Contacts of the helix formed by residues 592 - 605 (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 PRO 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A TYR* 3.4 43.7 - - + +
578A LEU* 5.8 0.4 - - + -
590A SER* 4.5 1.6 - - - +
591A LEU* 1.3 87.0 - - + +
593A VAL* 1.3 67.9 + - - +
594A HIS* 3.4 28.7 - - + +
595A VAL* 3.0 27.1 + - + +
596A ALA* 3.5 4.9 + - - +
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Residues in contact with VAL 593 (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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591A LEU 3.6 2.8 + - - +
592A PRO* 1.3 71.1 - - - +
594A HIS* 1.3 64.0 + - - +
595A VAL 3.1 0.3 + - - -
596A ALA* 3.1 9.5 + - + +
597A ASP* 3.0 39.1 + - - +
600A ARG* 6.1 0.7 - - - +
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Residues in contact with HIS 594 (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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548A ASP* 2.9 34.7 + - + +
549A GLN* 3.8 20.0 + - - +
552A THR* 4.7 9.9 - - + +
575A TYR* 4.8 0.2 - - - -
592A PRO* 3.4 24.8 - - + +
593A VAL* 1.3 79.3 + - - +
595A VAL* 1.3 67.9 + - + +
597A ASP* 3.7 13.9 - - - +
598A ALA* 3.3 19.6 + - - +
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Residues in contact with VAL 595 (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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548A ASP* 4.2 1.1 - - - +
571A LEU* 4.3 23.3 - - + -
572A LEU* 5.2 5.4 - - + -
575A TYR* 3.6 29.8 - - + -
591A LEU* 3.6 25.1 - - + -
592A PRO* 3.0 26.3 + - + +
594A HIS* 1.3 87.0 - - + +
596A ALA* 1.3 66.2 + - - +
598A ALA* 3.1 14.5 + - - +
599A PHE* 3.3 25.2 - - + -
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Residues in contact with ALA 596 (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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591A LEU* 4.6 7.5 - - + +
592A PRO 3.5 5.8 + - - +
593A VAL* 3.1 11.5 + - + +
595A VAL* 1.3 78.8 - - - +
597A ASP* 1.3 63.1 + - - +
599A PHE* 3.3 5.8 + - - +
600A ARG* 3.1 27.5 + - - +
648A LEU* 4.5 19.3 - - + -
651A GLU* 4.6 27.1 - - + +
652A LEU* 3.9 6.0 - - + +
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Residues in contact with ASP 597 (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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593A VAL* 3.0 39.0 + - - +
594A HIS* 3.7 11.3 - - - +
595A VAL 3.1 0.4 - - - -
596A ALA* 1.3 77.6 - - - +
598A ALA* 1.3 56.6 + - - +
600A ARG* 3.2 31.8 + - - +
601A ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 598 (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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552A THR* 3.9 25.6 - - + -
555A MET* 4.1 18.7 - - + +
571A LEU* 4.2 7.4 - - + -
594A HIS 3.3 10.6 + - - +
595A VAL 3.1 11.9 + - - +
597A ASP* 1.3 79.8 - - - +
599A PHE* 1.3 61.7 + - + +
601A ALA* 3.4 9.2 + - - +
602A VAL* 3.2 24.3 + - - +
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Residues in contact with PHE 599 (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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555A MET* 4.8 3.4 - - + -
568A ALA* 4.5 10.8 - - + -
571A LEU* 4.5 10.3 - - + -
572A LEU* 3.6 44.0 - - + -
595A VAL* 3.3 27.1 - - + -
596A ALA 3.3 6.1 + - - +
597A ASP 3.2 0.2 - - - -
598A ALA* 1.3 76.7 - - + +
600A ARG* 1.3 67.0 + - - +
601A ALA 3.2 0.4 - - - -
602A VAL* 3.3 6.6 + - - +
603A LEU* 3.1 25.5 + - - +
616A ILE* 3.5 42.8 - - + -
617A LEU* 4.2 15.1 - - + +
619A LEU* 5.5 4.3 - - + -
648A LEU* 4.7 19.7 - - + -
652A LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 600 (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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593A VAL* 6.1 0.8 - - - +
596A ALA* 3.1 13.7 + - - +
597A ASP* 3.2 32.4 + - - +
599A PHE* 1.3 77.1 - - - +
601A ALA* 1.3 63.1 + - - +
603A LEU* 3.2 8.4 + - - +
604A LEU* 3.0 34.0 + - + +
651A GLU* 3.0 38.6 + - - +
652A LEU* 3.4 25.5 - - + +
655A GLU* 2.8 49.1 + - + +
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Residues in contact with ALA 601 (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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597A ASP 2.9 12.8 + - - +
598A ALA* 3.4 12.8 - - - +
600A ARG* 1.3 79.2 - - - +
602A VAL* 1.3 61.4 + - + +
604A LEU* 3.4 5.8 + - - +
605A ASP* 3.0 26.4 + - - +
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Residues in contact with VAL 602 (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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555A MET* 3.9 26.0 - - + +
598A ALA 3.2 14.5 + - - +
599A PHE* 3.6 9.6 - - - +
600A ARG 3.2 0.4 - - - -
601A ALA* 1.3 78.6 - - + +
603A LEU* 1.3 63.1 + - - +
605A ASP* 3.4 15.2 + - - +
608A ILE* 3.9 21.1 - - + +
613A ALA* 4.0 32.9 - - + +
616A ILE* 4.1 26.2 - - + -
617A LEU* 4.5 8.3 - - + -
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Residues in contact with LEU 603 (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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599A PHE 3.1 10.2 + - - +
600A ARG* 3.2 9.4 + - - +
602A VAL* 1.3 80.8 - - - +
604A LEU* 1.3 60.2 + - - +
605A ASP 3.6 2.9 + - - +
613A ALA* 6.0 0.7 - - - -
617A LEU* 3.5 29.8 - - + -
652A LEU* 3.9 22.2 - - + -
655A GLU* 3.9 26.7 - - + +
656A LEU* 3.8 22.7 - - + -
659A ILE* 3.3 48.1 - - + +
680A LEU* 5.1 0.9 - - + -
684A CYS* 3.9 16.2 - - - -
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Residues in contact with LEU 604 (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* 3.0 29.2 + - + +
601A ALA* 3.7 5.4 - - - +
603A LEU* 1.3 78.6 - - - +
605A ASP* 1.3 59.1 + - - +
606A GLU* 3.0 20.8 + - - +
655A GLU* 3.9 34.8 - - + +
658A ALA* 6.1 2.9 - - + -
659A ILE* 5.2 7.2 - - + -
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Residues in contact with ASP 605 (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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556A ARG* 5.7 2.8 - - - +
564A ARG* 4.0 15.2 + - - -
601A ALA 3.0 16.9 + - - +
602A VAL* 3.8 4.9 - - - +
603A LEU 3.4 4.5 - - - +
604A LEU* 1.3 75.8 - - - +
606A GLU* 1.3 61.2 + - - +
607A LYS* 2.7 53.4 + - - -
608A ILE* 2.9 42.9 + - + +
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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