Contacts of the helix formed by residues 472 - 478 (chain A) in PDB entry 5IVH
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 THR 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 3.2 28.9 + - - +
354A PHE* 4.0 2.4 - - + -
455A ASN* 3.0 20.3 + - - -
457A TYR* 3.2 65.4 - - + +
458A ARG 5.1 0.2 + - - -
461A ARG* 4.5 5.7 + - - -
470A SER 3.2 0.4 + - - -
471A HIS* 1.3 88.8 + - + +
473A ASP* 1.3 61.6 + - - +
474A GLU* 3.1 14.0 + - - -
475A LEU* 3.2 11.8 + - - +
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Residues in contact with ASP 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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446A PHE* 4.3 1.8 - - + -
448A PHE 5.4 1.3 - - - +
449A ASP* 4.7 1.0 - - - +
455A ASN* 4.4 4.9 + - - +
458A ARG* 3.1 19.4 + - - +
461A ARG* 2.9 28.2 + - - -
468A GLY 3.5 6.4 - - - +
469A VAL* 3.3 23.0 - - + +
470A SER* 2.7 38.1 + - - +
471A HIS 3.2 1.2 + - - -
472A THR* 1.3 77.5 + - - +
474A GLU* 1.3 62.6 + - - +
475A LEU 3.3 0.6 + - - -
476A THR* 3.6 9.2 + - - -
477A TYR* 3.4 19.9 - - + -
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Residues in contact with GLU 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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217A GLU* 3.2 28.6 - - - +
243A MET* 3.7 33.1 - - + +
244A SER* 3.9 8.0 + - - -
348A THR* 3.6 14.2 - - - +
444A TYR* 4.6 5.7 + - + +
446A PHE* 3.7 40.6 - - + -
472A THR 3.4 20.0 + - - -
473A ASP* 1.3 71.1 + - - +
475A LEU* 1.3 68.7 + - + +
476A THR 2.9 4.9 + - - -
477A TYR* 2.9 15.9 + - - +
478A PHE* 3.3 16.7 - - + -
500A MET* 5.5 0.7 - - + -
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Residues in contact with LEU 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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132A TYR* 3.4 22.7 - - + +
148A TYR* 4.3 22.0 - - + +
217A GLU* 3.6 39.3 - - + +
243A MET* 4.6 10.5 - - + -
455A ASN* 4.0 9.6 - - + +
457A TYR* 4.5 9.6 - - + -
472A THR* 3.2 22.8 + - - +
474A GLU* 1.3 78.6 - - - +
476A THR* 1.3 61.2 + - - +
478A PHE* 3.1 6.1 + - + +
479A PHE* 3.1 46.1 + - + +
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Residues in contact with THR 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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152A TYR* 3.5 20.1 + - - -
453A LEU* 3.6 52.1 - - + +
454A ILE* 3.6 8.4 - - - +
455A ASN* 2.9 34.8 + - - +
473A ASP* 3.6 13.1 + - - -
474A GLU 2.9 0.2 + - - -
475A LEU* 1.3 78.8 - - - +
477A TYR* 1.3 66.0 + - + +
478A PHE 3.4 0.2 - - - -
479A PHE 3.8 6.3 - - - +
481A ASN* 4.9 2.2 + - - +
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Residues in contact with TYR 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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152A TYR* 4.1 3.4 - - - -
446A PHE* 3.5 28.3 - + - -
448A PHE* 3.5 32.9 + + - -
450A SER* 3.5 20.4 + - - -
453A LEU* 4.1 10.2 + - + -
473A ASP 3.4 18.6 - - - -
474A GLU 2.9 11.6 + - - +
476A THR* 1.3 94.3 - - + +
478A PHE* 1.3 61.0 + - - +
493A GLU* 3.9 27.8 - - + -
496A THR* 3.7 23.1 - - + -
497A ILE* 3.5 38.2 - - + +
500A MET* 4.0 13.0 - - + +
501A THR* 4.1 2.3 - - - +
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Residues in contact with PHE 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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149A GLY 4.5 1.0 - - - +
152A TYR* 3.7 16.4 - - - +
153A PHE* 3.5 43.7 + + + -
215A PHE* 4.9 2.2 - + - -
243A MET* 3.6 22.0 - - + -
474A GLU* 3.3 31.2 - - + -
475A LEU* 3.1 3.5 + - - +
477A TYR* 1.3 80.2 - - - +
479A PHE* 1.3 80.8 + + + +
500A MET* 3.4 52.7 - - + -
501A THR* 4.2 2.9 - - + +
504A TRP* 3.4 43.7 - + + -
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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