Contacts of the helix formed by residues 652 - 663 (chain A) in PDB entry 2DQM
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 LEU 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A ALA 3.9 7.9 - - - +
599A PHE* 4.2 22.0 - - + -
600A ARG* 3.4 49.1 - - + +
603A LEU* 3.9 20.0 - - + -
617A LEU* 5.3 3.8 - - + -
648A LEU* 2.9 35.1 + - + +
651A GLU* 1.3 82.6 - - + +
653A ALA* 1.3 65.2 + - - +
655A GLU* 3.2 12.3 + - - +
656A LEU* 2.8 37.7 + - + +
687A PHE* 6.4 1.8 - - + -
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Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A ALA 3.0 19.5 + - - +
650A THR* 3.8 10.8 - - - +
651A GLU 3.6 2.2 - - - -
652A LEU* 1.3 75.7 - - - +
654A ASP* 1.3 68.6 + - - +
656A LEU* 3.7 5.3 - - - +
657A LEU* 3.2 23.2 + - - +
688A LEU* 4.0 7.8 - - + +
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Residues in contact with ASP 654 (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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652A LEU 3.3 0.6 - - - -
653A ALA* 1.3 80.1 - - - +
655A GLU* 1.3 71.2 + - - +
657A LEU* 3.4 7.6 + - - +
658A ALA* 3.0 24.0 + - - +
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Residues in contact with GLU 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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600A ARG* 2.8 44.4 + - + -
603A LEU* 3.9 20.2 - - + -
604A LEU* 3.9 30.7 - - + +
651A GLU 4.1 0.9 - - - +
652A LEU* 3.2 22.4 - - - +
654A ASP* 1.3 82.8 + - + +
656A LEU* 1.3 62.5 + - - +
658A ALA* 3.3 6.9 + - - +
659A ILE* 3.0 30.0 + - - +
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Residues in contact with LEU 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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603A LEU* 3.8 18.6 - - + -
617A LEU* 5.4 2.5 - - + -
648A LEU 3.9 0.9 - - - +
649A ALA* 3.8 15.0 - - + +
652A LEU* 2.8 43.4 + - + +
653A ALA* 3.7 1.3 - - - +
655A GLU* 1.3 77.3 - - - +
657A LEU* 1.3 57.4 + - - +
659A ILE 3.4 0.2 + - - -
660A TYR* 2.9 29.8 + - - +
684A CYS* 3.8 24.4 - - - +
687A PHE* 3.5 47.8 - - + -
688A LEU* 3.7 19.7 - - + -
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Residues in contact with LEU 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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653A ALA 3.2 13.7 + - - +
654A ASP* 3.8 6.5 - - - +
656A LEU* 1.3 79.7 - - - +
658A ALA* 1.3 57.2 + - - +
660A TYR* 3.3 12.7 + - + +
661A ASN* 3.0 57.7 + - - +
688A LEU* 3.9 18.8 - - + +
695A LEU* 5.9 8.3 - - + -
699A LEU* 4.6 13.5 - - + -
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Residues in contact with ALA 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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604A LEU* 6.1 2.9 - - + -
654A ASP 3.0 17.4 + - - +
655A GLU* 3.6 8.7 - - - +
656A LEU 3.3 0.2 - - - -
657A LEU* 1.3 78.0 - - - +
659A ILE* 1.3 62.4 + - + +
661A ASN* 3.5 6.6 + - - +
662A ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 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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603A LEU* 3.3 39.0 - - + +
604A LEU* 5.2 7.4 - - + -
655A GLU* 3.0 16.4 + - - +
658A ALA* 1.3 78.4 - - + +
660A TYR* 1.3 66.2 + - - +
662A ALA* 4.2 7.9 - - + -
663A ASN* 2.9 46.2 + - - +
680A LEU* 3.9 19.3 - - + +
681A ARG* 5.0 0.3 - - - -
684A CYS* 3.7 22.4 - - - -
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Residues in contact with TYR 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 LEU 2.9 18.8 + - - +
657A LEU* 3.3 13.0 + - + +
659A ILE* 1.3 78.6 - - - +
661A ASN* 1.3 78.7 + - - +
663A ASN 3.5 1.7 + - - -
681A ARG* 3.0 89.6 + - + +
684A CYS* 4.2 6.3 - - + -
685A LEU* 4.0 13.6 - - + +
688A LEU* 3.8 18.2 - - + -
699A LEU* 3.7 30.7 + - + +
703A GLN* 2.6 38.3 + - - +
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Residues in contact with ASN 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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657A LEU* 3.0 41.8 + - - +
658A ALA* 3.9 6.0 - - - +
660A TYR* 1.3 93.4 - - - +
662A ALA* 1.3 63.9 + - - +
663A ASN 3.2 0.5 + - - -
664A TYR* 3.2 21.9 + - - +
681A ARG* 5.0 1.0 + - - +
699A LEU* 5.7 0.5 - - - +
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Residues in contact with ALA 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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658A ALA 2.9 18.6 + - - +
659A ILE* 3.3 13.9 + - + +
661A ASN* 1.3 76.8 - - - +
663A ASN* 1.3 63.6 + - - +
664A TYR 3.4 3.8 + - - +
677A LYS* 5.0 5.2 + - - -
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Residues in contact with ASN 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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610A PRO* 4.7 3.6 - - - +
659A ILE* 2.9 44.5 + - - +
660A TYR 3.5 0.2 + - - -
661A ASN 3.1 0.8 - - - -
662A ALA* 1.3 82.7 - - - +
664A TYR* 1.3 64.7 + - - +
665A GLN* 3.5 17.9 + - - +
677A LYS* 3.5 50.7 - - - +
678A ARG* 5.2 0.2 - - - -
680A LEU* 3.6 15.2 - - - +
681A ARG* 3.5 19.7 - - + +
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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