Contacts of the helix formed by residues 261 - 276 (chain A) in PDB entry 3QJQ
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 SER 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 3.3 23.9 - - - +
260A VAL* 1.3 84.1 - - - +
262A ASP* 1.3 61.3 + - - +
263A PRO* 3.2 11.0 - - - +
264A MET* 3.2 35.6 + - - +
265A ALA* 3.7 13.7 + - - +
315A THR* 4.4 7.3 - - - +
511A VAL* 4.4 0.2 - - - -
512A ILE 4.1 5.8 - - - -
8B HIS* 4.9 6.0 - - - -
11B ILE* 4.4 12.8 - - - -
12B LEU* 5.0 3.7 - - - +
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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
----------------------------------------------------------
181A LEU* 4.0 14.8 - - - +
259A LEU* 4.6 2.0 - - - -
261A SER* 1.3 71.6 - - - +
263A PRO* 1.4 76.8 - - + +
265A ALA* 3.3 8.4 + - - +
266A ARG* 2.6 64.5 + - - +
511A VAL* 3.4 27.1 - - + +
512A ILE 3.8 1.4 + - - -
513A SER* 3.6 12.9 + - - +
517A ASP* 6.4 0.2 - - - -
521A VAL* 3.9 6.9 - - - +
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Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER* 3.2 9.4 - - - +
262A ASP* 1.4 95.9 - - + +
264A MET* 1.3 74.6 + - + +
266A ARG 3.4 0.9 + - - -
267A LEU* 2.8 29.6 + - - +
517A ASP* 3.6 37.9 - - + +
520A LEU* 4.3 15.0 - - + +
521A VAL* 4.2 8.3 - - + -
524A MET* 3.6 13.3 - - + +
8B HIS* 4.6 6.5 - - + -
12B LEU* 5.1 5.4 - - + -
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Residues in contact with MET 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 5.0 0.2 - - - -
261A SER* 3.2 22.3 + - - +
263A PRO* 1.3 82.2 - - + +
265A ALA* 1.3 59.4 + - - +
267A LEU* 3.1 15.2 + - + -
268A ALA* 2.7 36.5 + - - +
311A MET* 3.6 17.3 - - + +
315A THR* 3.6 20.2 - - + +
520A LEU* 4.8 9.0 - - + -
11B ILE* 5.4 2.2 - - + -
12B LEU* 3.7 35.7 - - + -
15B GLU* 3.4 40.6 - - + +
19B LEU* 6.0 0.7 - - - -
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Residues in contact with ALA 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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181A LEU* 4.0 5.8 - - + -
185A MET* 3.4 25.8 - - + -
248A TYR* 4.1 26.7 - - + -
259A LEU* 4.7 3.8 - - + -
261A SER 3.7 13.7 + - - +
262A ASP* 3.3 10.9 + - - +
264A MET* 1.3 78.0 - - - +
266A ARG* 1.3 61.3 + - - +
268A ALA* 3.9 1.0 - - - +
269A PHE* 3.1 31.9 + - - -
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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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178A VAL* 3.7 20.7 - - - +
179A THR* 2.6 31.5 + - - +
180A PRO* 3.8 1.6 - - - +
181A LEU* 3.6 27.7 - - + +
184A TYR* 3.4 49.6 - - + +
185A MET* 5.7 0.2 - - - -
262A ASP* 2.6 44.9 + - - +
263A PRO 3.8 5.6 - - - +
265A ALA* 1.3 72.6 - - - +
267A LEU* 1.3 56.4 + - - +
269A PHE* 3.0 4.1 + - - +
270A LEU* 2.7 35.7 + - - +
521A VAL* 4.1 21.2 - - - +
524A MET* 3.9 14.1 - - + -
525A ASP* 5.0 3.4 + - - +
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Residues in contact with LEU 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 PRO 2.8 21.5 + - - +
264A MET* 3.5 20.0 - - + +
266A ARG* 1.3 69.6 - - - +
268A ALA* 1.3 67.3 + - - +
270A LEU* 2.9 22.8 + - + +
271A LEU* 2.9 37.2 + - + +
311A MET* 3.7 26.7 - - + -
520A LEU* 5.2 7.0 - - + -
524A MET* 3.6 18.3 - - - -
19B LEU* 5.4 6.7 - - + -
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Residues in contact with ALA 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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244A TYR* 6.1 0.2 - - + -
248A TYR* 3.8 23.1 - - + +
264A MET 2.7 19.8 + - - +
265A ALA 3.9 3.4 - - - +
267A LEU* 1.3 75.7 - - - +
269A PHE* 1.3 63.0 + - + +
271A LEU* 3.5 5.3 + - - +
272A PHE* 3.0 27.6 + - + -
308A PRO* 3.8 15.8 - - + +
311A MET* 3.7 14.1 - - + +
312A THR* 4.0 9.6 - - - +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 4.3 7.0 - - + -
184A TYR* 4.7 1.3 - - + -
185A MET* 3.6 63.9 - - + -
188A VAL* 3.6 20.9 - - + +
