Contacts of the strand formed by residues 654 - 661 (chain B) in PDB entry 1QAS
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 PRO 654 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B LEU* 3.7 27.1 - - + -
652B VAL* 3.0 31.2 - - + +
653B ASP* 1.3 76.8 - - - +
655B LYS* 1.3 61.3 + - - +
673B ALA 3.7 1.4 - - - +
674B VAL* 3.2 3.7 - - - -
675B ILE* 2.8 43.0 + - + +
678B ASN 3.1 24.7 - - - +
682B PRO* 4.4 1.8 - - + -
684B TRP* 3.7 14.8 + - + -
704B VAL* 4.2 4.5 - - + -
705B GLU 3.3 10.1 - - - +
716B ILE* 4.3 0.2 - - + -
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Residues in contact with LYS 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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654B PRO* 1.3 78.0 - - - +
656B VAL* 1.3 62.8 + - - +
657B ILE* 3.5 18.8 - - + +
671B GLN* 3.0 45.2 + - - +
672B THR* 3.7 21.1 - - - +
673B ALA 4.0 3.1 - - - +
674B VAL* 3.7 22.7 - - + -
684B TRP* 4.3 1.6 - - - +
703B MET 3.6 0.3 - - - +
704B VAL* 3.3 3.9 - - - -
705B GLU* 2.9 46.4 + - + +
707B TYR* 4.2 10.3 - - + -
713B ASN* 3.9 23.1 - - - +
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Residues in contact with VAL 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B ILE* 4.0 26.7 - - + -
655B LYS* 1.3 78.8 - - - +
657B ILE* 1.3 70.4 + - - +
658B VAL* 4.1 2.8 + - + -
671B GLN* 3.4 2.3 - - - -
672B THR* 3.0 37.1 + - + +
684B TRP* 3.7 31.4 - - + -
688B PHE* 4.6 0.9 - - - -
702B PHE* 4.9 0.9 - - + -
703B MET 3.1 11.9 - - - +
704B VAL* 4.2 5.6 - - + -
748B LEU* 3.5 37.9 - - + -
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Residues in contact with ILE 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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655B LYS* 3.5 32.5 - - - +
656B VAL* 1.3 73.7 - - - +
658B VAL* 1.3 63.9 + - - +
659B GLU* 3.6 21.1 - - - +
669B SER* 3.4 23.1 - - - +
670B ARG 3.4 6.5 - - - +
671B GLN* 3.9 11.7 - - + +
701B ARG 3.7 0.5 - - - +
702B PHE* 3.6 2.1 - - - -
703B MET* 2.6 58.0 + - + +
705B GLU* 3.6 33.4 - - + +
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Residues in contact with VAL 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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633B VAL* 4.6 9.0 - - + -
635B ILE* 3.8 35.0 - - + -
656B VAL* 4.4 3.6 - - + +
657B ILE* 1.3 76.7 - - - +
659B GLU* 1.3 63.5 + - - +
669B SER* 3.3 1.6 - - - -
670B ARG 2.7 36.6 + - - +
688B PHE* 4.1 14.4 - - + -
690B PHE* 3.5 31.4 - - + -
700B VAL* 4.2 18.4 - - + -
701B ARG 3.4 7.0 - - - +
702B PHE* 4.1 12.1 - - + -
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Residues in contact with GLU 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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584B PRO* 5.0 1.0 - - - +
657B ILE* 3.6 21.0 - - + +
658B VAL* 1.3 77.4 - - - +
660B ILE* 1.3 64.9 - - - +
661B HIS* 2.9 33.0 + - + +
668B GLY 3.4 11.2 - - - +
669B SER* 4.0 9.3 + - - -
690B PHE* 4.8 0.4 - - - -
699B LEU 3.7 0.2 - - - +
700B VAL* 3.5 5.0 - - - +
701B ARG* 2.6 75.3 + - + +
703B MET* 5.0 5.1 - - + +
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Residues in contact with ILE 660 (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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631B LEU* 3.9 17.9 - - + -
659B GLU* 1.3 78.3 - - - +
661B HIS* 1.3 65.2 + - - +
666B ASP* 3.2 32.5 - - + +
667B THR* 3.4 8.5 - - - +
668B GLY 2.9 27.7 + - - +
690B PHE* 3.6 33.2 - - + -
692B VAL* 4.3 12.8 - - + -
698B ALA* 4.2 15.0 - - + -
699B LEU 3.5 4.0 - - - +
700B VAL* 3.4 34.1 - - + -
723B TRP* 4.6 0.7 - - + -
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Residues in contact with HIS 661 (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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563B SER* 5.8 1.4 + - - -
565B VAL* 4.1 23.3 - - + +
584B PRO* 5.6 4.9 - - + -
588B VAL* 3.7 34.7 - - + +
659B GLU* 2.9 39.9 + - + +
660B ILE* 1.3 77.9 + - - +
662B GLY* 1.3 57.9 + - - +
667B THR* 4.3 8.8 - - + +
697B LEU 3.6 1.4 - - - +
698B ALA* 3.0 2.5 - - - -
699B LEU* 2.7 46.7 + - + +
701B ARG* 3.8 17.8 - - + +
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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