Contacts of the strand formed by residues 651 - 659 (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 TRP 651 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A GLY* 3.0 23.2 + - - +
437A PRO* 3.5 20.2 - - + +
440A PRO* 4.3 6.5 - - + +
441A VAL* 4.4 12.1 - - + -
442A GLU* 3.8 22.9 - - + -
443A GLN* 6.2 0.2 - - - +
457B ASN 5.7 1.3 - - - -
458B PHE* 4.7 6.3 - + - -
460B TRP* 3.7 40.8 - + + -
559B ILE* 3.3 3.9 - - + +
560B CYS* 3.0 28.9 + - - +
575B TYR* 3.7 43.7 - + + -
642B ALA* 4.2 11.9 - - + -
643B VAL 3.6 2.0 - - - -
644B ARG* 3.7 46.6 - - + +
649B ASP* 3.7 7.9 + - - -
650B ARG* 1.3 76.4 - - - +
652B VAL* 1.3 62.5 + - - +
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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
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559B ILE* 3.5 6.2 - - - +
560B CYS* 3.5 9.9 - - + -
561B LEU 3.5 5.6 - - - +
562B PRO* 3.3 44.4 - - + -
567B PHE* 3.7 31.4 - - + -
642B ALA* 3.2 5.5 - - - -
643B VAL 2.9 36.5 + - - +
645B ASP* 4.7 2.5 - - + -
650B ARG* 4.0 18.4 - - + +
651B TRP* 1.3 80.2 - - - +
653B ALA* 1.3 64.1 + - - +
654B THR* 3.2 5.5 + - + +
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Residues in contact with ALA 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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481B LEU* 4.6 11.9 - - + -
559B ILE* 3.6 28.2 - - + +
560B CYS 2.9 12.3 + - - +
561B LEU* 5.0 2.7 - - + -
562B PRO* 3.5 6.1 - - - +
640B VAL* 3.8 22.7 - - + -
641B PHE 3.6 6.5 - - - -
652B VAL* 1.3 71.0 - - - +
654B THR* 1.3 60.2 + - - +
655B GLY 3.3 2.7 - - - +
673B VAL* 3.1 25.1 - - + +
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Residues in contact with THR 654 (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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562B PRO* 4.4 2.7 - - + -
567B PHE* 3.7 35.4 - - + +
568B TYR* 2.6 45.9 + - - +
621B PHE* 3.5 2.4 - - - -
641B PHE* 3.1 32.2 + - - -
643B VAL* 3.5 25.6 - - + +
652B VAL* 4.1 7.4 - - + +
653B ALA* 1.3 72.6 - - - +
655B GLY* 1.3 58.4 + - - +
673B VAL* 2.8 12.8 + - - -
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Residues in contact with GLY 655 (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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621B PHE* 3.7 14.1 - - - -
640B VAL* 3.1 13.0 - - - +
641B PHE* 2.8 27.8 + - - -
653B ALA 3.3 1.4 - - - -
654B THR* 1.3 85.0 + - - +
656B ILE* 1.3 64.5 + - - +
670B TYR* 4.4 0.2 - - - -
671B THR 3.1 11.9 - - - -
673B VAL* 3.4 4.4 - - - +
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Residues in contact with ILE 656 (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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481B LEU* 3.8 18.4 - - + -
482B THR* 3.6 10.8 - - - +
483B ALA* 3.8 26.5 - - + +
540B ASP 4.3 4.5 - - - +
541B ILE* 3.5 41.7 - - + -
638B GLY* 3.9 9.6 - - - +
639B GLY 3.4 5.2 - - - +
640B VAL* 4.9 2.9 - - + -
655B GLY* 1.3 79.2 - - - +
657B VAL* 1.3 77.9 + - - +
658B SER* 3.0 2.1 + - - -
670B TYR* 3.2 7.3 - - - +
671B THR* 3.0 34.2 + - - +
673B VAL* 3.7 11.7 - - + -
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Residues in contact with VAL 657 (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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483B ALA* 3.9 4.2 - - - +
576B VAL* 3.6 31.0 - - + -
632B ALA* 3.6 24.7 - - + -
633B CYS 5.9 0.2 - - - +
636B ASP 3.9 13.2 - - - +
637B SER* 3.8 22.1 - - - +
638B GLY 3.1 20.3 + - - -
639B GLY 2.8 23.0 + - - +
640B VAL* 4.5 1.1 - - - +
656B ILE* 1.3 75.6 - - - +
658B SER* 1.3 61.2 + - - +
659B TRP 5.3 0.4 - - - +
669B PHE 4.5 0.4 - - - +
670B TYR* 3.7 23.6 - - + -
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Residues in contact with SER 658 (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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485B HIS* 3.0 23.1 + - - -
537B PHE* 3.6 6.8 + - - +
540B ASP* 2.6 32.8 + - - +
620B MET* 6.2 0.8 - - - +
637B SER* 4.1 3.8 + - - -
656B ILE 3.0 8.1 + - - -
657B VAL* 1.3 78.9 - - - +
659B TRP* 1.3 78.5 + - - +
669B PHE 3.2 14.3 + - - -
670B TYR 4.4 0.7 - - - -
671B THR* 3.9 16.1 + - - -
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Residues in contact with TRP 659 (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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537B PHE* 3.5 51.8 - + + +
607B LEU* 4.1 13.9 - - + -
612B ARG* 5.5 0.2 - - - -
614B ASP* 3.6 36.8 - - + -
615B VAL 3.6 20.1 + - - -
616B PHE* 4.8 1.3 - - + -
620B MET* 3.6 19.2 - - - -
657B VAL* 5.3 0.6 - - - +
658B SER* 1.3 87.6 - - - +
660B GLY* 1.3 86.9 + - - +
661B ILE* 4.6 4.3 - - + -
668B GLY* 4.0 1.6 - - - -
669B PHE* 2.9 84.1 + + + +
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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