Contacts of the helix formed by residues 262 - 270 (chain A) in PDB entry 1WNZ
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A THR* 2.9 43.7 + - + +
249A ALA* 4.1 18.6 - - + -
251A PHE* 3.7 10.0 - - + -
260A LEU 3.3 4.6 + - - -
261A GLU* 1.3 79.0 - - - +
263A GLY* 1.3 65.3 + - - +
265A GLY 3.5 0.2 + - - -
266A ARG* 2.4 72.0 + - - +
278A THR* 5.8 1.1 - - + -
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Residues in contact with GLY 263 (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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261A GLU* 3.0 11.8 + - - -
262A GLU* 1.3 81.5 + - - +
264A LEU* 1.3 66.5 + - - +
266A ARG* 3.3 22.2 + - - +
267A LYS* 3.0 42.1 + - - +
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Residues in contact with LEU 264 (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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260A LEU* 4.2 2.0 - - + -
261A GLU* 2.8 17.9 + - + +
263A GLY* 1.3 76.0 - - - +
265A GLY* 1.3 57.8 + - - +
267A LYS* 3.4 20.9 + - + +
268A LEU* 2.9 31.4 + - - +
311A GLN 3.5 31.2 - - - +
312A GLU 3.8 17.5 - - - +
313A ASP 3.4 16.8 - - - +
314A GLY 3.4 27.7 - - - +
315A THR* 3.4 22.7 - - - +
316A GLY* 3.4 4.9 - - - +
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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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251A PHE* 3.7 19.1 - - - -
260A LEU* 3.7 19.9 - - - +
261A GLU 2.8 16.5 + - - -
262A GLU 3.5 0.2 + - - -
263A GLY 3.2 0.2 - - - -
264A LEU* 1.3 75.6 - - - +
266A ARG* 1.3 58.0 - - - +
268A LEU* 4.6 0.9 - - - -
269A LEU* 2.8 36.6 + - - +
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Residues in contact with ARG 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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251A PHE* 3.8 13.7 - - + -
262A GLU* 2.4 64.8 + - - +
263A GLY* 3.9 11.7 + - - +
265A GLY* 1.3 76.1 - - - +
267A LYS* 1.3 59.7 + - + +
270A GLY* 2.7 40.4 + - - +
271A GLU* 2.9 49.6 + - - +
275A VAL* 5.7 4.9 - - + -
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Residues in contact with LYS 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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261A GLU* 5.0 0.4 + - - -
263A GLY* 3.0 37.9 + - - +
264A LEU* 3.6 26.0 - - + +
266A ARG* 1.3 82.3 - - + +
268A LEU* 1.3 60.9 + - - +
270A GLY* 4.2 2.9 + - - -
311A GLN 4.4 8.3 + - - -
312A GLU* 4.8 8.7 + - - +
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Residues in contact with LEU 268 (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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206A TYR* 3.8 37.7 - - + +
225A LEU* 3.7 30.3 - - + -
260A LEU* 3.8 14.1 - - + -
264A LEU 2.9 17.3 + - - +
265A GLY 4.0 2.0 - - - +
267A LYS* 1.3 78.9 - - - +
269A LEU* 1.3 69.1 + - + +
314A GLY 5.7 1.6 - - - +
377A PHE* 4.2 8.5 - - + -
378A LYS* 3.4 37.1 + - - +
380A GLU* 5.1 1.6 - - - +
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Residues in contact with LEU 269 (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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251A PHE* 3.5 43.5 - - + -
253A VAL* 4.0 19.5 - - + -
258A LEU* 4.5 5.4 - - + -
260A LEU* 4.1 13.2 - - + -
265A GLY 2.8 20.0 + - - +
268A LEU* 1.3 85.9 - - + +
270A GLY* 1.3 55.8 + - - +
273A THR* 2.8 27.5 + - + +
377A PHE* 3.6 35.0 - - + -
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Residues in contact with GLY 270 (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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251A PHE* 5.4 0.9 - - - -
266A ARG* 2.7 27.9 + - - +
267A LYS 4.2 2.8 + - - -
268A LEU 3.6 1.2 - - - -
269A LEU* 1.3 74.7 - - - +
271A GLU* 1.3 65.4 + - - -
272A GLY 3.1 3.8 - - - -
273A THR* 3.1 20.5 + - - +
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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