Contacts of the helix formed by residues 459 - 467 (chain A) in PDB entry 6S1M
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 MET 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A THR* 5.3 5.4 - - - -
395A GLY 3.3 17.7 + - - +
396A TYR* 4.0 15.0 - - + -
457A MET* 3.4 10.2 + - - +
458A ASP* 1.3 71.3 + - - +
460A LEU* 1.3 60.4 + - - +
462A VAL* 3.4 14.6 + - + +
463A LEU* 3.0 48.9 + - + +
519A PRO* 4.3 20.4 - - + +
522A LEU* 4.5 22.9 - - + +
523A LEU* 4.3 15.0 - - + -
526A LEU* 4.7 3.4 - - + -
528A VAL* 4.0 36.1 - - + -
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Residues in contact with LEU 460 (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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396A TYR* 3.7 39.4 - - + +
397A ASN* 3.7 35.0 - - + +
400A ASN* 6.2 0.7 - - - +
458A ASP* 3.2 15.0 + - - +
459A MET* 1.3 77.9 - - - +
461A GLN* 1.3 74.4 + - - +
463A LEU* 3.3 2.8 + - - +
464A LEU* 2.9 58.1 + - + +
472A TYR 5.0 6.3 - - - +
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Residues in contact with GLN 461 (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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399A GLN* 4.5 13.2 - - + +
400A ASN* 4.8 8.1 + - - +
444A ARG* 4.8 15.9 - - - +
446A THR* 4.0 22.3 + - + +
458A ASP* 3.4 23.4 + - + +
459A MET 3.3 0.4 - - - -
460A LEU* 1.3 93.5 - - + +
462A VAL* 1.3 62.2 + - - +
464A LEU* 3.8 11.5 - - - +
465A ARG* 3.0 44.6 + - - +
547A LEU* 4.8 14.2 + - + +
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Residues in contact with VAL 462 (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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457A MET* 4.2 17.0 - - + -
458A ASP 3.3 17.3 - - - +
459A MET* 3.7 17.0 - - + +
460A LEU 3.3 0.6 - - - -
461A GLN* 1.3 75.2 - - - +
463A LEU* 1.3 61.3 + - + +
465A ARG* 3.5 13.9 + - - +
466A GLU* 3.0 32.7 + - + +
467A TYR* 4.9 1.4 - - + -
528A VAL* 4.3 25.1 - - + -
547A LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 463 (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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396A TYR* 3.4 28.9 - - + +
459A MET* 3.0 30.7 + - + +
460A LEU* 3.7 4.5 - - - +
462A VAL* 1.3 77.6 - - + +
464A LEU* 1.3 57.6 + - + +
467A TYR* 2.9 58.1 + - + +
469A LEU* 5.4 0.9 - - + -
472A TYR* 4.0 14.5 - - + -
477A VAL* 3.8 30.3 - - + -
481A PHE* 4.5 9.0 - - + -
522A LEU* 5.0 6.3 - - + -
526A LEU* 4.5 20.4 - - + -
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Residues in contact with LEU 464 (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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396A TYR* 5.9 0.4 - - - +
441A THR* 5.3 2.1 - - - -
444A ARG* 3.7 51.7 + - - +
460A LEU* 2.9 48.6 + - + +
461A GLN* 3.9 12.3 - - - +
462A VAL 3.4 0.2 - - - -
463A LEU* 1.3 75.8 - - + +
465A ARG* 1.3 61.3 + - + +
467A TYR 4.4 5.2 - - - +
472A TYR* 3.6 47.1 + - + -
919A GLY 5.9 1.6 - - - +
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Residues in contact with ARG 465 (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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441A THR* 4.8 23.4 - - + +
444A ARG* 5.4 6.7 - - - +
461A GLN* 3.0 29.5 + - + +
462A VAL* 4.0 15.7 - - - +
464A LEU* 1.3 82.7 - - + +
466A GLU* 1.3 62.2 + - - +
467A TYR 5.1 0.2 - - - -
546A LEU* 3.0 34.1 + - - +
547A LEU* 4.2 26.0 - - - +
549A ARG 5.1 10.5 + - - -
551A GLN* 5.7 5.1 - - - +
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Residues in contact with GLU 466 (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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462A VAL* 3.0 19.9 + - + +
465A ARG* 1.3 79.0 - - + +
467A TYR* 1.3 102.0 + - + +
468A LYS* 4.2 3.7 + - - +
688A GLY* 4.9 1.8 - - - +
691A LEU* 3.3 32.6 - - - +
692A ALA* 5.8 0.2 - - - +
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Residues in contact with TYR 467 (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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462A VAL* 4.9 1.1 - - + -
463A LEU* 2.9 39.2 + - + +
464A LEU 4.4 5.5 - - - +
466A GLU* 1.3 112.4 + - + +
468A LYS* 1.3 58.9 + - - +
469A LEU* 4.1 24.0 - - + -
472A TYR* 2.3 23.6 + - - -
480A HIS* 6.1 0.4 - - - -
481A PHE* 4.5 19.0 - + - -
526A LEU* 3.7 28.4 - - + +
684A GLN* 4.7 12.9 + - - -
685A VAL* 5.1 3.6 - - - +
688A GLY* 5.8 3.5 - - - -
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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