Contacts of the helix formed by residues 257 - 264 (chain A) in PDB entry 2W5X
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 GLN 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A THR* 3.0 28.7 + - - +
220A MET 2.9 26.0 + - - -
221A PRO 3.7 7.3 + - - -
222A THR* 3.4 18.4 - - - +
227A ARG* 3.8 10.3 - - - +
255A GLY 3.4 0.6 - - - -
256A SER* 1.3 76.5 - - - +
258A ILE* 1.3 65.6 + - - +
259A ASP 3.1 2.2 - - - -
260A TRP* 3.1 44.6 + - + +
261A GLY* 3.1 9.2 + - - -
269A TYR* 2.8 29.6 + - - +
273A GLU* 3.6 24.8 + - - +
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Residues in contact with ILE 258 (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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42A SER* 3.7 29.2 - - - -
43A ASP 3.3 10.8 - - - +
44A GLY 4.6 2.9 - - - +
45A ALA* 4.2 17.9 - - + +
49A GLN* 4.6 2.2 - - + -
255A GLY 3.7 13.0 - - - +
256A SER 3.4 1.0 - - - -
257A GLN* 1.3 76.1 - - - +
259A ASP* 1.3 62.7 + - - +
261A GLY* 3.1 4.5 + - - -
262A GLY* 3.1 17.0 + - - -
270A LEU* 4.0 28.2 - - + +
273A GLU* 3.8 12.1 - - + +
274A ILE* 3.7 42.8 - - + +
277A PHE* 3.9 11.4 - - + -
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Residues in contact with ASP 259 (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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43A ASP* 2.9 34.9 + - - +
44A GLY* 4.2 4.5 - - - -
84A SEP 2.6 11.3 + - - -
256A SER 4.0 6.5 - - - +
258A ILE* 1.3 77.1 - - - +
260A TRP* 1.3 75.3 + - + +
262A GLY* 3.0 3.6 + - - -
263A HIS* 3.0 29.1 + - - -
302A HIS* 3.5 2.3 - - - -
304A THR* 2.7 27.5 + - - +
1377A ZN 2.4 36.4 - - - -
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Residues in contact with TRP 260 (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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84A SEP 5.2 2.0 + - - -
131A SER* 3.7 27.1 - - - -
132A SER 5.2 0.2 - - - -
135A GLU* 4.6 22.7 + - + -
219A ALA* 3.5 30.3 - - + -
256A SER 3.9 11.0 + - - -
257A GLN* 3.1 33.9 + - + +
259A ASP* 1.3 98.2 + - + +
261A GLY* 1.3 63.3 + - - +
263A HIS* 3.3 9.2 + + - +
264A ALA* 3.0 25.6 + - - +
269A TYR* 3.4 28.1 - - + +
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Residues in contact with GLY 261 (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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257A GLN 3.1 10.8 + - - -
258A ILE 3.1 4.9 + - - -
260A TRP* 1.3 77.1 - - - +
262A GLY* 1.3 60.0 + - - +
264A ALA* 3.3 1.6 + - - -
265A ASN* 3.1 3.3 + - - -
266A ASN 3.1 29.7 + - - +
269A TYR* 3.7 25.9 - - - -
270A LEU* 4.0 15.3 - - - -
332A PHE* 4.4 0.5 - - - -
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Residues in contact with GLY 262 (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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258A ILE 3.1 8.4 + - - -
259A ASP 3.0 7.9 + - - -
261A GLY* 1.3 75.1 - - - +
263A HIS* 1.3 62.1 + - - +
265A ASN* 2.9 23.4 + - - +
270A LEU* 3.8 13.1 - - - +
304A THR* 3.6 26.5 - - - -
305A GLY* 3.9 7.0 - - - -
332A PHE* 4.0 4.1 - - - -
334A THR 4.4 0.3 - - - +
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Residues in contact with HIS 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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259A ASP* 3.0 29.6 + - - -
260A TRP* 3.3 11.0 + + - +
262A GLY* 1.3 75.7 - - - +
264A ALA* 1.3 61.4 + - - +
265A ASN* 3.3 5.4 + - - +
304A THR* 3.6 2.3 + - - -
335A GLY* 2.6 38.9 + - - +
336A GLY* 3.8 8.7 - - - -
337A HIS* 3.6 17.3 - + - -
1377A ZN 2.1 37.1 - - - -
325B TYR* 4.5 3.6 - - - -
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Residues in contact with ALA 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 TRP 3.0 17.5 + - - +
261A GLY* 3.9 4.0 - - - +
262A GLY 3.2 0.2 - - - -
263A HIS* 1.3 76.4 - - - +
265A ASN* 1.3 70.2 + - - +
266A ASN* 3.1 16.6 + - + +
269A TYR* 4.9 6.5 - - + -
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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