Contacts of the strand formed by residues 654 - 661 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A LEU* 3.7 28.9 - - + -
652A VAL 3.2 13.5 - - - +
653A ASP* 1.4 83.6 - - - +
655A LYS* 1.3 61.5 + - - +
673A ALA 3.7 1.2 - - - +
674A VAL* 3.2 3.3 - - - -
675A ILE* 2.8 45.1 + - + +
678A ASN 3.2 29.8 - - - +
679A GLY* 4.1 1.1 - - - -
682A PRO* 4.4 2.0 - - + -
684A TRP* 3.7 15.6 + - + -
704A VAL* 4.2 4.7 - - + -
705A GLU 3.2 10.1 - - - +
716A ILE* 4.3 2.7 - - + -
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Residues in contact with LYS 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A PRO* 1.3 77.4 - - - +
656A VAL* 1.3 63.4 + - - +
657A ILE* 3.5 20.2 - - + +
671A GLN* 3.1 44.7 + - - +
672A THR* 3.7 21.8 - - - +
673A ALA 3.9 2.5 - - - +
674A VAL* 3.6 22.9 - - + -
684A TRP* 4.3 1.6 - - - +
703A MET 3.6 0.7 - - - +
704A VAL* 3.4 3.9 - - - -
705A GLU* 2.9 46.1 + - + +
707A TYR* 4.2 9.9 - - + -
713A ASN* 3.9 23.3 - - - +
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A ILE* 4.0 26.2 - - + -
655A LYS* 1.3 78.1 - - - +
657A ILE* 1.3 71.4 + - - +
658A VAL* 4.1 3.5 + - + -
671A GLN* 3.4 2.3 - - - -
672A THR* 3.0 37.3 + - + +
684A TRP* 3.7 33.7 - - + -
688A PHE* 4.6 1.0 - - - -
702A PHE* 4.9 0.7 - - + -
703A MET 3.1 12.3 - - - +
704A VAL* 4.2 5.2 - - + -
748A LEU* 3.5 35.2 - - + -
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Residues in contact with ILE 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LYS* 3.5 33.2 - - - +
656A VAL* 1.3 74.9 - - - +
658A VAL* 1.3 64.2 + - - +
659A GLU* 3.6 21.3 - - - +
669A SER* 3.5 22.9 - - - +
670A ARG 3.4 6.3 - - - +
671A GLN* 4.0 11.0 - - + +
701A ARG 3.6 0.5 - - - +
702A PHE* 3.6 2.1 - - - -
703A MET* 2.6 59.4 + - + +
705A GLU* 3.6 31.6 - - + +
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Residues in contact with VAL 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A VAL* 4.7 9.4 - - + -
635A ILE* 3.8 35.0 - - + -
656A VAL* 4.4 3.1 - - + -
657A ILE* 1.3 76.9 - - - +
659A GLU* 1.3 64.0 + - - +
669A SER* 3.4 1.9 + - - -
670A ARG 2.7 41.5 + - - +
688A PHE* 4.1 14.4 - - + -
690A PHE* 3.6 30.5 - - + -
700A VAL* 4.2 19.3 - - + -
701A ARG 3.3 6.5 - - - +
702A PHE* 4.1 11.4 - - + -
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Residues in contact with GLU 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A PRO* 5.1 0.9 - - - +
657A ILE* 3.6 20.1 - - + +
658A VAL* 1.3 76.5 - - - +
660A ILE* 1.3 65.3 - - - +
661A HIS* 2.8 33.5 + - + +
668A GLY 3.4 11.7 - - - +
669A SER* 4.0 9.7 + - - +
690A PHE* 4.9 0.4 - - - -
699A LEU 3.7 0.5 - - - +
700A VAL* 3.5 4.5 - - - +
701A ARG* 2.6 77.7 + - + +
703A MET* 5.0 4.9 - - + +
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Residues in contact with ILE 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A LEU* 3.8 18.2 - - + -
659A GLU* 1.3 77.3 - - - +
661A HIS* 1.3 65.7 + - - +
666A ASP* 3.3 34.1 - - + +
667A THR* 3.4 8.1 - - - +
668A GLY 2.9 28.1 + - - +
690A PHE* 3.7 34.3 - - + -
692A VAL* 4.3 11.4 - - + -
698A ALA* 4.2 14.6 - - + -
699A LEU 3.5 4.0 - - - +
700A VAL* 3.5 33.7 - - + -
723A TRP* 4.7 0.7 - - + -
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Residues in contact with HIS 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A VAL* 4.2 21.4 - - + +
584A PRO* 5.7 4.9 - - + -
588A VAL* 3.8 29.2 - - + +
659A GLU* 2.8 40.8 + - + +
660A ILE* 1.3 79.3 + - - +
662A GLY* 1.3 58.9 + - - +
667A THR* 4.4 8.4 - - + +
697A LEU 3.6 1.4 - - - +
698A ALA* 3.0 2.9 - - - -
699A LEU* 2.7 50.2 + - + +
701A 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