Contacts of the helix formed by residues 263 - 267 (chain A) in PDB entry 1O94
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 GLU 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASP* 2.8 23.8 + - - +
262A ALA* 1.3 86.3 - - + +
264A TRP* 1.3 56.2 + - - +
265A GLY 3.1 6.5 - - - +
266A GLU* 3.1 39.4 + - + +
575A PRO* 3.4 25.6 - - + +
579A ARG* 2.6 49.0 + - - -
608B TRP* 3.9 7.7 - - + -
624B ARG* 4.2 2.6 + - - -
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Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 5.7 1.7 - + - -
172A HIS* 3.8 27.8 - + + -
259A GLY 5.6 0.4 - - - -
260A ASP 3.2 22.0 + - - +
261A ILE* 3.0 28.2 - - + +
262A ALA 3.7 1.5 - - - -
263A GLU* 1.3 73.0 - - - +
265A GLY* 1.3 54.5 + - - +
266A GLU 2.9 5.4 - - - +
267A ASP* 3.0 20.4 + - + +
268A ALA* 3.0 27.1 + - + -
352A ILE* 3.6 37.9 - - + -
355A TRP* 3.7 24.8 - + - -
356A GLU* 2.8 21.9 + - - -
572A LEU* 3.5 16.3 - - + +
1730A FMN 3.6 42.6 - + - -
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Residues in contact with GLY 265 (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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263A GLU 3.1 3.0 - - - -
264A TRP* 1.3 75.7 - - - +
266A GLU* 1.3 64.5 + - - +
267A ASP 3.3 0.4 - - - -
268A ALA 3.8 7.9 - - - -
269A GLY* 3.3 20.8 - - - -
270A PRO* 3.3 8.9 - - - +
274A TYR* 3.9 5.0 - - - -
572A LEU* 3.5 41.2 + - - +
576A ASN* 5.4 0.6 + - - -
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Residues in contact with GLU 266 (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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228A VAL* 4.0 23.6 - - + -
258A ILE* 3.7 7.6 - - - +
259A GLY* 4.5 6.1 - - - -
263A GLU* 3.1 26.9 + - + +
264A TRP 2.9 1.6 - - - -
265A GLY* 1.3 80.7 - - - +
267A ASP* 1.3 59.2 + - - +
274A TYR* 2.3 26.2 + - - -
278A HIS* 3.4 13.6 - - - -
576A ASN* 2.9 26.4 + - - +
614B ARG* 2.8 40.9 + - - +
624B ARG* 3.1 19.0 + - - +
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Residues in contact with ASP 267 (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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172A HIS* 2.7 31.8 + - + +
257A THR* 4.1 10.6 - - - -
258A ILE* 3.3 25.2 + - - +
264A TRP* 3.0 10.9 + - + +
266A GLU* 1.3 76.9 - - - +
268A ALA* 1.3 59.2 + - - +
269A GLY 2.8 11.4 + - - -
278A HIS* 3.5 14.8 + - - -
279A THR* 4.8 4.2 - - - +
297A VAL* 3.5 11.8 - - - +
298A GLY* 5.9 0.2 - - - -
1730A FMN 2.7 45.4 + - - +
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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