Contacts of the helix formed by residues 592 - 603 (chain A) in PDB entry 5A7R
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 SER 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A HIS* 3.1 27.3 + - - -
590A TYR 3.6 0.2 - - - -
591A GLN* 1.3 82.1 - - - +
593A ILE* 1.3 67.6 + - - +
594A LEU 3.5 1.3 - - - -
595A PRO* 3.5 2.1 - - - +
596A ASP* 3.1 33.2 + - - +
684A ARG* 2.2 30.4 + - - -
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Residues in contact with ILE 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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588A HIS* 3.1 40.3 + - + +
589A LEU* 3.8 15.0 - - + +
592A SER* 1.3 80.5 - - - +
594A LEU* 1.3 65.4 + - - +
596A ASP* 3.3 2.1 + - - +
597A MET* 3.0 42.8 + - + +
680A PHE* 4.2 17.5 - - + +
683A PHE 5.0 0.4 - - - -
684A ARG* 4.0 45.1 - - + +
687A THR* 5.0 0.3 + - - -
1982A GOL 3.8 23.6 - - - +
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Residues in contact with LEU 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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547A PHE* 4.1 19.1 - - + -
553A LEU* 4.2 11.2 - - + -
577A TRP* 3.6 34.8 - - + -
589A LEU* 2.8 38.7 + - + +
590A TYR* 4.2 3.6 - - - -
593A ILE* 1.3 73.6 - - - +
595A PRO* 1.3 66.0 - - + +
597A MET* 3.1 15.6 + - - +
598A VAL* 2.9 31.7 + - - +
638A PHE* 4.0 31.0 - - + -
639A PHE* 4.1 8.4 - - + -
680A PHE* 4.4 6.7 - - + -
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Residues in contact with PRO 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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547A PHE* 5.2 4.5 - - + -
590A TYR 3.3 22.9 - - - +
591A GLN* 3.3 24.9 - - - +
592A SER 3.5 8.3 - - - +
594A LEU* 1.3 93.7 - - + +
596A ASP* 1.3 63.3 - - - +
598A VAL* 3.4 9.3 + - + +
599A LYS* 3.1 39.4 + - - +
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Residues in contact with ASP 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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592A SER* 3.1 22.6 + - - +
593A ILE 3.7 3.8 - - - +
595A PRO* 1.3 80.2 - - - +
597A MET* 1.3 61.5 + - - +
599A LYS* 3.4 22.7 + - - +
600A ILE* 3.1 24.4 + - - +
684A ARG* 3.2 23.8 + - - +
687A THR* 3.8 29.2 - - - +
688A ALA* 5.5 0.7 - - - -
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Residues in contact with MET 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 ILE* 3.0 31.6 + - + +
594A LEU* 3.1 12.5 + - - +
596A ASP* 1.3 73.9 - - - +
598A VAL* 1.4 67.8 + - - +
600A ILE* 3.4 10.4 - - - +
601A ALA* 3.0 24.1 + - - +
635A ALA* 3.6 5.1 - - + +
638A PHE* 3.6 42.4 - - + -
639A PHE* 3.7 11.0 - - + -
680A PHE* 3.9 10.5 - - - -
683A PHE* 3.6 54.7 - - + -
687A THR* 4.3 7.2 - - + -
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Residues in contact with VAL 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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543A LEU* 3.8 39.9 - - + +
544A LEU* 4.1 11.4 - - + -
547A PHE* 4.2 10.3 - - + -
594A LEU 2.9 18.0 + - - +
595A PRO* 3.7 10.8 - - + +
596A ASP 3.3 0.2 - - - -
597A MET* 1.4 76.6 - - - +
599A LYS* 1.3 59.1 + - + +
601A ALA* 3.2 3.7 + - - +
602A LEU* 2.9 50.3 + - + +
639A PHE* 3.6 26.0 - - + -
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Residues in contact with LYS 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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544A LEU* 5.3 10.1 - - + -
595A PRO* 3.1 24.3 + - - +
596A ASP* 3.8 23.7 + - - +
597A MET 3.3 0.4 - - - -
598A VAL* 1.3 85.5 - - + +
600A ILE* 1.3 61.4 + - - +
602A LEU* 3.4 5.7 + - - +
603A CYS* 3.1 23.2 + - - +
1966A BME 5.3 0.3 - - - -
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Residues in contact with ILE 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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596A ASP 3.1 17.4 + - - +
597A MET* 3.4 13.7 - - - +
599A LYS* 1.3 74.1 - - - +
601A ALA* 1.4 67.2 + - - +
603A CYS* 3.3 12.4 + - - +
604A LEU 3.7 0.5 + - - -
607A ILE* 4.2 9.9 - - + -
628A GLU* 4.5 16.4 - - + +
631A ALA* 4.0 28.7 - - + +
632A SER* 2.8 32.2 + - - +
635A ALA* 3.8 14.8 - - + -
683A PHE* 6.1 0.9 - - + -
686A VAL 4.7 11.9 - - - +
687A THR* 4.1 14.8 - - + -
691A PRO* 6.4 0.4 - - + -
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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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536A TRP* 3.7 4.1 - - - -
543A LEU* 5.4 3.4 - - + -
597A MET 3.0 18.9 + - - +
598A VAL* 3.5 4.7 - - - +
600A ILE* 1.4 77.9 - - - +
602A LEU* 1.3 64.3 + - + +
604A LEU* 3.1 18.0 + - - +
632A SER 4.0 4.3 - - - -
635A ALA* 3.8 13.9 - - + -
636A ASN* 3.1 40.7 + - - +
639A PHE* 4.3 10.1 - - + -
641A THR* 6.2 0.4 - - + -
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Residues in contact with LEU 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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536A TRP* 3.5 31.2 - - + -
539A ILE* 4.1 20.4 - - + -
540A GLN* 4.1 27.0 + - + +
543A LEU* 4.5 9.2 - - + -
544A LEU* 3.8 31.2 - - + -
598A VAL* 2.9 39.4 + - + +
599A LYS* 3.8 6.1 - - - +
600A ILE 3.3 0.2 - - - -
601A ALA* 1.3 73.9 - - + +
603A CYS* 1.3 59.6 + - - +
604A LEU 3.1 5.8 + - - -
605A PRO* 3.7 5.4 - - - +
606A ASN* 5.1 0.3 - - - +
636A ASN* 5.8 0.2 - - - +
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Residues in contact with CYS 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 LYS 3.1 15.7 + - - +
600A ILE* 3.8 4.3 - - - +
601A ALA 3.2 1.0 - - - -
602A LEU* 1.3 76.6 - - - +
604A LEU* 1.3 65.6 + - - +
605A PRO* 3.3 2.2 - - - -
606A ASN* 2.9 29.4 + - - -
607A ILE* 3.3 26.4 + - + +
1966A BME 1.9 63.3 - - + -
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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