Contacts of the helix formed by residues 262 - 284 (chain A) in PDB entry 1P5Q
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 ASN 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLU 3.4 4.5 + - - +
261A MSE 1.3 78.0 - - - +
263A SER* 1.3 74.3 + - - +
264A GLU* 3.5 30.2 + - - +
265A GLU* 3.0 59.0 + - - +
266A LYS* 3.2 8.8 + - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 1.3 80.6 - - - +
264A GLU* 1.3 62.5 + - - +
266A LYS* 3.2 17.0 + - - +
267A LEU* 3.5 4.9 + - - +
303A GLU* 4.0 16.3 - - - -
305A SER* 3.7 14.5 + - - -
306A PHE* 3.0 38.4 - - - -
310A GLU* 3.4 15.3 + - - -
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 3.5 23.1 + - - +
263A SER* 1.3 78.5 + - - +
265A GLU* 1.3 61.8 + - - +
266A LYS 3.2 0.2 - - - -
267A LEU* 3.5 12.4 + - + +
268A GLU* 3.4 34.7 + - - +
310A GLU* 3.8 17.1 + - + +
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Residues in contact with GLU 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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256A LYS* 2.7 43.1 + - - -
260A GLU 3.8 1.6 - - - +
261A MSE 3.6 7.9 - - + -
262A ASN* 3.0 45.5 + - - +
264A GLU* 1.3 77.3 - - - +
266A LYS* 1.3 56.1 + - - +
268A GLU* 3.1 13.3 + - - +
269A GLN* 2.8 47.5 + - - +
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Residues in contact with LYS 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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258A SER* 2.8 43.2 + - - +
259A TRP* 4.9 0.6 - - - +
261A MSE 3.3 44.3 - - + +
262A ASN 3.2 5.1 + - - +
263A SER 3.2 8.0 + - - +
265A GLU* 1.3 74.8 - - - +
267A LEU* 1.3 61.8 + - - +
268A GLU 2.9 5.4 + - - -
270A SER* 2.7 32.0 + - - +
299A TRP* 4.1 20.0 + - + +
300A LEU* 4.1 13.2 - - + -
303A GLU* 3.3 39.9 - - + +
306A PHE* 5.0 1.3 - - + -
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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
----------------------------------------------------------
263A SER 3.5 10.6 + - - +
264A GLU* 3.5 12.1 + - + +
265A GLU 3.3 0.4 - - - -
266A LYS* 1.3 77.7 - - - +
268A GLU* 1.3 59.5 + - + +
270A SER* 4.2 0.9 - - - -
271A THR* 2.8 27.4 + - - -
300A LEU* 3.7 17.0 - - + -
306A PHE* 3.7 8.5 - - + -
310A GLU* 3.4 26.5 - - + +
313A LYS* 3.4 42.6 - - + +
314A ALA* 3.6 31.4 - - + -
317A LEU* 3.7 10.3 - - + +
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Residues in contact with GLU 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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264A GLU* 3.4 24.1 + - - +
265A GLU* 3.1 17.5 + - - +
266A LYS 2.9 1.4 - - - -
267A LEU* 1.3 78.7 - - + +
269A GLN* 1.3 75.3 + - - +
270A SER 3.0 1.8 - - - -
271A THR* 3.2 4.9 + - - -
272A ILE* 3.0 28.9 + - + +
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Residues in contact with GLN 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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256A LYS* 5.1 12.1 - - + +
261A MSE 3.7 31.4 - - + -
265A GLU* 2.8 33.4 + - + +
266A LYS 4.5 0.2 - - - +
268A GLU* 1.3 81.8 + - - +
270A SER* 1.3 58.2 + - - +
272A ILE* 3.4 24.7 + - - +
273A VAL* 2.8 36.2 + - - +
276A ARG* 5.6 2.9 + - - -
299A TRP* 3.5 20.6 - - + -
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Residues in contact with SER 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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266A LYS 2.7 23.0 + - - -
268A GLU 3.0 0.2 - - - -
269A GLN* 1.3 76.0 - - - +
271A THR* 1.3 65.7 + - - +
273A VAL* 3.0 4.0 + - - +
274A LYS* 2.9 22.3 + - - +
296A ILE* 3.9 18.9 - - - +
299A TRP* 3.3 23.8 - - - +
300A LEU* 3.9 17.5 - - - +
317A LEU* 3.7 20.9 - - - -
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Residues in contact with THR 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 2.8 21.7 + - - -
268A GLU* 3.2 7.1 + - - -
270A SER* 1.3 75.1 - - - +
272A ILE* 1.3 68.8 + - - +
274A LYS* 3.4 17.0 + - - +
275A GLU* 3.3 18.9 + - - +
317A LEU* 3.8 18.1 - - + +
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Residues in contact with ILE 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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268A GLU* 3.0 18.5 + - + +
269A GLN* 3.5 33.2 - - - +
270A SER 3.1 0.2 - - - -
271A THR* 1.3 81.1 - - - +
273A VAL* 1.3 65.9 + - + +
275A GLU* 3.1 6.3 + - - +
276A ARG* 3.1 45.1 + - + +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLN* 2.8 20.4 + - + +
270A SER* 3.0 4.0 + - - +
272A ILE* 1.3 80.5 - - + +
274A LYS* 1.3 56.5 + - - +
276A ARG* 4.0 15.0 - - - +
277A GLY 2.8 23.2 + - - -
292A GLN* 2.7 60.6 - - + +
295A LYS* 3.7 7.6 - - + +
296A ILE* 4.8 2.5 - - + -
299A TRP* 3.5 26.7 - - + -