189A PHE* 5.0 0.9 - - + -
241A LEU* 3.5 39.5 - - + -
244A TYR* 4.0 6.7 - + + -
245A ALA* 3.9 18.8 - - + -
248A TYR* 4.1 21.8 - + - -
265A ALA 3.1 24.4 + - - +
266A ARG* 3.0 13.7 + - - +
268A ALA* 1.3 70.3 - - + +
270A LEU* 1.3 68.0 - - - +
272A PHE* 3.0 19.7 + + - +
273A LEU 3.1 8.1 + - - -
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Residues in contact with LEU 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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184A TYR* 3.6 19.0 + - + +
188A VAL* 4.3 3.5 - - + +
266A ARG 2.7 16.1 + - - +
267A LEU* 2.9 20.4 + - + +
269A PHE* 1.3 70.2 - - - +
271A LEU* 1.3 57.9 + - + +
273A LEU* 2.6 41.6 + - + +
274A LEU* 2.8 20.1 + - + -
524A MET* 4.0 26.2 - - + -
527A ILE* 6.4 0.2 - - + -
530A TRP* 3.7 56.8 - - + +
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Residues in contact with LEU 271 (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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267A LEU* 2.9 41.3 + - + +
268A ALA 3.7 4.9 - - - +
270A LEU* 1.3 74.4 - - + +
272A PHE* 1.3 53.8 + - - +
274A LEU* 3.5 23.1 - - + +
275A LEU* 2.6 54.9 + - + +
307A VAL* 4.9 10.8 - - + -
308A PRO* 3.6 32.4 - - + +
311A MET* 4.5 11.9 - - - -
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Residues in contact with PHE 272 (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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192A MET* 3.4 3.6 - - + +
237A TYR* 3.3 35.9 - + - -
240A LEU* 4.7 1.3 - - + -
241A LEU* 4.0 37.7 - - + -
244A TYR* 4.0 17.7 - + - -
268A ALA* 3.0 24.8 + - + -
269A PHE* 3.0 12.0 + + - +
270A LEU 2.9 1.0 - - - -
271A LEU* 1.3 74.3 - - - +
273A LEU* 1.3 61.4 + - - +
275A LEU 5.0 0.2 - - - -
276A SER* 2.3 52.1 + - - +
305A VAL* 4.6 7.9 - - + -
308A PRO* 3.2 32.8 - - + -
309A SER* 3.6 17.3 - - - -
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Residues in contact with LEU 273 (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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188A VAL* 3.4 49.1 + - + +
191A LEU* 4.0 10.8 - - + -
192A MET* 3.4 31.9 - - + +
195A LEU* 4.9 4.9 - - + +
269A PHE 3.1 4.4 + - - -
270A LEU* 2.6 30.4 + - + +
272A PHE* 1.3 73.9 - - - +
274A LEU* 1.3 62.0 + - + +
276A SER 4.4 1.0 + - - -
277A THR* 5.3 1.4 + - - -
527A ILE* 5.0 7.0 - - + -
530A TRP* 4.4 4.3 - - + +
531A PHE* 4.4 28.0 - - + +
534A ALA* 3.7 18.9 - - + +
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Residues in contact with LEU 274 (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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270A LEU* 2.8 25.3 + - + +
271A LEU* 3.5 26.5 - - + +
273A LEU* 1.3 78.0 - - + +
275A LEU* 1.3 69.2 + - + +
276A SER 3.8 0.3 + - - -
277A THR* 4.7 0.7 + - - -
278A PRO* 4.1 10.0 - - - +
530A TRP* 3.7 62.1 - - + +
533A VAL* 4.5 16.4 - - + -
534A ALA* 4.6 7.9 - - - +
537A LEU* 4.0 20.6 - - + +
538A VAL* 6.1 0.3 - - - +
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Residues in contact with LEU 275 (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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271A LEU* 2.6 43.1 + - + +
272A PHE 3.8 0.2 - - - -
274A LEU* 1.3 79.5 - - + +
276A SER* 1.3 64.1 + - - +
277A THR 3.4 2.2 - - - -
278A PRO* 3.8 11.7 - - + +
279A VAL* 4.0 9.4 - - - +
301A LEU* 4.4 22.7 - - + +
304A PHE* 3.5 50.9 - - + +
305A VAL* 3.3 25.0 - - + +
308A PRO* 5.2 0.9 - - + -
537A LEU* 5.6 7.9 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 3.4 26.3 - - - -
233A HIS* 3.4 12.2 - - - -
234A PRO* 3.4 19.6 - - - +
237A TYR* 4.1 18.4 - - - +
272A PHE* 2.3 52.3 + - - +
273A LEU 4.4 0.6 + - - -
274A LEU 3.6 1.2 - - - -
275A LEU* 1.3 75.1 - - - +
277A THR* 1.3 60.5 + - - +
278A PRO* 3.8 0.2 - - - -
279A VAL* 3.6 2.6 - - - +
305A VAL* 4.5 5.2 - - - -
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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