Contacts of the helix formed by residues 472 - 483 (chain A) in PDB entry 2H3W
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LYS 5.2 2.5 - - - -
53A ALA* 5.3 3.1 - - - +
56A PRO* 3.5 13.6 - - - +
469A ARG 4.7 6.3 - - - -
470A SER 3.5 3.7 + - - -
471A ALA* 1.3 75.5 - - - +
473A ILE* 1.3 64.6 + - - +
474A ASP* 3.5 7.3 + - - +
475A SER* 2.9 26.4 + - - -
476A LEU* 3.1 24.8 + - - +
499A ALA 5.5 0.7 + - - -
502A ALA* 4.8 7.9 - - - +
503A HIS 5.8 0.2 + - - -
506A TYR* 5.8 5.4 - - - -
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Residues in contact with ILE 473 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.8 41.0 + - + +
55A GLN* 3.6 42.8 - - + +
56A PRO* 4.3 4.0 - - + -
472A SER* 1.3 76.1 - - - +
474A ASP* 1.3 66.2 + - - +
476A LEU* 4.0 3.7 - - - +
477A ALA* 3.1 28.1 + - + +
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Residues in contact with ASP 474 (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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472A SER* 3.3 2.9 + - - +
473A ILE* 1.3 84.6 - - - +
475A SER* 1.3 64.8 + - - +
477A ALA* 3.3 7.8 + - - +
478A PHE* 3.1 22.3 + - - +
495A LEU* 4.5 2.3 - - - +
498A LYS* 3.7 33.2 - - + +
499A ALA* 3.7 16.0 - - - +
502A ALA* 3.2 34.2 - - + +
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Residues in contact with SER 475 (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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435A VAL* 5.4 7.0 - - - -
438A GLN* 4.2 18.2 + - - -
470A SER 3.4 16.4 + - - -
471A ALA* 3.7 3.5 - - - -
472A SER* 2.9 31.8 + - - -
474A ASP* 1.3 77.9 - - - +
476A LEU* 1.3 67.1 + - - +
478A PHE* 3.1 4.2 + - - +
479A VAL* 2.9 28.8 + - - +
499A ALA* 3.9 16.7 - - - +
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Residues in contact with LEU 476 (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 GLN 5.4 0.2 - - - +
56A PRO* 3.8 32.1 - - + +
442A TYR* 4.0 12.3 - - + -
448A ALA* 4.2 19.3 - - + +
472A SER 3.1 14.8 + - - +
473A ILE* 4.0 4.0 - - - +
475A SER* 1.3 82.1 + - - +
477A ALA* 1.3 63.1 + - - +
479A VAL* 3.1 19.3 - - + +
480A LYS* 3.1 57.3 + - + +
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Residues in contact with ALA 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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473A ILE* 3.1 20.6 + - + +
474A ASP* 3.6 9.6 - - - +
475A SER 3.2 0.2 - - - -
476A LEU* 1.3 76.7 - - - +
478A PHE* 1.3 57.8 + - - +
480A LYS* 4.0 6.9 - - - +
481A GLY* 3.1 20.4 + - - -
495A LEU* 3.6 26.5 - - + +
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Residues in contact with PHE 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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435A VAL* 3.5 32.3 - - + -
439A LEU* 4.2 15.5 - - + -
474A ASP 3.1 12.3 + - - +
475A SER 3.1 7.7 + - - +
477A ALA* 1.3 74.2 - - - +
479A VAL* 1.3 64.5 + - + +
480A LYS 3.1 1.6 - - - -
481A GLY 3.3 0.7 + - - -
482A MET* 2.7 68.1 + - + +
492A LYS* 3.9 8.5 - - - -
495A LEU* 3.7 19.2 - - + +
496A LEU* 3.5 52.7 - - + -
499A ALA* 4.1 3.6 - - + -
614A MET* 3.8 17.3 - - + -
617A LEU* 4.4 0.2 - - + -
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Residues in contact with VAL 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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438A GLN* 3.8 13.0 - - + -
439A LEU* 3.4 48.1 - - + +
442A TYR* 3.6 40.5 - - + -
448A ALA* 6.1 0.4 - - + -
475A SER 2.9 15.4 + - - +
476A LEU* 3.1 28.3 - - + +
478A PHE* 1.3 80.7 - - + +
480A LYS* 1.3 65.1 + - - +
482A MET* 3.7 1.2 + - - +
483A GLY* 3.4 14.6 + - - -
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Residues in contact with LYS 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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442A TYR* 2.9 42.5 + - + +
446A GLY 5.4 0.6 + - - -
476A LEU* 3.1 49.6 + - + +
477A ALA* 4.0 6.1 - - - +
479A VAL* 1.3 75.9 - - - +
481A GLY* 1.3 66.5 + - - +
482A MET 3.2 0.2 + - - -
483A GLY* 3.3 4.5 + - - -
484A ASP* 3.2 21.6 + - - +
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Residues in contact with GLY 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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477A ALA 3.1 13.7 + - - -
478A PHE 3.8 1.6 - - - -
480A LYS* 1.3 80.7 - - - +
482A MET* 1.3 58.9 + - - +
484A ASP* 3.3 14.3 + - - +
487A VAL* 3.7 9.8 - - - +
492A LYS* 2.9 32.0 + - - +
495A LEU* 4.2 13.5 - - - -
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Residues in contact with MET 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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439A LEU* 3.8 31.2 - - + -
443A ARG* 4.0 21.5 + - - +
478A PHE* 2.7 37.0 + - + +
479A VAL 3.8 5.6 - - - +
480A LYS 3.1 0.2 - - - -
481A GLY* 1.3 76.5 - - - +
483A GLY* 1.3 57.6 + - - +
484A ASP 3.4 2.8 + - - -
492A LYS* 3.7 27.8 - - - +
613A ASP* 4.1 29.4 - - + +
614A MET* 4.5 1.8 - - - +
617A LEU* 3.9 29.6 - - + -
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Residues in contact with GLY 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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439A LEU* 5.4 1.0 - - - +
442A TYR* 6.3 1.1 - - - -
443A ARG* 6.0 5.8 - - - -
479A VAL 3.4 6.9 + - - -
480A LYS 3.3 8.6 + - - -
482A MET* 1.3 76.9 - - - +
484A ASP* 1.3 59.3 + - - +
485A SER* 3.6 3.1 + - - -
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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