Contacts of the helix formed by residues 463 - 469 (chain B) 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 463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.0 12.6 + - - +
462B GLY* 1.3 69.7 - - - -
464B GLY* 1.3 66.6 + - - +
466B PHE* 4.5 0.2 - - - -
467B HIS* 3.0 20.6 + - - +
487B VAL* 4.3 3.3 - - - +
488B VAL 3.3 4.8 + - - +
489B ASN* 3.1 26.0 - - + +
490B ASN 3.1 11.1 + - - -
491B ASP* 3.2 8.8 + - - -
492B THR 3.0 24.4 + - - +
514B PHE* 3.6 7.4 - - - -
519B PHE* 3.6 25.1 - - + -
601B MG 2.3 26.9 - - - -
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Residues in contact with GLY 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.7 7.0 + - - +
438B PHE* 4.0 7.1 - - - -
463B ASP* 1.3 75.6 - - - +
465B GLY* 1.3 60.1 + - - +
468B SER* 3.3 21.8 + - - -
493B ASN* 3.3 25.1 - - - -
514B PHE* 3.7 15.1 - - - -
600B TP9 2.8 17.4 + - - -
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Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ASP* 4.1 7.2 - - - -
410B ILE 4.7 0.2 - - - -
438B PHE* 3.5 30.5 - - - -
439B GLY* 3.2 14.0 + - - -
462B GLY 5.5 0.2 - - - -
464B GLY* 1.3 70.2 - - - +
466B PHE* 1.3 63.7 + - - +
468B SER* 2.7 22.7 + - - -
600B TP9 2.8 20.5 + - - -
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Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ASP* 4.3 6.2 + - - -
439B GLY* 5.2 0.4 - - - -
442B ILE* 3.6 36.6 - - + -
459B LEU* 4.4 1.6 - - + -
461B ALA* 3.7 26.3 - - + +
462B GLY 2.8 26.1 + - - +
463B ASP 4.3 1.1 - - - +
465B GLY* 1.3 72.1 - - - +
467B HIS* 1.3 59.8 + - - +
469B ASN* 3.1 6.9 + - - +
470B SER* 3.0 39.7 + - - -
473B LEU* 3.9 15.9 - - + -
485B THR* 3.8 17.7 - - + -
487B VAL* 3.9 17.5 - - + -
519B PHE* 3.9 24.0 - + - -
522B LEU* 4.6 0.4 - - + -
554B LEU* 3.7 21.8 - - + -
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Residues in contact with HIS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.3 29.6 - - - +
471A SER* 2.5 63.3 + - - -
474A GLU* 4.5 0.2 - - + -
526A ASN* 2.9 27.9 + - - -
463B ASP 3.0 20.7 + - - +
466B PHE* 1.3 72.8 - - - +
468B SER* 1.3 62.3 + - - +
469B ASN 3.0 2.5 + - - -
470B SER* 2.8 30.4 + - - -
517B VAL* 3.8 15.7 - - + +
519B PHE* 3.9 11.7 - + + -
522B LEU* 3.8 27.5 - - + +
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Residues in contact with SER 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.4 27.3 + - - +
56A HIS* 3.7 13.3 - - - +
471A SER* 4.6 3.2 + - - -
1501A K 3.3 19.6 - - - -
438B PHE* 3.5 28.3 + - - -
439B GLY* 3.4 16.1 + - - -
464B GLY 3.3 8.9 + - - -
465B GLY 2.7 19.0 + - - -
466B PHE 3.2 0.2 - - - -
467B HIS* 1.3 75.8 - - - +
469B ASN* 1.3 57.9 + - - +
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Residues in contact with ASN 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B HIS* 4.3 12.1 - - - +
58B PHE* 3.7 17.8 - - + -
59B THR* 3.0 28.1 + - - -
439B GLY* 3.0 38.7 + - - +
442B ILE* 3.7 13.3 - - + +
443B PRO* 3.5 11.9 - - - +
466B PHE 3.1 6.0 + - - +
467B HIS 3.0 0.4 - - - -
468B SER* 1.3 83.6 + - - +
470B SER* 1.3 62.0 + - - +
471B SER* 3.3 5.1 + - - -
472B ASP* 3.8 9.4 + - - +
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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