Contacts of the helix formed by residues 476 - 488 (chain A) in PDB entry 5OC9
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 ALA 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A VAL* 3.8 23.0 - - + +
470A LEU* 3.8 25.6 - - + -
471A LYS 6.2 3.4 - - - +
475A ASP* 1.3 70.7 - - - +
477A THR* 1.3 58.5 + - - +
478A LEU 3.6 1.3 - - - -
479A TYR* 3.8 12.8 - - + -
480A GLU* 3.1 26.5 + - - +
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Residues in contact with THR 477 (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 ASP* 2.9 32.5 + - - -
476A ALA* 1.3 73.6 + - - +
478A LEU* 1.4 58.1 + - - +
480A GLU* 3.5 6.4 + - - +
481A GLN* 3.2 25.2 + - - +
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Residues in contact with LEU 478 (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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17A PRO* 3.8 22.9 - - + -
53A ARG* 3.7 26.2 - - - +
55A LEU* 4.1 13.9 - - + +
71A LEU* 3.7 18.2 - - + -
173A LEU* 4.7 3.4 - - + -
475A ASP* 4.8 2.9 + - - +
476A ALA* 4.6 0.2 - - - +
477A THR* 1.4 74.5 - - - +
479A TYR* 1.4 60.1 + - - +
481A GLN* 3.3 24.4 + - - +
482A VAL* 2.9 36.2 + - + +
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Residues in contact with TYR 479 (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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55A LEU* 3.7 21.0 - - + +
56A LEU* 3.7 37.2 - - + -
67A GLN* 5.2 10.2 - - + +
69A LEU* 6.0 0.2 - - + -
466A LYS* 4.8 7.1 + - + +
467A VAL* 3.6 37.7 - - + -
470A LEU* 3.8 38.6 - - + +
475A ASP 5.4 0.2 + - - -
476A ALA* 3.7 18.0 + - + +
478A LEU* 1.4 78.9 - - - +
480A GLU* 1.3 55.8 + - - +
482A VAL* 3.3 2.1 + - - +
483A ILE* 3.0 58.6 + - + +
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Residues in contact with GLU 480 (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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460A GLY 4.8 1.4 - - - +
463A VAL* 3.7 8.9 - - + +
464A LYS* 3.4 52.1 + - - +
467A VAL* 3.5 35.9 - - + +
476A ALA 3.1 14.4 + - - +
477A THR* 3.7 5.6 - - - +
479A TYR* 1.3 78.1 - - - +
481A GLN* 1.4 56.6 + - - +
483A ILE* 3.6 0.8 + - - -
484A LEU* 3.0 35.8 + - + +
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Residues in contact with GLN 481 (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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173A LEU* 3.7 13.1 - - - +
174A HIS 2.8 28.1 + - - +
176A SER* 3.5 21.3 + - - +
477A THR 3.2 14.3 + - - +
478A LEU* 3.3 30.6 + - - +
480A GLU* 1.4 75.0 - - - +
482A VAL* 1.4 57.9 + - - +
484A LEU* 3.9 6.7 - - + +
485A GLU* 3.2 48.3 + - - +
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Residues in contact with VAL 482 (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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20A VAL* 4.1 15.0 - - + -
55A LEU* 3.7 34.5 - - + -
69A LEU* 3.9 25.4 - - + -
71A LEU* 4.0 14.6 - - + -
171A PHE* 4.4 2.4 - - + -
173A LEU* 4.0 22.4 - - + -
478A LEU* 2.9 24.6 + - + +
479A TYR 3.3 3.1 + - - +
481A GLN* 1.4 73.8 - - - +
483A ILE* 1.4 56.9 + - - +
484A LEU 3.3 0.2 + - - -
485A GLU* 3.3 1.5 + - - +
486A LYS* 2.8 36.6 + - - +
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Residues in contact with ILE 483 (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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55A LEU* 4.5 0.4 - - + -
67A GLN* 4.9 10.1 - - + -
69A LEU* 3.8 24.9 - - + -
463A VAL* 3.7 24.7 - - + +
466A LYS* 4.2 19.5 - - + -
467A VAL* 4.7 0.9 - - + -
479A TYR* 3.0 62.2 + - + +
480A GLU* 4.0 0.9 - - - +
482A VAL* 1.4 73.5 - - - +
484A LEU* 1.4 61.8 + - - +
486A LYS* 3.7 9.5 + - - +
487A GLU* 3.4 40.0 + - - +
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Residues in contact with LEU 484 (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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456A GLN* 4.6 8.2 + - - +
459A HIS 4.4 0.4 - - - +
460A GLY* 3.7 33.7 - - - +
463A VAL* 3.6 25.3 - - + +
480A GLU* 3.0 23.4 + - + +
481A GLN* 3.9 7.2 - - + +
482A VAL 3.2 0.2 - - - -
483A ILE* 1.4 78.5 - - - +
485A GLU* 1.3 60.0 + - + +
487A GLU* 3.4 2.6 + - - +
488A MET* 3.2 52.2 + - + +
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Residues in contact with GLU 485 (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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171A PHE* 3.9 13.4 - - + -
172A PRO 4.1 3.1 - - - +
173A LEU* 3.4 16.7 - - - +
174A HIS* 2.8 56.4 + - + +
176A SER* 5.3 0.3 + - - -
481A GLN* 3.2 38.7 + - - +
482A VAL* 4.1 1.3 - - - +
484A LEU* 1.3 78.8 - - + +
486A LYS* 1.3 64.3 + - - +
488A MET* 3.4 27.0 - - + +
542A LYS* 3.3 25.4 - - + +
543A ARG 5.3 0.2 + - - -
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Residues in contact with LYS 486 (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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22A GLU* 3.3 31.0 + - - +
67A GLN* 5.0 12.1 + - - +
69A LEU* 3.7 31.1 - - + +
169A GLN* 3.0 27.8 + - - +
171A PHE* 3.6 16.1 - - + -
482A VAL 2.8 23.3 + - - +
483A ILE* 3.8 8.0 - - - +
484A LEU 3.3 0.2 - - - -
485A GLU* 1.3 72.2 - - - +
487A GLU* 1.4 91.3 + - - +
488A MET 3.3 0.4 - - - +
542A LYS* 3.0 20.4 + - - -
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A GLN* 4.8 2.9 - - - +
459A HIS* 5.5 6.3 + - + -
462A ARG* 4.8 13.9 + - - +
463A VAL* 3.5 20.0 - - + +
466A LYS* 3.7 23.8 + - - -
483A ILE* 3.4 29.6 + - - +
484A LEU 3.8 2.9 - - - +
486A LYS* 1.4 102.5 + - - +
488A MET* 1.4 65.1 + - - +
489A GLY 3.9 0.2 + - - -
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Residues in contact with MET 488 (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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174A HIS* 4.8 5.4 - - + -
456A GLN* 3.6 33.4 - - + +
484A LEU* 3.2 43.2 + - + +
485A GLU* 3.4 28.3 - - + +
486A LYS 3.3 1.6 - - - +
487A GLU* 1.4 80.1 - - - +
489A GLY* 1.3 57.8 + - - +
490A THR* 3.8 0.7 + - - -
538A CYS 5.5 3.6 - - - +
539A ARG* 5.2 6.7 - - - +
540A VAL 3.9 4.9 - - - +
541A PHE 3.8 10.3 - - - +
542A LYS* 2.8 51.2 + - + +
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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