Contacts of the helix formed by residues 476 - 484 (chain A) in PDB entry 2IHM
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 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A PRO* 3.6 17.8 - - - +
475A THR* 1.3 81.0 - - - +
477A GLU* 1.3 64.1 + - - +
478A GLU* 3.2 27.1 + - - +
479A ASP* 3.2 25.1 + - - +
480A VAL* 3.3 8.7 + - - +
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Residues in contact with GLU 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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322A ARG* 2.7 37.7 + - - -
430A PRO* 4.3 15.3 - - + +
433A LEU* 3.9 18.2 - - + -
434A LEU* 3.5 24.2 + - + +
476A SER* 1.3 72.8 - - - +
478A GLU* 1.3 72.0 + - - +
480A VAL* 3.2 9.4 + - - +
481A PHE* 3.0 28.2 + - - -
488A TYR* 4.0 13.9 + - + -
494A ARG* 2.7 35.9 + - - +
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A SER* 3.1 19.6 + - - +
477A GLU* 1.3 81.8 + - - +
479A ASP* 1.3 63.2 + - - +
481A PHE* 3.0 5.3 + - - +
482A ARG* 3.0 44.0 + - - +
488A TYR* 3.5 55.6 + - + -
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Residues in contact with ASP 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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473A HIS 5.0 1.6 - - - +
474A ALA* 3.7 10.4 - - + -
475A THR* 2.7 44.4 + - - +
476A SER* 3.2 17.7 + - - +
478A GLU* 1.3 77.6 - - - +
480A VAL* 1.3 58.6 + - - +
482A ARG* 2.8 42.3 + - - +
483A LEU* 3.0 18.4 + - + +
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Residues in contact with VAL 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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430A PRO* 4.2 11.7 - - + +
431A PHE* 3.6 43.1 - - + -
434A LEU* 3.5 30.1 - - + -
458A LEU* 5.2 2.0 - - + -
463A LEU* 6.0 2.0 - - + -
474A ALA* 3.7 13.7 - - + -
476A SER 3.3 6.2 + - - +
477A GLU* 3.2 10.4 + - - +
479A ASP* 1.3 79.8 - - - +
481A PHE* 1.3 61.1 + - + +
483A LEU* 3.6 8.8 + - + +
484A LEU* 3.4 34.8 + - + +
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Residues in contact with PHE 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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143A CYS 4.6 5.6 - - - -
434A LEU* 3.8 26.7 - - + -
442A PHE* 4.2 24.5 - + - -
446A LEU* 5.1 3.8 - - + -
477A GLU* 3.0 24.7 + - + -
478A GLU 3.0 9.8 + - - +
480A VAL* 1.3 76.9 - - + +
482A ARG* 1.3 62.5 + - - +
484A LEU* 3.5 3.5 + - - -
485A GLY 3.2 2.6 + - - -
486A LEU* 2.8 58.9 + - + +
487A LYS 3.5 24.0 - - - -
488A TYR* 3.5 30.3 - + + -
489A LEU* 3.8 23.6 - - + -
494A ARG* 4.0 6.5 - - - -
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Residues in contact with ARG 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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478A GLU* 3.0 33.3 + - - +
479A ASP* 2.8 29.7 + - - +
481A PHE* 1.3 72.7 - - - +
483A LEU* 1.3 58.7 + - + +
484A LEU 3.0 2.0 - - - -
485A GLY* 2.6 27.9 + - - +
486A LEU 5.0 0.9 - - - -
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Residues in contact with LEU 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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431A PHE* 4.8 6.3 - - + -
454A LYS* 5.7 1.4 - - - +
456A LEU* 5.2 4.2 - - - +
463A LEU* 4.1 17.9 - - + +
472A PHE* 3.8 42.1 - - + -
473A HIS 3.3 27.8 - - - +
474A ALA* 4.9 0.2 - - + -
479A ASP* 3.0 14.2 + - + +
480A VAL* 3.9 14.6 - - - +
481A PHE 3.5 0.2 - - - -
482A ARG* 1.3 80.2 - - + +
484A LEU* 1.3 61.6 + - - +
485A GLY 3.3 0.4 + - - -
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Residues in contact with LEU 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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434A LEU* 5.7 0.2 - - + -
446A LEU* 4.8 9.0 - - + +
449A PHE* 3.8 13.1 - - + -
450A SER* 4.0 17.5 - - - +
454A LYS* 3.6 30.3 - - + +
456A LEU* 4.9 5.2 - - + -
458A LEU* 4.3 22.9 - - + -
463A LEU* 3.4 39.5 - - + -
480A VAL* 3.4 26.1 + - + +
481A PHE* 3.5 2.0 + - - +
482A ARG 3.0 0.8 - - - -
483A LEU* 1.3 78.3 - - - +
485A GLY* 1.3 65.7 + - - +
486A LEU* 3.4 25.5 + - + -
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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