Contacts of the helix formed by residues 260 - 269 (chain A) in PDB entry 2Q5E
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ARG* 3.4 38.1 + - - +
258A ALA* 4.2 2.4 - - - +
259A GLU* 1.3 82.0 - - + +
261A VAL* 1.3 63.8 + - - +
262A TYR* 2.6 41.6 + - - +
263A THR* 3.1 25.6 + - - +
264A SER* 3.3 22.0 + - - -
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Residues in contact with VAL 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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102A ILE* 3.9 28.0 - - + -
210A LEU 4.0 2.7 - - - +
211A ARG 2.8 25.1 + - - +
212A LYS* 4.3 4.9 - - - -
213A THR 3.6 20.0 - - - +
214A LEU* 3.8 29.4 - - + -
229A ASN* 3.9 13.5 - - - +
255A LEU* 5.3 3.1 - - + -
258A ALA* 4.9 1.8 - - + -
260A ASP* 1.3 70.8 - - - +
262A TYR* 1.3 71.3 + - + +
264A SER* 4.4 6.5 - - - -
265A LEU* 2.9 36.2 + - + +
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Residues in contact with TYR 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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210A LEU* 3.5 22.7 + - + +
211A ARG* 3.8 25.4 - - + -
228A GLU* 3.5 43.3 + - + +
229A ASN* 2.8 41.7 + - - -
260A ASP* 2.6 24.2 + - - +
261A VAL* 1.3 75.0 - - + +
263A THR* 1.3 59.5 + - - +
265A LEU* 4.3 2.8 - - - +
266A GLY* 3.4 14.0 + - - -
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Residues in contact with THR 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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260A ASP* 3.1 26.4 + - - +
262A TYR* 1.3 74.1 - - - +
264A SER* 1.3 55.9 + - - +
266A GLY* 2.8 22.7 + - - -
267A GLN* 2.9 39.3 + - - +
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Residues in contact with SER 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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254A GLU 5.6 0.6 + - - -
255A LEU* 3.7 23.1 - - - -
258A ALA* 3.0 31.2 - - - +
260A ASP 3.3 7.4 + - - -
261A VAL* 4.0 2.0 - - - -
263A THR* 1.3 73.3 - - - +
265A LEU* 1.3 67.6 + - - +
267A GLN* 3.0 18.3 + - - +
268A LEU* 2.8 27.6 + - - +
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Residues in contact with LEU 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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214A LEU* 4.3 15.7 - - + -
228A GLU 3.3 27.1 - - - +
229A ASN* 4.3 1.8 - - - -
230A ALA 3.9 9.9 - - - +
231A VAL* 4.1 16.6 - - + -
251A ILE* 6.2 0.7 - - + -
255A LEU* 3.7 32.3 - - + +
261A VAL* 2.9 26.0 + - + +
262A TYR* 4.5 2.2 - - - +
264A SER* 1.3 73.6 - - - +
266A GLY* 1.3 57.2 + - - +
268A LEU* 3.9 7.3 - - + +
269A ARG* 3.0 63.2 + - - +
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Residues in contact with GLY 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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262A TYR 3.4 10.2 + - - -
263A THR* 2.8 11.0 + - - -
265A LEU* 1.3 78.3 - - - +
267A GLN* 1.3 55.4 - - - -
269A ARG* 3.2 7.1 + - - +
270A ALA* 3.1 25.3 + - - +
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Residues in contact with GLN 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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263A THR* 2.9 43.4 + - - +
264A SER* 3.6 19.0 + - - +
266A GLY* 1.3 72.4 - - - +
268A LEU* 1.3 70.9 + - + +
270A ALA* 3.0 25.1 + - + +
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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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251A ILE* 3.8 43.1 - - + +
254A GLU* 3.8 44.2 - - + +
255A LEU* 4.5 12.6 - - + -
264A SER* 2.8 25.7 + - - +
265A LEU* 3.9 10.1 - - + +
267A GLN* 1.3 80.5 - - + +
269A ARG* 1.3 66.0 + - + +
270A ALA 3.0 5.9 + - - +
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Residues in contact with ARG 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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227A PRO 5.7 2.0 + - - -
228A GLU* 5.2 1.8 + - - +
230A ALA 3.5 19.6 + - - -
231A VAL* 4.2 6.3 - - - +
232A PRO* 3.7 19.2 - - - +
265A LEU* 3.0 55.4 + - - +
266A GLY* 3.2 5.8 + - - +
268A LEU* 1.3 78.3 - - + +
270A ALA* 1.3 62.5 + - - +
126C ILE* 4.5 33.1 - - + +
137C GLN* 4.3 15.3 - - - +
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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