Contacts of the helix formed by residues 657 - 671 (chain A) in PDB entry 3QFS
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 GLU 657 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A MET* 1.3 78.7 - - - +
658A HIS* 1.3 68.6 + - - +
659A ALA* 4.4 7.2 - - + +
660A GLN* 2.9 35.3 + - + +
661A ALA* 2.9 11.5 + - - +
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Residues in contact with HIS 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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644A ASN* 5.7 0.9 - - - -
647A TYR* 4.1 34.0 - + + +
648A ASP* 4.7 10.6 + - - -
651A ALA* 4.6 9.5 - - + +
656A MET 3.9 0.4 + - - -
657A GLU* 1.3 73.7 + - - +
659A ALA* 1.3 59.7 + - - +
661A ALA* 2.8 25.8 + - - +
662A VAL* 2.8 34.0 + - + +
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Residues in contact with ALA 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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657A GLU* 3.2 6.4 - - + +
658A HIS* 1.3 81.8 - - - +
660A GLN* 1.3 64.8 + - + +
662A VAL* 3.2 11.4 + - - +
663A ASP* 3.0 22.0 + - - +
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Residues in contact with GLN 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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656A MET* 3.0 27.4 - - + +
657A GLU* 2.9 39.9 + - + +
659A ALA* 1.3 78.4 - - + +
661A ALA* 1.3 56.2 + - - +
663A ASP* 3.4 9.1 + - - +
664A TYR* 2.9 27.2 + - - +
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Residues in contact with ALA 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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647A TYR* 3.5 30.5 - - + +
650A VAL* 4.4 3.1 - - + -
651A ALA* 3.8 19.1 - - + +
656A MET* 3.7 9.6 - - - -
657A GLU 2.9 9.6 + - - +
658A HIS* 2.8 12.8 + - - +
660A GLN* 1.3 76.7 - - - +
662A VAL* 1.3 62.2 + - - +
663A ASP 3.1 0.2 - - - -
664A TYR* 3.2 4.7 + - - +
665A ILE* 3.0 29.5 + - - +
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A TYR* 3.7 28.3 - - + +
658A HIS* 2.8 47.9 + - + +
659A ALA* 3.5 9.6 - - - +
661A ALA* 1.3 75.7 - - - +
663A ASP* 1.3 57.4 + - - +
665A ILE* 3.6 1.4 + - - +
666A LYS* 3.0 66.2 + - + +
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Residues in contact with ASP 663 (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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659A ALA 3.0 12.4 + - - +
660A GLN* 3.6 12.4 - - - +
662A VAL* 1.3 76.0 - - - +
664A TYR* 1.3 60.0 + - - +
666A LYS* 3.8 7.3 - - - +
667A LYS* 2.9 70.1 + - - +
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Residues in contact with TYR 664 (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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620A TRP* 3.9 12.2 - + - -
623A ILE* 3.6 33.8 + - + +
624A GLU* 2.7 32.7 + - - -
650A VAL* 3.7 24.2 - - + -
656A MET* 3.9 17.5 - - + -
660A GLN 2.9 15.0 + - - +
661A ALA 3.4 9.9 - - - +
663A ASP* 1.3 78.0 - - - +
665A ILE* 1.3 63.5 + - - +
667A LYS* 3.3 9.7 + - - +
668A LEU* 3.2 37.6 + - + +
673A ARG* 5.3 1.6 + - - -
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Residues in contact with ILE 665 (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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623A ILE* 5.6 0.4 - - + -
629A ILE* 5.2 2.2 - - + -
643A GLN* 4.8 4.3 - - + -
646A PHE* 4.2 18.6 - - + +
647A TYR* 3.5 37.2 - - + +
650A VAL* 3.9 27.1 - - + -
661A ALA 3.0 15.8 + - - +
664A TYR* 1.3 72.8 - - + +
666A LYS* 1.3 62.3 + - - +
668A LEU* 2.9 41.0 + - + +
669A MET* 3.0 20.5 + - + +
674A TYR* 3.9 27.4 - - + -
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Residues in contact with LYS 666 (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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643A GLN* 5.9 0.7 - - - +
647A TYR* 4.2 11.9 - - - +
662A VAL* 3.0 47.4 + - + +
663A ASP* 3.8 8.7 - - - +
665A ILE* 1.3 77.4 - - + +
667A LYS* 1.3 62.0 + - + +
669A MET* 3.3 19.4 + - - +
670A THR* 3.1 29.5 + - + +
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Residues in contact with LYS 667 (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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663A ASP* 2.9 46.9 + - - +
664A TYR* 3.6 8.1 - - - +
665A ILE 3.1 0.2 - - - -
666A LYS* 1.3 75.0 - - + +
668A LEU* 1.3 62.2 + - + +
670A THR* 2.6 24.2 + - + +
671A LYS* 2.9 38.3 - - - +
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Residues in contact with LEU 668 (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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623A ILE* 4.2 11.2 - - + -
627A ALA 5.9 0.2 - - - +
629A ILE* 4.6 13.0 - - + -
664A TYR* 3.2 36.8 + - + +
665A ILE* 2.9 34.5 + - + +
667A LYS* 1.3 78.7 - - - +
669A MET* 1.3 56.2 + - - +
671A LYS* 3.3 6.3 + - + -
672A GLY 3.1 4.2 + - - -
673A ARG* 2.7 78.2 + - + +
674A TYR* 3.9 12.8 - - + -
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Residues in contact with MET 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN* 3.9 17.7 - - - +
665A ILE* 3.0 20.3 + - + +
666A LYS* 3.5 20.4 - - - +
667A LYS 3.2 0.4 - - - -
668A LEU* 1.3 77.6 - - - +
670A THR* 1.3 61.3 + - + +
672A GLY* 3.2 12.5 + - - -
674A TYR* 3.7 41.8 - - + +
676A LEU* 3.8 30.3 - - + -
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Residues in contact with THR 670 (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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666A LYS* 3.1 16.7 + - + +
667A LYS* 2.6 27.6 + - + +
669A MET* 1.3 76.9 - - + +
671A LYS* 1.3 65.1 + - - +
672A GLY 3.2 2.6 + - - -
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Residues in contact with LYS 671 (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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628A HIS* 5.6 0.5 + - - -
667A LYS* 2.9 38.4 + - - +
668A LEU* 3.3 7.8 + - + +
669A MET 3.2 0.2 - - - -
670A THR* 1.3 81.6 + - - +
672A GLY* 1.3 61.5 + - - +
673A ARG* 3.3 19.1 + - + +
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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