Contacts of the helix formed by residues 262 - 283 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG* 3.7 10.7 - - - +
420A GLU* 3.5 27.7 + - - +
421A GLU* 4.6 2.5 - - - +
260B GLU 3.7 3.0 + - - -
261B MSE 1.3 79.2 - - - +
263B SER* 1.3 66.2 + - - +
264B GLU* 3.4 29.2 - - - +
265B GLU* 2.9 51.0 + - - +
266B LYS* 3.2 11.7 + - - +
303B GLU* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLU* 4.5 6.5 + - - -
424A LYS* 5.9 2.9 - - - -
262B ASN* 1.3 78.7 + - - +
264B GLU* 1.3 69.6 + - - +
266B LYS* 3.5 9.0 + - - +
267B LEU* 3.5 16.3 + - - +
303B GLU* 4.4 14.3 + - - -
305B SER* 4.5 11.0 + - - -
306B PHE* 3.8 26.0 - - - -
310B GLU* 3.4 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ASN* 3.3 17.6 - - - +
263B SER* 1.3 81.7 + - - +
265B GLU* 1.3 64.9 + - + +
267B LEU* 3.1 12.5 + - - +
268B GLU* 2.9 39.4 + - - +
310B GLU* 4.1 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 2.8 39.4 + - - +
260B GLU 4.0 7.2 - - - +
261B MSE 3.5 29.3 - - + +
262B ASN* 2.9 30.4 + - - +
264B GLU* 1.3 77.7 - - + +
266B LYS* 1.3 52.3 + - - +
268B GLU* 2.9 16.1 + - + +
269B GLN* 2.6 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG* 4.5 4.1 - - - +
258B SER* 2.6 40.4 + - - +
261B MSE 3.4 30.6 + - + -
262B ASN 3.2 12.4 + - - +
263B SER 4.0 5.4 - - - +
264B GLU 3.3 0.4 - - - -
265B GLU* 1.3 74.3 - - - +
267B LEU* 1.3 53.0 + - - +
269B GLN* 4.0 0.6 - - - +
270B SER* 2.6 43.8 + - - +
299B TRP* 3.1 30.3 - - + +
300B LEU* 4.2 13.7 - - + -
303B GLU* 2.9 39.5 - - + -
306B PHE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER 3.5 13.9 + - - +
264B GLU* 3.1 9.7 + - - +
266B LYS* 1.3 75.1 - - - +
268B GLU* 1.3 65.8 + - - +
270B SER* 4.1 4.3 - - - -
271B THR* 3.5 20.6 + - - -
300B LEU* 4.4 7.0 - - + -
306B PHE* 4.2 10.3 - - + -
310B GLU* 4.0 30.7 - - + +
313B LYS* 4.1 29.9 + - + +
314B ALA* 3.7 29.4 - - + +
317B LEU* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLU* 2.9 32.8 + - - +
265B GLU* 2.9 21.4 + - + +
267B LEU* 1.3 77.9 - - - +
269B GLN* 1.3 65.2 + - + +
271B THR* 3.0 16.1 + - - -
272B ILE* 3.2 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 3.7 37.0 - - + +
261B MSE 3.8 23.6 - - + -
265B GLU 2.6 17.3 + - - +
266B LYS 4.0 0.9 - - - +
268B GLU* 1.3 72.6 - - + +
270B SER* 1.3 66.0 + - - +
271B THR 3.0 0.2 + - - -
272B ILE* 3.1 27.8 + - - +
273B VAL* 2.9 34.5 + - - +
276B ARG* 4.9 6.6 + - - -
299B TRP* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LYS 2.6 28.9 + - - -
267B LEU 4.1 3.1 - - - -
268B GLU 3.2 0.2 - - - -
269B GLN* 1.3 74.6 - - - +
271B THR* 1.3 57.2 + - - +
273B VAL* 4.7 0.4 - - - -
274B LYS* 3.2 17.8 + - - +
296B ILE* 3.3 33.7 - - - +
299B TRP* 4.0 17.1 - - - +
300B LEU* 3.8 23.6 - - - +
317B LEU* 3.9 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 3.5 10.5 + - - -
268B GLU* 3.0 9.7 + - - -
269B GLN 3.0 1.0 - - - -
270B SER* 1.3 77.7 - - - +
272B ILE* 1.3 69.2 + - + +
274B LYS* 3.1 12.7 + - + +
275B GLU* 2.9 23.0 + - + +
317B LEU* 4.0 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.2 14.5 + - + +
269B GLN* 3.1 34.6 + - - +
271B THR* 1.3 79.6 - - + +
273B VAL* 1.3 65.2 + - + +
