Contacts of the helix formed by residues 472 - 482 (chain A) in PDB entry 5WRS
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 ARG 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.2 15.6 - - - +
466A LEU 3.7 3.6 - - - +
467A ALA 5.8 2.4 + - - +
468A GLN 3.0 9.9 + - - +
469A ALA* 3.4 34.2 + - - +
470A ASP 3.7 0.2 - - - -
471A TYR* 1.3 75.5 - - - +
473A LEU* 1.3 69.4 + - - +
474A SER* 3.3 15.9 - - - +
475A ASP* 2.6 48.7 + - - +
476A VAL* 2.9 21.1 + - - +
499A ASP* 3.3 26.0 - - - +
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Residues in contact with LEU 473 (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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269A LEU* 3.8 28.5 - - + -
272A ILE* 4.0 17.9 - - + -
273A LEU* 5.1 1.1 - - + -
405A LEU* 4.3 16.6 - - + -
466A LEU* 3.1 32.1 + - + +
471A TYR 3.3 1.5 + - - -
472A ARG* 1.3 72.9 - - - +
474A SER* 1.3 59.3 + - - +
476A VAL* 3.3 7.4 - - - +
477A MET* 3.0 37.9 + - + +
498A LEU* 3.7 37.0 - - + +
499A ASP* 3.7 6.9 + - - +
502A LEU* 4.2 17.0 - - + -
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Residues in contact with SER 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 ARG* 3.3 9.9 - - - -
473A LEU* 1.3 76.6 - - - +
475A ASP* 1.3 63.7 + - - +
477A MET* 3.9 4.3 - - - +
478A ARG* 3.0 36.7 + - - +
495A LEU* 3.3 36.1 - - - +
496A LEU* 4.4 9.3 - - - +
498A LEU* 5.0 1.1 - - - +
499A ASP* 2.5 34.5 + - - -
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Residues in contact with ASP 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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91A LYS* 2.8 32.7 + - + -
472A ARG* 2.6 46.8 + - - +
474A SER* 1.3 81.1 + - - +
476A VAL* 1.3 61.0 + - - +
478A ARG* 2.7 34.9 + - - +
479A GLU* 3.0 32.7 + - - +
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Residues in contact with VAL 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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91A LYS* 3.7 38.4 - - + +
92A LEU* 3.8 16.7 - - + +
95A LEU* 4.5 9.2 - - + -
272A ILE* 3.6 26.4 - - + +
466A LEU* 4.2 5.4 - - + -
471A TYR* 4.2 10.5 - - - +
472A ARG 2.9 17.0 + - - +
473A LEU* 3.3 18.4 - - - +
475A ASP* 1.3 77.1 - - - +
477A MET* 1.3 60.4 + - - +
479A GLU* 3.8 6.0 - - - +
480A SER* 2.8 30.1 + - - -
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Residues in contact with MET 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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265A ALA* 3.6 20.4 - - + +
268A HIS* 3.8 6.7 - - + -
269A LEU* 3.5 33.2 - - + -
272A ILE* 3.7 17.0 - - + -
435A PHE* 4.6 2.0 - - + -
473A LEU* 3.0 29.2 + - + +
474A SER 3.9 0.2 - - - +
476A VAL* 1.3 76.3 - - - +
478A ARG* 1.3 65.5 + - - +
480A SER* 3.1 1.2 + - - -
481A LEU* 2.9 39.9 + - + +
490A LEU* 3.9 26.2 - - + -
495A LEU* 3.8 13.5 - - + -
498A LEU* 3.8 21.1 - - + -
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Residues in contact with ARG 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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474A SER* 3.0 27.2 + - - +
475A ASP* 2.7 33.7 + - - +
477A MET* 1.3 77.7 - - - +
479A GLU* 1.3 62.3 + - - +
481A LEU* 3.5 5.4 + - - +
482A LEU* 3.4 30.1 + - + +
488A PRO* 6.1 4.3 - - + -
492A GLU* 2.7 46.0 + - - -
495A LEU* 3.4 36.7 - - + +
496A LEU* 4.6 7.9 - - - +
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Residues in contact with GLU 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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90A SER* 2.2 33.2 + - - -
91A LYS* 3.5 12.9 + - - +
92A LEU* 3.2 35.8 + - + +
475A ASP* 3.0 17.9 + - - +
476A VAL 3.8 3.6 - - - +
478A ARG* 1.3 75.8 - - - +
480A SER* 1.3 64.9 + - - +
482A LEU* 3.3 27.8 + - + +
483A GLU* 4.4 4.9 + - - +
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Residues in contact with SER 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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92A LEU* 3.7 19.9 - - - +
268A HIS* 2.7 40.6 + - - +
271A ARG* 3.8 12.0 + - - -
272A ILE* 4.0 15.8 - - - +
476A VAL 2.8 19.6 + - - -
477A MET* 3.7 4.0 - - - -
479A GLU* 1.3 75.8 - - - +
481A LEU* 1.3 62.6 + - - +
482A LEU 3.3 0.9 + - - -
483A GLU* 3.4 20.6 + - - -
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Residues in contact with LEU 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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264A ILE* 4.3 0.4 - - + -
265A ALA* 4.1 6.1 - - - -
268A HIS* 3.4 41.5 - - + +
477A MET* 2.9 27.2 + - + +
478A ARG* 4.1 4.9 - - - +
479A GLU 3.3 0.4 - - - -
480A SER* 1.3 71.8 - - - +
482A LEU* 1.3 64.5 + - - +
483A GLU 3.1 4.0 + - - -
484A ASP* 3.3 16.7 + - - +
487A SER* 3.9 9.7 - - - -
488A PRO 3.7 20.0 - - - +
489A VAL* 4.0 23.5 - - + +
490A LEU* 3.7 38.6 - - + -
495A LEU* 4.3 6.3 - - + -
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Residues in contact with LEU 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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478A ARG* 3.4 23.7 + - + +
479A GLU* 3.5 19.3 - - + +
480A SER 3.2 1.6 - - - -
481A LEU* 1.3 77.1 - - - +
483A GLU* 1.3 61.9 + - + +
484A ASP 3.2 6.7 + - - +
487A SER* 3.3 24.5 - - - +
488A PRO* 5.2 6.5 - - + -
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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