Contacts of the helix formed by residues 477 - 486 (chain A) in PDB entry 4X61
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 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY* 3.6 7.6 - - - -
475A ILE* 4.4 5.6 - - - +
476A SER* 1.3 75.9 + - - +
478A SER* 1.3 58.2 + - - +
479A LYS* 3.6 2.6 + - - +
480A LEU* 3.0 31.2 + - - +
481A TYR* 2.9 27.0 + - - +
508A ASN 2.7 25.1 + - - -
509A PHE* 3.8 9.9 - - - -
549A HIS* 2.9 17.5 + - - +
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Residues in contact with SER 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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193A ARG* 2.6 43.1 + - - -
198A TYR* 3.9 11.6 - - - -
223A GLY 3.1 7.6 + - - -
224A GLU* 3.9 8.5 + - - -
225A PRO* 4.5 7.0 - - - -
476A SER* 5.1 0.4 + - - -
477A SER* 1.3 72.8 - - - +
479A LYS* 1.3 62.0 + - - +
481A TYR* 3.9 4.0 - - - +
482A ASN* 3.2 24.8 + - - +
549A HIS* 3.2 25.6 + - - -
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Residues in contact with LYS 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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223A GLY 3.2 6.7 + - - +
225A PRO* 4.8 15.1 - - + +
227A LYS* 5.4 9.7 - - - +
306A ASP* 4.3 23.8 - - - +
477A SER* 3.7 7.6 - - - +
478A SER* 1.3 77.4 - - - +
480A LEU* 1.3 60.0 + - - +
482A ASN* 3.1 9.5 + - - +
483A GLU* 3.1 52.1 + - + +
508A ASN* 3.6 36.1 - - + +
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Residues in contact with LEU 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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306A ASP* 3.8 49.8 - - + +
308A LEU* 4.1 22.2 - - + -
475A ILE* 4.5 6.5 - - + -
477A SER* 3.0 28.4 + - - +
479A LYS* 1.3 72.1 - - + +
481A TYR* 1.3 65.4 - - - +
482A ASN 3.1 1.6 - - - -
483A GLU* 3.1 7.7 + - + +
484A VAL* 3.0 29.4 + - - +
504A VAL* 4.1 4.7 - - + -
506A LEU* 3.7 28.0 - - + -
509A PHE* 4.4 8.5 - - + -
583A LEU* 4.4 11.2 - - + -
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Residues in contact with TYR 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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198A TYR* 4.1 31.2 - + - -
477A SER 2.9 18.5 + - - +
478A SER* 3.9 4.0 - - - +
480A LEU* 1.3 76.4 - - - +
482A ASN* 1.3 58.6 + - - +
484A VAL* 3.6 6.1 + - + +
485A ARG* 3.1 54.1 + - - +
498A PHE* 3.7 21.9 - + - -
549A HIS* 3.5 35.8 - + + +
585A PRO* 6.2 1.3 - - + -
586A ILE 3.7 16.4 - - - -
587A LYS 3.2 16.1 + - - -
588A GLN* 4.1 7.3 + - - -
589A PRO* 3.4 29.4 - - + +
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Residues in contact with ASN 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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198A TYR* 2.9 38.0 + - - +
199A SER 4.0 2.2 + - - -
200A LYS* 3.8 24.8 + - - +
225A PRO* 6.3 0.6 - - - +
478A SER 3.2 13.0 + - - +
479A LYS* 3.1 12.3 + - - +
480A LEU 3.1 0.6 - - - -
481A TYR* 1.3 79.5 - - + +
483A GLU* 1.3 64.2 + - - +
485A ARG* 3.5 20.8 + - - +
486A ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 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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306A ASP 4.1 17.7 - - - +
308A LEU* 3.7 20.3 - - + +
479A LYS* 3.1 48.0 + - + +
480A LEU* 3.5 15.5 - - + +
482A ASN* 1.3 75.5 - - - +
484A VAL* 1.3 64.9 + - - +
486A ALA* 3.2 17.6 + - - +
487A CYS* 3.5 13.5 - - - -
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Residues in contact with VAL 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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308A LEU* 3.8 19.5 - - + -
480A LEU 3.0 17.6 + - - +
481A TYR* 3.9 6.1 - - - +
483A GLU* 1.3 74.1 - - - +
485A ARG* 1.3 55.4 - - - +
487A CYS* 2.8 32.3 + - - +
497A GLN* 3.3 35.8 - - - +
498A PHE* 3.7 24.0 - - + -
502A TYR* 4.0 6.3 - - + +
583A LEU* 4.1 14.8 - - + -
585A PRO* 3.9 23.1 - - + -
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Residues in contact with ARG 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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197A ASP* 2.8 45.3 + - - -
198A TYR* 3.3 23.2 + - - +
199A SER* 4.3 1.6 - - - +
200A LYS 5.6 0.2 - - - +
481A TYR* 3.1 45.0 + - - +
482A ASN* 3.5 17.3 + - - +
484A VAL* 1.3 75.9 - - - +
486A ALA* 1.3 58.2 + - - +
487A CYS 3.2 4.3 + - - -
488A ARG* 3.7 11.8 + - - +
497A GLN* 4.0 8.4 + - - +
498A PHE* 3.7 22.6 - - + -
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Residues in contact with ALA 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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200A LYS* 5.9 7.4 - - + -
482A ASN 3.1 16.7 + - - +
483A GLU* 3.5 10.1 - - - +
484A VAL 3.1 0.8 - - - -
485A ARG* 1.3 74.1 - - - +
487A CYS* 1.3 56.1 + - - +
488A ARG* 3.2 12.1 + - - +
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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