Contacts of the helix formed by residues 660 - 669 (chain A) in PDB entry 3QHE
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 ASN 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657A ARG* 3.0 18.7 + - - +
658A GLU 4.7 4.4 + - - -
659A ASN* 1.3 83.7 - - - +
661A CYS* 1.3 64.7 + - - +
662A LEU 3.4 2.5 - - - -
663A GLN* 3.0 39.7 + - + +
664A THR* 3.2 25.5 + - - +
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Residues in contact with CYS 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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617A VAL* 4.1 15.5 - - + -
620A LEU* 4.1 5.8 - - - -
639A LEU* 3.9 20.9 - - - -
656A LEU* 3.1 50.9 + - + +
657A ARG* 4.9 0.6 - - - +
659A ASN 3.3 1.0 - - - -
660A ASN* 1.3 75.9 - - - +
662A LEU* 1.3 60.3 + - + +
664A THR* 3.1 6.7 + - - -
665A LEU* 2.8 51.2 + - - +
687A LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 662 (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 LEU* 6.4 1.8 - - + -
657A ARG* 5.3 9.1 - - + +
660A ASN 3.4 0.4 - - - -
661A CYS* 1.3 78.9 - - + +
663A GLN* 1.3 63.6 + - - +
665A LEU* 3.1 6.4 + - + +
666A LEU* 3.0 26.3 + - - +
684A LEU* 4.1 19.1 - - + +
687A LEU* 3.9 35.4 - - + -
694A ASP* 3.6 45.8 - - + +
697A ALA* 4.3 12.1 - - + -
698A LEU* 4.2 10.5 - - + -
701A MET* 3.7 16.6 - - + -
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Residues in contact with GLN 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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660A ASN* 3.0 44.9 + - + +
661A CYS 3.4 0.2 - - - -
662A LEU* 1.3 78.2 - - - +
664A THR* 1.3 64.3 + - - +
666A LEU* 3.4 6.8 + - - +
667A GLN* 3.3 22.8 + - - +
701A MET* 3.4 29.0 - - + -
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Residues in contact with THR 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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617A VAL* 5.5 2.2 - - - +
620A LEU* 3.7 28.0 - - + -
621A THR* 3.6 32.3 - - + +
659A ASN 4.9 2.3 + - - -
660A ASN* 3.2 14.1 + - - +
661A CYS* 3.1 9.9 + - - -
663A GLN* 1.3 75.6 - - - +
665A LEU* 1.3 65.8 + - - +
667A GLN* 3.1 11.2 + - + +
668A HIS* 3.0 32.0 + - + +
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Residues in contact with LEU 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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620A LEU* 4.1 22.2 - - + -
639A LEU* 4.6 2.9 - - + -
661A CYS* 2.8 33.1 + - - +
662A LEU* 3.1 7.6 + - + +
664A THR* 1.3 75.6 - - - +
666A LEU* 1.3 63.4 + - - +
668A HIS* 3.2 19.6 + - - +
669A LEU* 3.2 14.6 + - - +
680A ALA* 3.7 19.0 - - + +
683A THR* 3.6 41.1 - - + +
684A LEU* 3.9 28.7 - - + -
687A LEU* 3.9 11.9 - - + -
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Residues in contact with LEU 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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662A LEU 3.0 13.3 + - - +
663A GLN* 3.6 8.5 - - - +
665A LEU* 1.3 76.2 - - - +
667A GLN* 1.3 56.2 + - - +
669A LEU* 3.1 46.8 + - + +
670A LYS* 4.0 2.1 + - - +
684A LEU* 4.0 12.8 - - + -
698A LEU* 4.0 17.9 - - + -
701A MET* 3.6 37.7 - - + +
703A ALA* 3.8 26.5 - - + -
706A MET* 3.7 32.9 - - + +
707A LEU* 5.4 0.4 - - + -
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Residues in contact with GLN 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 GLN 3.3 10.4 + - - +
664A THR* 3.1 13.8 + - + +
666A LEU* 1.3 77.5 - - - +
668A HIS* 1.3 60.7 + - + +
670A LYS* 3.0 46.0 + - + +
671A SER* 3.8 2.9 + - - -
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Residues in contact with HIS 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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620A LEU* 2.8 57.5 + - + +
632A ILE* 3.6 20.9 - - + +
664A THR* 3.0 24.4 + - + +
665A LEU* 3.2 15.6 + - - +
667A GLN* 1.3 74.3 - - + +
669A LEU* 1.3 64.1 + - - +
670A LYS 3.1 0.4 - - - -
671A SER* 3.2 21.0 + - - -
676A ILE* 3.5 21.4 + - + +
677A VAL* 3.3 12.3 - - - +
679A ASN* 6.2 1.0 - - - +
680A ALA* 3.7 17.3 + - + +
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Residues in contact with LEU 669 (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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665A LEU 3.2 9.5 + - - +
666A LEU* 3.1 41.2 + - + +
668A HIS* 1.3 77.3 - - - +
670A LYS* 1.3 57.2 + - + +
671A SER 3.3 1.3 + - - +
677A VAL* 3.7 19.8 - - + +
680A ALA* 4.2 9.2 - - + -
681A CYS* 3.8 29.4 - - - +
684A LEU* 4.0 14.4 - - + -
706A MET* 3.8 25.6 - - + +
707A LEU* 3.9 20.4 - - + -
710A LEU* 4.5 21.0 - - + +
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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