Contacts of the helix formed by residues 508 - 515 (chain A) in PDB entry 4H1S
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 PHE 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ASN* 4.9 0.4 - - + -
434A ALA* 3.3 45.5 - - + -
437A HIS* 3.7 16.4 - + - -
438A SER* 4.5 0.7 - - - -
448A GLU* 3.2 42.8 - - + -
450A LEU* 3.6 20.2 - - + -
501A LEU* 3.5 24.2 - - + +
504A GLY* 3.3 16.7 + - - -
505A GLY 3.1 19.3 + - - +
506A ASP* 3.9 4.3 - - + -
507A GLY* 1.3 72.3 - - - +
509A GLN* 1.3 62.7 + - - +
510A MET* 3.2 15.9 - - - -
511A ILE* 3.2 31.1 + - + +
512A LYS 3.6 0.7 + - - -
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Residues in contact with GLN 509 (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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183A PHE* 4.6 19.2 - - - -
503A ASN 5.5 0.2 + - - -
504A GLY* 4.7 13.8 + - - -
507A GLY* 2.9 14.1 + - - +
508A PHE* 1.3 72.1 - - - +
510A MET* 1.3 59.1 + - + +
511A ILE 3.3 0.2 + - - -
512A LYS* 3.2 24.1 + - - +
513A ASP* 2.8 62.3 + - - +
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Residues in contact with MET 510 (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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430A THR* 3.5 28.0 - - + +
433A LYS* 3.9 44.0 - - + +
434A ALA* 4.0 5.2 - - - -
437A HIS* 4.0 18.2 - - + +
507A GLY 4.5 2.2 - - - +
508A PHE* 3.2 33.3 - - - -
509A GLN* 1.3 82.6 - - + +
511A ILE* 1.3 63.9 + - + +
513A ASP* 4.8 1.3 - - - -
514A GLU* 3.0 46.1 + - - +
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Residues in contact with ILE 511 (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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388A ILE* 4.1 16.6 - - + -
424A VAL* 5.2 1.1 - - + -
426A LEU* 4.3 20.9 - - + -
430A THR* 4.2 7.2 - - + -
434A ALA* 4.5 7.4 - - + -
497A LEU* 4.0 25.1 - - + -
501A LEU* 3.6 20.4 - - + +
502A ALA* 4.0 12.8 - - + +
508A PHE* 3.2 32.9 + - + +
509A GLN 3.2 0.6 - - - -
510A MET* 1.3 87.6 - - + +
512A LYS* 1.3 62.8 + - - +
515A LEU* 3.0 33.2 + - + +
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Residues in contact with LYS 512 (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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502A ALA 3.6 19.0 + - - +
503A ASN* 3.4 23.8 - - - +
504A GLY* 3.9 11.4 - - - +
508A PHE 3.6 1.8 + - - -
509A GLN* 3.2 33.5 + - - +
511A ILE* 1.3 82.0 - - - +
513A ASP* 1.3 65.8 + - - +
514A GLU 3.5 0.2 + - - -
515A LEU* 3.9 13.3 - - - +
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Residues in contact with ASP 513 (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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509A GLN* 2.8 51.8 + - - +
510A MET* 4.8 0.7 - - - -
512A LYS* 1.3 85.9 + - - +
514A GLU* 1.3 69.5 + - + +
515A LEU 4.9 1.3 - - - +
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Residues in contact with GLU 514 (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 LEU* 5.1 0.2 - - - -
427A LYS* 4.4 20.9 + - - +
429A SER* 4.8 2.1 + - - -
430A THR* 2.7 41.9 + - + +
433A LYS* 2.5 36.8 + - - +
510A MET* 3.0 26.2 + - - +
513A ASP* 1.3 84.6 - - + +
515A LEU* 1.3 68.8 + - - +
516A LEU* 3.6 14.7 + - - +
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Residues in contact with LEU 515 (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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424A VAL* 4.1 19.1 - - + -
425A GLN 3.6 6.5 - - - +
426A LEU* 3.5 20.5 - - + +
502A ALA 3.9 18.6 - - - +
511A ILE* 3.0 24.3 + - + +
512A LYS* 3.9 10.9 - - - +
513A ASP 3.7 2.1 - - - +
514A GLU* 1.3 82.4 - - - +
516A LEU* 1.3 59.6 + - - +
517A ARG* 3.7 27.4 - - - +
518A HIS* 3.8 16.6 - - + +
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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