Contacts of the helix formed by residues 258 - 267 (chain A) in PDB entry 1QL6
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR 5.6 0.2 - - - -
257A SER* 1.3 72.9 - - - +
259A THR* 1.3 60.8 + - - +
260A VAL 3.4 0.2 - - - -
261A LYS* 3.9 21.2 + - - +
262A ASP* 2.9 31.4 + - - +
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Residues in contact with THR 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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257A SER* 3.3 12.7 + - - -
258A ASP* 1.3 79.0 - - - +
260A VAL* 1.3 62.5 + - - -
262A ASP* 3.5 4.2 + - - +
263A LEU* 3.2 16.8 + - - +
284A HIS* 3.4 17.8 - - + -
285A PRO* 4.3 8.5 - - + -
286A PHE* 3.6 38.8 - - + +
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Residues in contact with VAL 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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123A GLU* 3.4 24.0 - - + +
126A THR* 5.5 0.9 - - + -
219A MET* 3.6 15.9 - - + +
223A LEU* 4.1 20.6 - - + -
253A TRP* 5.2 0.7 - - + -
256A TYR* 3.7 13.2 - - + -
257A SER* 3.1 30.8 + - - +
259A THR* 1.3 75.3 - - - +
261A LYS* 1.3 61.2 - - + +
262A ASP 3.2 0.2 - - - -
263A LEU* 3.4 1.6 + - - +
264A VAL* 3.1 29.9 + - + +
286A PHE* 3.3 36.9 - - + -
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Residues in contact with LYS 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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248A PHE* 3.3 46.5 - - + +
253A TRP* 3.5 49.3 + - + +
254A ASP* 5.7 0.8 + - - +
256A TYR* 3.8 12.6 + - + -
257A SER 3.2 22.2 + - - +
258A ASP* 3.3 20.6 + - - +
259A THR 3.3 0.4 - - - -
260A VAL* 1.3 77.8 - - + +
262A ASP* 1.3 67.4 + - - +
264A VAL* 3.3 1.9 + - - -
265A SER* 3.0 20.3 + - - -
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Residues in contact with ASP 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 ASP 2.9 19.2 + - - +
259A THR* 3.8 5.2 - - - +
261A LYS* 1.3 74.9 - - - +
263A LEU* 1.3 63.3 + - - +
265A SER* 2.9 23.7 + - - -
266A ARG* 2.7 48.1 + - - +
284A HIS* 2.6 27.7 + - + +
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Residues in contact with LEU 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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134A LEU* 5.5 0.2 - - + -
219A MET* 3.6 23.1 - - + -
259A THR 3.2 10.4 + - - +
260A VAL* 3.7 8.5 - - - +
261A LYS 3.3 0.4 - - - -
262A ASP* 1.3 74.3 - - - +
264A VAL* 1.3 65.3 + - - +
266A ARG* 2.9 20.2 + - - +
267A PHE* 3.5 23.8 + - + -
276A TYR* 3.9 23.3 - - + -
281A ALA* 4.2 3.8 - - + -
284A HIS* 3.7 32.6 - - + +
286A PHE* 3.7 16.4 - - + -
287A PHE* 3.5 32.8 - - + -
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Residues in contact with VAL 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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216A GLY 4.5 3.8 - - - +
219A MET* 3.3 37.0 - - + -
220A TYR* 4.1 16.2 - - + +
223A LEU* 4.4 9.0 - - + -
248A PHE* 3.7 22.0 - - + -
253A TRP* 4.5 7.0 - - + -
260A VAL 3.1 9.6 + - - +
261A LYS 3.6 6.5 - - - +
263A LEU* 1.3 77.8 - - - +
265A SER* 1.3 56.7 + - - +
267A PHE* 2.8 29.9 + - - +
268A LEU* 3.1 29.4 + - + +
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Residues in contact with SER 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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246A TYR* 3.1 24.8 + - - -
248A PHE* 4.0 7.2 - - - -
261A LYS 3.0 12.5 + - - -
262A ASP* 2.9 20.5 + - - -
264A VAL* 1.3 73.3 - - - +
266A ARG* 1.3 63.4 + - - +
267A PHE 3.3 0.6 + - - -
268A LEU 3.7 8.4 + - - +
269A VAL* 3.4 17.8 - - - +
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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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262A ASP* 2.7 53.5 + - - +
263A LEU* 2.9 11.7 + - - +
265A SER* 1.3 78.3 + - - +
267A PHE* 1.3 60.1 + - - +
268A LEU 3.4 0.2 - - - -
269A VAL* 3.8 12.0 - - - +
274A LYS 5.1 0.2 - - - +
276A TYR* 2.9 73.1 + - + +
284A HIS* 5.1 0.4 - - - +
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Residues in contact with PHE 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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130A MET* 4.8 0.9 - - + -
134A LEU* 4.2 14.1 - - + -
212A MET* 3.4 34.3 - - + +
213A TRP* 3.8 6.9 - - - -
215A THR* 4.3 9.2 - - + -
216A GLY* 3.4 31.9 - - - -
219A MET* 3.4 31.9 - - - -
263A LEU* 3.8 25.6 - - + -
264A VAL* 2.8 7.3 + - - +
266A ARG* 1.3 78.6 - - - +
268A LEU* 1.4 62.1 + - - +
269A VAL 3.1 8.5 + - - -
275A ARG* 3.2 26.4 + - - -
276A TYR* 4.1 12.8 - - + -
281A ALA* 3.4 34.8 - - + -
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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