Contacts of the helix formed by residues 472 - 479 (chain D) in PDB entry 2IHU
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 ASP 472 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D THR* 3.4 5.7 - - - -
55D ARG* 2.7 19.7 + - - +
56D HIS* 3.4 17.8 + - - +
59D THR* 2.6 35.9 + - + +
442D ILE* 3.8 24.1 - - + +
469D ASN* 3.8 7.6 + - - +
470D SER 3.1 2.2 - - - -
471D SER* 1.3 73.9 - - - +
473D LEU* 1.3 63.6 + - - +
474D GLU 3.1 1.3 - - - +
475D THR* 2.6 38.7 + - - -
476D ILE* 3.2 16.1 + - - +
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Residues in contact with LEU 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D ILE* 4.0 9.2 - - + +
466D PHE* 3.8 35.4 - - + -
470D SER 3.0 21.7 + - - +
471D SER 3.0 0.2 - - - -
472D ASP* 1.3 77.7 - - - +
474D GLU* 1.3 61.1 + - - +
476D ILE* 3.2 17.0 + - + +
477D ALA 3.1 17.8 + - - -
485D THR* 5.2 4.3 - - - +
519D PHE 5.5 0.2 - - - +
522D LEU* 4.3 7.4 - - + -
523D ALA* 3.9 27.1 - - + +
526D ASN* 3.7 22.0 - - + +
528D VAL* 3.6 28.7 - - + +
554D LEU* 4.1 11.7 - - + -
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Residues in contact with GLU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C PHE* 3.7 0.7 - - - -
515C GLY* 2.8 32.6 + - - +
516C GLY 4.6 2.5 - - - +
517C VAL* 3.6 25.8 - - + -
55D ARG* 2.9 25.3 + - + +
471D SER 3.3 10.5 + - - +
472D ASP 3.1 0.6 - - - -
473D LEU* 1.3 77.2 - - - +
475D THR* 1.3 56.8 + - - +
477D ALA* 3.4 2.4 + - + +
478D ARG* 2.8 60.6 + - - +
526D ASN* 3.4 31.4 + - - +
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Residues in contact with THR 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 5.1 0.9 - - + -
53D LEU 3.6 18.2 - - - +
54D THR* 3.7 10.9 - - + -
55D ARG* 3.8 3.8 + - - +
446D ILE* 4.2 12.8 - - + -
472D ASP* 2.6 36.0 + - - +
474D GLU* 1.3 76.7 + - - +
476D ILE* 1.3 59.7 + - - +
478D ARG* 3.2 20.7 + - - +
479D LEU* 2.9 52.3 + - + +
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Residues in contact with ILE 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D ILE* 3.8 33.9 - - + +
445D ALA* 5.5 0.4 - - + -
446D ILE* 3.8 20.9 - - + -
459D LEU* 6.0 0.2 - - + -
472D ASP 3.2 8.8 + - - +
473D LEU* 3.2 18.8 + - + +
475D THR* 1.3 78.1 - - - +
477D ALA* 1.3 56.5 + - - +
479D LEU 3.7 0.3 + - - -
480D ASN* 3.0 21.0 + - - -
481D LEU* 3.1 29.1 + - - +
483D ILE* 4.1 28.0 - - + -
485D THR* 5.0 4.3 - - - +
528D VAL* 5.0 2.2 - - + -
552D PRO* 3.4 29.0 - - + +
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Residues in contact with ALA 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D LEU 3.1 10.1 + - - +
474D GLU* 3.6 5.6 - - + +
476D ILE* 1.3 76.0 - - - +
478D ARG* 1.3 61.6 + - - +
480D ASN* 3.0 22.2 + - - +
526D ASN 3.6 24.0 - - - +
527D GLY* 4.0 11.0 - - - +
528D VAL* 3.8 11.2 - - + -
552D PRO* 4.1 10.8 - - + -
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Residues in contact with ARG 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C LYS 3.7 20.7 + - - -
514C PHE* 3.9 15.7 - - - +
515C GLY* 3.9 11.4 - - - +
53D LEU* 2.8 43.1 + - - +
55D ARG* 4.1 2.6 - - - +
474D GLU* 2.8 54.6 + - - +
475D THR* 3.2 22.8 + - - +
477D ALA* 1.3 73.3 - - - +
479D LEU* 1.3 73.1 + - + +
480D ASN* 3.4 2.3 + - - +
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Residues in contact with LEU 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.7 35.7 - - + -
446D ILE* 4.5 7.9 - - + -
450D MET* 4.7 6.1 - - - -
475D THR* 2.9 33.9 + - + +
476D ILE 4.3 0.2 - - - +
478D ARG* 1.3 91.2 - - + +
480D ASN* 1.3 69.1 + - - +
481D LEU* 3.3 34.0 + - + +
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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