 + - - +
478B ARG 3.7 0.3 + - - -
479B TRP* 2.9 41.2 + - + +
481B LEU* 4.1 29.4 - - + +
543B LEU* 4.5 6.7 - - + -
559B ILE* 3.4 34.1 - - + +
561B LEU* 4.2 24.7 - - + -
680B ILE* 3.9 27.8 - - + -
684B MET* 4.3 9.6 - - - -
801B GOL 3.5 11.0 - - - +
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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