Contacts of the strand formed by residues 473 - 478 (chain A) in PDB entry 5HQG
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 ILE 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A SER* 2.6 26.9 + - - -
439A ALA* 3.6 20.4 - - + -
440A GLY* 3.1 17.4 + - - +
441A VAL* 5.9 0.5 - - - +
443A LYS* 3.5 29.2 - - - +
444A LYS 3.7 7.0 - - - +
445A ILE* 3.5 28.3 - - + -
469A CYS* 3.9 16.2 - - + -
471A SER 3.8 8.7 - - - +
472A LYS* 1.3 74.8 - - - +
474A SER* 1.3 54.5 + - - +
475A CYS 3.7 16.2 - - - +
476A ILE* 4.2 4.3 - - + -
488A SER* 4.4 6.3 - - - -
489A SER 3.4 16.2 - - - +
490A ASP* 4.6 0.2 - - + -
491A TYR* 4.6 3.4 - - - -
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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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425A SER* 3.7 22.9 + - - +
426A SER* 4.3 0.2 - - - -
472A LYS 3.9 1.2 + - - -
473A ILE* 1.3 73.1 - - - +
475A CYS* 1.3 61.5 + - - +
489A SER* 2.8 29.6 + - - -
491A TYR* 4.1 17.9 - - - -
516A CYS 2.6 28.9 + - - -
517A TRP* 3.3 27.0 + - - +
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Residues in contact with CYS 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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426A SER* 3.8 13.7 - - - -
428A GLU* 6.0 1.1 - - - -
473A ILE* 3.6 3.2 - - - +
474A SER* 1.3 83.7 + - - +
476A ILE* 1.3 84.2 + - - +
488A SER* 3.4 0.3 - - - -
489A SER* 3.0 38.0 + - - +
517A TRP 3.7 10.3 - - - +
518A SER* 3.8 9.9 - - - -
519A VAL* 3.6 29.6 - - - +
606A LYS* 6.0 3.4 - - - -
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Residues in contact with ILE 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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426A SER* 3.1 26.0 + - - +
428A GLU* 3.3 30.6 - - + +
437A ALA* 3.4 47.6 - - + +
438A ILE* 4.0 5.6 - - - +
439A ALA* 3.8 18.8 - - + -
445A ILE* 4.4 11.0 - - + -
473A ILE* 4.2 0.7 - - + -
475A CYS* 1.3 90.3 - - - +
477A SER* 1.3 63.7 + - - +
486A LEU* 4.1 7.2 - - + -
487A ALA 3.1 13.2 - - - +
488A SER* 4.1 12.3 - - - -
519A VAL* 4.2 1.8 - - - -
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 4.5 7.0 - - - -
476A ILE* 1.3 78.2 - - - +
478A TRP* 1.3 67.5 + - - +
486A LEU* 3.3 4.6 - - - +
487A ALA* 2.9 32.4 + - - -
519A VAL* 3.6 23.6 - - - -
520A ASP* 3.6 13.7 + - - -
521A PHE* 3.4 28.9 + - - +
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Residues in contact with TRP 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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428A GLU* 3.2 32.0 + - + +
429A PHE 3.1 29.1 - - - +
430A ASP* 3.6 25.4 - - + -
431A ARG 4.7 0.2 - - - +
435A TYR* 4.8 2.5 - - + -
436A PHE 4.7 2.0 - - - -
437A ALA* 3.5 28.5 - - + +
447A VAL* 4.3 21.3 - - + -
477A SER* 1.3 82.4 + - - +
479A SER* 1.3 68.1 + - - +
480A SER* 3.6 1.9 + - - -
483A LYS 3.4 27.1 - - - -
484A ASN* 4.1 14.4 - - - -
485A LEU 3.6 14.4 - - - -
486A LEU* 4.0 24.4 - - + +
500A GLY* 4.4 8.7 - - - -
501A PHE* 4.4 12.3 - + - -
521A PHE* 3.7 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