Contacts of the helix formed by residues 427 - 432 (chain B) in PDB entry 1O95
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 HIS 427 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PRO* 4.0 14.1 - - + -
426B GLY* 1.3 72.0 - - - -
428B LEU* 1.3 62.5 + - - +
429B ASN* 2.8 4.2 + - - -
430B GLN* 3.5 15.7 + - - +
431B VAL* 3.1 35.0 + - + +
489B ALA 5.7 2.5 - - - +
540B PHE* 6.3 0.4 - + - -
644B ARG* 4.5 17.2 + - - -
674B ASP* 3.9 6.3 - - - -
679B ARG 5.8 1.5 + - - -
681B ILE* 3.9 25.3 - - + +
684B ALA* 6.0 0.7 - - + -
1731B ADP 2.5 52.8 + - - +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 6.1 0.7 - - + -
399B PRO* 5.3 3.1 - - + -
425B GLY* 2.8 17.3 + - - +
426B GLY 2.7 4.8 + - - -
427B HIS* 1.3 80.5 + - + +
429B ASN* 1.3 61.3 + - - +
431B VAL* 3.4 16.8 - - + -
432B ALA* 2.9 30.3 + - + +
440B TRP* 3.0 37.0 - - + +
441B SER* 4.9 1.8 - - - +
443B HIS* 3.5 30.3 - - + +
444B ARG* 4.1 13.5 - - + +
681B ILE* 3.6 34.5 - - + -
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Residues in contact with ASN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS* 4.1 22.7 + - + +
424B ILE 3.3 7.7 + - - -
425B GLY* 3.3 35.8 - - - +
426B GLY 3.1 7.0 + - - +
427B HIS 2.8 2.8 - - - -
428B LEU* 1.3 84.0 - - - +
430B GLN* 1.3 62.9 + - - +
432B ALA* 3.5 7.7 + - - +
433B ALA* 3.6 8.7 + - - +
441B SER* 5.6 0.5 + - - -
444B ARG* 3.3 27.2 + - - +
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Residues in contact with GLN 430 (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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426B GLY 4.8 0.4 + - - -
427B HIS* 3.5 15.9 + - - +
429B ASN* 1.3 74.8 - - - +
431B VAL* 1.3 67.7 + - - +
433B ALA* 2.5 23.2 + - + +
434B LEU* 3.4 5.9 + - - +
490B ARG* 4.9 4.5 + - - +
518B GLU* 4.2 20.2 + - - +
521B MET* 3.2 47.4 - - + +
522B ASP* 2.9 32.8 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B HIS* 3.1 36.5 + - + +
428B LEU* 2.9 19.8 + - + +
430B GLN* 1.3 77.9 - - + +
432B ALA* 1.3 61.7 + - - +
433B ALA 3.1 0.7 + - - -
434B LEU* 3.1 24.6 + - - +
437B LEU* 3.6 6.1 - - + +
440B TRP* 3.7 25.1 - - + -
521B MET* 5.2 1.8 - - + -
540B PHE* 3.7 35.9 - - + -
541B MET* 4.7 11.9 - - + -
681B ILE* 4.6 2.0 - - + -
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Residues in contact with ALA 432 (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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428B LEU* 2.9 15.4 + - + +
429B ASN* 4.3 4.5 - - - +
431B VAL* 1.3 79.4 - - - +
433B ALA* 1.3 61.3 + - - +
434B LEU 3.4 1.4 + - - +
437B LEU* 3.3 31.2 - - - +
438B GLY* 3.6 11.7 + - - -
440B TRP* 4.1 3.6 - - + -
441B SER* 3.5 38.4 - - - +
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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