Contacts of the helix formed by residues 474 - 482 (chain A) in PDB entry 4I5L
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 GLY 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A VAL* 2.6 25.9 + - - +
471A GLU 4.7 0.4 + - - -
472A LYS 3.7 0.8 - - - -
473A PHE* 1.3 74.9 - - - +
475A LYS* 1.3 64.6 + - - -
476A GLU* 3.2 8.5 - - - -
477A TRP* 3.3 7.0 + - - +
478A ALA* 3.1 19.8 + - - +
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Residues in contact with LYS 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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470A VAL* 4.1 5.1 - - - +
474A GLY* 1.3 69.4 - - - -
476A GLU* 1.3 85.3 + - - +
478A ALA* 3.4 9.4 + - - +
479A HIS 2.9 23.4 + - - -
511A VAL 3.9 8.2 + - - +
512A CYS* 3.5 42.0 - - - +
513A GLY* 5.1 3.8 - - - -
516A ILE* 3.6 23.6 - - + +
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Residues in contact with GLU 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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473A PHE 5.3 0.9 - - - +
474A GLY* 4.4 4.3 - - - -
475A LYS* 1.3 109.1 + - + +
477A TRP* 1.3 60.0 + - - +
479A HIS* 3.3 6.4 + - - +
480A ALA* 2.9 29.9 + - - +
516A ILE* 5.0 3.4 - - + -
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Residues in contact with TRP 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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436A VAL* 3.6 19.3 - - + +
439A PHE* 3.5 28.7 - + - -
440A ASP* 2.7 28.7 + - - -
444A ASN* 5.2 0.2 - - - -
469A LEU* 3.7 41.7 - - + -
470A VAL* 4.0 7.9 - - + -
473A PHE* 3.5 41.5 + + + +
474A GLY 3.3 6.7 + - - +
476A GLU* 1.3 77.3 - - - +
478A ALA* 1.3 65.6 + - + +
480A ALA* 3.2 5.2 + - - -
481A THR* 2.7 62.5 + - + -
482A ILE* 3.6 27.6 - - + -
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Residues in contact with ALA 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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470A VAL* 3.7 29.2 - - + -
474A GLY 3.1 10.3 + - - +
475A LYS* 3.4 9.6 - - - +
477A TRP* 1.3 85.3 - - - +
479A HIS* 1.3 57.8 + - - +
482A ILE* 2.9 33.3 + - + -
483A ILE* 2.9 16.8 + - + -
508A LEU* 5.3 0.7 - - + -
512A CYS* 3.9 17.7 - - - -
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Residues in contact with HIS 479 (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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475A LYS 2.9 16.5 + - - +
476A GLU* 3.3 6.0 + - - +
478A ALA* 1.3 76.0 - - - +
480A ALA* 1.3 62.0 + - - +
483A ILE* 3.9 18.5 - - + +
484A PRO* 3.3 21.4 - - + +
516A ILE* 4.2 17.0 - - + +
520A HIS* 3.3 56.7 + + + -
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Residues in contact with ALA 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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476A GLU 2.9 18.1 + - - +
477A TRP* 3.8 5.4 - - - +
479A HIS* 1.3 80.0 - - - +
481A THR* 1.3 67.8 + - + +
484A PRO* 4.3 9.6 - - - +
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Residues in contact with THR 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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440A ASP* 4.2 14.8 - - + +
444A ASN* 3.4 23.5 + - - -
477A TRP* 2.7 64.4 + - + +
480A ALA* 1.3 85.1 - - + +
482A ILE* 1.3 60.3 + - - +
484A PRO* 4.4 3.4 - - - -
485A LYS* 4.1 16.3 - - - +
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Residues in contact with ILE 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 PHE* 5.1 3.4 - - + -
444A ASN* 3.5 27.1 - - - +
447A CYS* 6.1 0.7 - - + -
448A MET* 4.0 15.3 - - - +
466A LEU* 4.0 28.0 - - + -
470A VAL* 5.6 0.9 - - + -
477A TRP* 3.6 38.1 - - + -
478A ALA* 2.9 15.3 + - + +
481A THR* 1.3 81.9 - - - +
483A ILE* 1.3 66.9 + - + +
484A PRO* 3.4 2.0 - - - +
485A LYS* 3.1 8.9 + - - +
486A VAL* 3.1 33.4 + - + +
508A LEU* 4.4 13.7 - - + -
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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