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Residues in contact with LYS 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 SER 2.9 12.6 + - - +
271A THR* 3.6 18.6 - - - +
272A ILE 3.2 0.2 - - - -
273A VAL* 1.3 75.0 - - - +
275A GLU* 1.3 56.4 + - - +
277A GLY* 3.0 3.1 + - - -
278A THR* 2.7 47.8 + - - -
293A TYR* 3.4 20.1 - - + -
296A ILE* 3.6 21.5 - - + +
317A LEU* 4.4 17.9 - - + -
320A ALA* 4.2 23.5 - - + +
321A SER 5.5 0.7 - - - +
324A ASN* 4.1 9.6 - - - +
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Residues in contact with GLU 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 THR 3.3 7.9 + - - +
272A ILE* 3.1 10.0 + - - +
274A LYS* 1.3 80.6 - - - +
276A ARG* 1.3 66.9 + - - +
278A THR* 3.0 8.3 + - - +
279A VAL* 2.9 30.9 + - + +
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Residues in contact with ARG 276 (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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167A GLY 4.8 3.6 + - - -
169A ILE* 4.1 22.2 - - - +
191A GLU* 3.1 22.0 + - - -
269A GLN* 5.6 3.2 + - - -
272A ILE* 3.1 32.0 + - + +
273A VAL* 3.5 17.0 - - - +
275A GLU* 1.3 78.6 - - - +
277A GLY* 1.3 61.2 + - - +
279A VAL* 3.3 10.3 - - - +
280A TYR* 3.1 36.9 + - + -
292A GLN* 3.5 23.3 + - - +
295A LYS* 4.0 12.7 - - - +
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Residues in contact with GLY 277 (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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273A VAL 2.8 15.2 + - - -
274A LYS 3.3 4.0 - - - -
276A ARG* 1.3 76.0 - - - +
278A THR* 1.3 65.8 + - - +
280A TYR* 3.0 9.2 + - - +
281A PHE* 2.8 19.8 + - - +
289A ALA* 3.7 6.8 - - - +
292A GLN* 3.8 17.9 - - - +
293A TYR* 3.5 14.4 - - - -
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Residues in contact with THR 278 (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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274A LYS* 2.7 29.3 + - - -
275A GLU* 3.0 8.7 + - - -
277A GLY* 1.3 70.7 - - - +
279A VAL* 1.3 67.0 + - + +
281A PHE* 2.8 17.4 + - + +
282A LYS* 2.9 41.4 + - + +
293A TYR* 2.9 20.6 + - - -
324A ASN* 4.6 2.4 + - - -
327A MET* 6.1 0.2 - - - +
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Residues in contact with VAL 279 (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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275A GLU* 2.9 21.6 + - + +
276A ARG* 3.3 10.5 - - - +
278A THR* 1.3 80.4 - - + +
280A TYR* 1.3 70.2 + - + +
282A LYS* 3.1 17.1 + - + +
283A GLU* 3.1 29.8 + - + +
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Residues in contact with TYR 280 (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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191A GLU* 5.1 2.9 + - - +
194A GLU* 3.0 30.0 + - - -
276A ARG* 3.1 26.9 + - + +
277A GLY* 3.0 8.1 + - - +
279A VAL* 1.3 80.9 - - + +
281A PHE* 1.3 64.7 + - - +
283A GLU* 3.0 19.9 + - - +
285A LYS* 3.0 55.7 + - + +
288A GLN* 3.7 36.3 - - + -
289A ALA* 3.8 6.1 - - + -
292A GLN* 3.8 29.8 + - + -
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Residues in contact with PHE 281 (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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277A GLY 2.8 11.2 + - - +
278A THR* 2.8 20.9 + - + +
280A TYR* 1.3 77.1 - - - +
282A LYS* 1.3 66.1 + - + +
284A GLY* 2.8 22.2 + - - -
286A TYR* 3.4 42.5 + + - -
289A ALA* 4.0 5.8 - - + +
293A TYR* 4.4 6.5 - + - +
327A MET* 4.0 45.5 - - + -
328A CYS* 3.9 21.3 - - - -
331A LYS* 4.2 17.5 - - + -
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Residues in contact with LYS 282 (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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278A THR* 2.9 35.1 + - + +
279A VAL* 3.6 9.9 - - + +
281A PHE* 1.3 84.4 - - + +
283A GLU* 1.3 61.5 + - + +
284A GLY* 3.0 1.5 + - - -
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Residues in contact with GLU 283 (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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279A VAL* 3.1 30.0 + - + +
280A TYR* 3.0 13.8 + - - +
282A LYS* 1.3 75.5 - - + +
284A GLY* 1.3 59.0 + - - +
285A LYS* 3.2 44.6 + - + +
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Residues in contact with GLY 284 (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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280A TYR 3.9 0.2 - - - -
281A PHE 2.8 15.6 + - - -
282A LYS 3.0 2.5 + - - -
283A GLU* 1.3 80.0 - - - +
285A LYS* 1.3 52.6 + - - +
286A TYR* 2.8 48.4 + - - -
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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
------------------------------------------------------------
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