Contacts of the helix formed by residues 676 - 680 (chain A) in PDB entry 4MS0
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 CYS 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A THR* 3.7 32.5 - - - -
533A VAL* 4.6 1.1 - - - -
536A CYS* 3.7 28.9 - - - -
672A ALA 3.2 9.2 + - - +
673A CYS 3.1 21.3 + - - +
674A ASP 3.4 1.4 + - - -
675A LEU* 1.3 70.7 - - - +
677A SER* 1.4 56.3 + - - +
678A VAL 3.0 2.7 - - - -
679A THR* 2.5 42.9 + - + +
680A LYS* 3.5 16.5 - - - +
738A TYR* 3.4 8.5 - - - +
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Residues in contact with SER 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 4.6 8.8 + - - -
532A THR* 5.2 4.6 - - - +
674A ASP 5.1 0.8 + - - -
675A LEU 3.0 5.1 + - - -
676A CYS* 1.4 79.7 - - - +
678A VAL* 1.3 61.3 + - - +
679A THR 3.2 1.1 + - - -
680A LYS* 3.7 13.7 - - - +
684A VAL* 6.2 0.2 - - - -
685A THR* 2.8 37.5 + - - +
688A THR* 3.6 36.5 - - - +
692A ILE* 4.3 5.9 - - - +
900A 2ZX 4.2 9.9 + - - -
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Residues in contact with VAL 678 (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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675A LEU* 2.9 23.8 - - + +
676A CYS 3.0 1.4 - - - -
677A SER* 1.3 80.2 + - - +
679A THR* 1.3 57.7 + - + +
685A THR* 4.2 1.6 - - + -
729A PHE* 5.0 2.9 - - + -
730A TYR* 3.3 37.7 - - + +
734A ALA* 4.2 13.5 - - + -
738A TYR* 3.5 29.6 - - + +
755A CYS* 3.3 18.7 - - - -
758A ASN* 3.0 19.9 + - - +
900A 2ZX 3.5 27.8 - - + +
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Residues in contact with THR 679 (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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475A PHE* 4.9 1.4 + - - +
476A HIS* 4.5 12.1 - - - +
676A CYS* 2.5 23.4 + - - +
678A VAL* 1.3 80.8 - - + +
680A LYS* 1.3 69.2 + - - +
738A TYR* 3.4 42.8 - - + +
751A LEU* 3.5 44.9 - - + +
754A ALA* 2.8 26.3 - - - +
755A CYS* 4.4 0.7 - - + -
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Residues in contact with LYS 680 (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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475A PHE 3.0 23.4 + - - +
476A HIS* 3.7 21.1 - - - +
477A PHE 3.0 17.4 + - - +
478A ASP* 4.9 3.4 - - + +
532A THR* 4.4 12.8 - - + +
535A HIS* 4.1 11.1 + - - -
536A CYS* 5.2 2.0 - - - +
676A CYS* 3.5 41.3 - - - +
677A SER* 3.7 11.0 + - - +
678A VAL 3.5 1.2 - - - -
679A THR* 1.3 85.6 + - - +
681A LEU* 1.3 63.1 + - - +
682A TRP 3.6 0.3 + - - -
684A VAL* 3.6 29.2 - - + -
685A THR* 3.6 6.5 - - - +
754A ALA* 4.6 3.8 - - - +
758A ASN* 2.9 22.3 + - - +
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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