275B GLU* 2.8 25.8 + - + +
276B ARG* 3.1 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLN* 2.9 22.4 + - - +
270B SER* 4.2 4.0 - - - +
272B ILE* 1.3 81.6 - - + +
274B LYS* 1.3 58.3 + - - +
276B ARG* 3.1 13.3 + - - +
277B GLY 2.8 25.6 + - - -
292B GLN* 3.0 55.3 - - - +
295B LYS* 3.5 13.7 - - + +
296B ILE* 4.7 4.9 - - + -
299B TRP* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER 3.2 16.2 + - - +
271B THR* 3.1 12.6 + - - +
272B ILE 3.1 1.0 - - - -
273B VAL* 1.3 79.5 - - - +
275B GLU* 1.3 63.6 + - - +
277B GLY* 3.4 1.3 + - - +
278B THR* 3.0 27.1 + - - +
293B TYR* 3.7 6.6 - - + -
296B ILE* 3.5 21.5 - - + -
317B LEU* 4.3 15.9 - - + -
320B ALA* 4.1 22.5 - - + +
324B ASN* 4.0 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 2.9 12.5 + - + +
272B ILE* 2.8 18.0 + - + +
274B LYS* 1.3 75.0 - - - +
276B ARG* 1.3 65.2 + - + +
278B THR* 3.1 7.8 + - - -
279B VAL* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLY 4.8 2.8 + - - -
169B ILE* 3.3 28.0 - - - +
191B GLU* 3.0 24.4 + - - -
269B GLN* 4.9 7.7 + - - -
272B ILE* 3.1 34.8 + - + +
273B VAL* 3.4 12.0 - - - +
275B GLU* 1.3 75.2 - - + +
277B GLY* 1.3 69.4 + - - +
279B VAL* 3.0 18.6 + - - +
280B TYR* 3.1 25.1 + - + -
292B GLN* 3.8 25.3 - - + +
295B LYS* 4.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL 2.8 11.5 + - - -
274B LYS 3.6 4.3 - - - -
275B GLU 3.2 0.2 - - - -
276B ARG* 1.3 78.9 - - - +
278B THR* 1.3 56.5 + - - +
280B TYR* 3.4 1.3 + - - +
281B PHE 2.9 20.6 + - - -
289B ALA* 3.5 16.5 - - - +
292B GLN* 3.7 19.0 - - - +
293B TYR* 3.2 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 3.0 17.3 + - - +
275B GLU* 3.1 8.4 + - - -
277B GLY* 1.3 71.9 - - - +
279B VAL* 1.3 70.0 + - - +
281B PHE* 3.0 13.6 + - + +
282B LYS* 3.1 35.5 + - + +
293B TYR* 2.9 19.4 + - - +
324B ASN* 4.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 2.9 23.3 + - + +
276B ARG* 3.0 9.8 + - - +
278B THR* 1.3 70.6 - - - +
280B TYR* 1.3 60.5 + - + +
282B LYS* 2.6 35.3 + - - +
283B GLU* 3.2 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 5.0 1.4 + - - +
194B GLU* 3.0 37.2 + - - -
276B ARG* 3.1 24.8 + - + -
277B GLY 3.5 5.2 - - - +
279B VAL* 1.3 83.8 - - + +
281B PHE* 1.3 61.2 + - - +
283B GLU* 3.1 22.2 + - - -
285B LYS* 2.8 50.1 + - + -
288B GLN* 3.7 30.3 - - + -
289B ALA* 3.9 9.9 - - - +
292B GLN* 3.9 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLY 2.9 14.5 + - - +
278B THR* 3.3 17.5 - - + +
279B VAL 2.9 0.6 + - - -
280B TYR* 1.3 77.2 - - - +
282B LYS* 1.3 69.7 + - + +
284B GLY* 3.3 7.4 + - - -
286B TYR* 3.2 50.0 + + - -
289B ALA* 4.3 5.2 - - + -
293B TYR* 4.1 8.1 - + - +
327B MET* 4.0 33.2 - - + -
328B CYS* 4.0 22.4 - - - -
331B LYS* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B THR* 3.5 28.2 - - + +
279B VAL* 2.6 17.5 + - - +
281B PHE* 1.3 77.1 - - + +
283B GLU* 1.3 56.9 + - + +
284B GLY 3.0 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 3.6 32.9 - - + +
280B TYR* 3.1 15.8 + - - +
282B LYS* 1.3 76.5 - - + +
284B GLY* 1.3 61.5 + - - +
285B LYS* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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