Contacts of the helix formed by residues 258 - 276 (chain B) in PDB entry 4LEY
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 258 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE 2.6 22.4 + - - +
253B GLU* 3.8 29.8 + - - -
256B VAL 3.4 1.6 + - - -
257B LEU* 1.3 72.0 - - - +
259B ALA* 1.3 61.7 + - - +
260B THR* 3.5 3.8 + - - -
261B LYS* 3.5 25.6 + - - +
262B MET* 3.4 22.7 + - - +
360B GLY* 3.2 15.6 + - - -
361B GLU* 4.3 5.1 - - - +
363B TRP* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU 3.6 4.0 + - - -
258B SER* 1.3 71.4 - - - +
260B THR* 1.3 56.8 + - - +
262B MET* 3.8 1.6 - - - +
263B LEU* 2.9 32.4 + - - +
349B PRO* 3.8 26.1 - - + +
350B LYS 5.1 0.2 - - - +
351B ASN* 5.7 2.7 - - + +
360B GLY* 2.7 16.0 + - - +
361B GLU* 4.6 0.2 - - - -
362B THR 4.3 9.2 - - - +
363B TRP* 3.5 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B SER* 4.0 4.0 - - - -
259B ALA* 1.3 75.9 - - - +
261B LYS* 1.3 56.8 + - + +
263B LEU* 3.5 6.1 + - - +
264B SER* 2.5 44.4 + - - +
351B ASN* 4.0 16.1 + - - +
353B LYS* 4.3 17.4 + - - +
360B GLY* 3.1 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B HIS 3.5 19.4 + - - +
251B PHE* 3.7 26.7 - - + -
252B LEU 3.2 23.8 + - - -
253B GLU* 3.5 31.5 - - - +
258B SER* 3.5 13.6 + - - +
259B ALA 3.4 0.4 - - - -
260B THR* 1.3 75.8 - - + +
262B MET* 1.3 68.2 + - - +
264B SER* 3.1 7.6 + - - -
265B LYS* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.3 25.4 - - + -
218B LEU* 4.1 13.2 - - + -
248B LEU* 4.1 19.1 - - + -
251B PHE* 3.4 34.8 - - + -
257B LEU* 3.8 19.3 - - - -
258B SER 3.4 11.6 + - - +
259B ALA* 3.8 4.7 - - - +
261B LYS* 1.3 78.7 - - - +
263B LEU* 1.3 58.5 + - - +
265B LYS* 3.3 0.3 + - - -
266B PHE* 3.0 30.1 + - - +
310B LEU* 4.0 15.3 - - + -
312B LEU* 3.6 20.0 - - + -
363B TRP* 3.7 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA 2.9 18.4 + - - +
260B THR* 3.7 5.2 - - - +
262B MET* 1.3 76.6 - - - +
264B SER* 1.3 56.8 + - - +
266B PHE* 3.4 10.4 - - + +
267B ARG* 2.9 33.3 + - - +
287B GLU* 4.8 3.6 - - - +
291B SER 3.9 11.4 - - - +
292B PRO* 4.0 18.6 - - + +
293B ALA 4.9 3.8 - - - +
294B VAL* 4.8 8.7 - - + -
310B LEU* 3.9 24.6 - - + +
349B PRO* 3.9 17.5 - - + -
351B ASN* 3.7 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B THR* 2.5 32.5 + - - +
261B LYS* 3.1 8.1 + - - -
263B LEU* 1.3 75.2 - - - +
265B LYS* 1.3 59.6 + - - +
267B ARG* 3.4 8.2 + - - +
268B LYS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU* 2.8 36.3 + - - +
189B PHE* 3.8 9.9 - - + -
251B PHE* 3.5 37.4 - - + -
261B LYS 3.0 7.3 + - - +
262B MET 3.9 0.7 - - - +
264B SER* 1.3 73.4 - - - +
266B PHE* 1.3 66.1 + - - +
268B LYS* 3.1 35.3 + - + +
269B ILE* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B MET* 4.0 22.0 - - + -
189B PHE* 3.5 35.5 - + + -
192B VAL* 5.2 1.8 - - + -
216B PHE* 3.9 24.7 - + + -
262B MET 3.0 17.8 + - - +
263B LEU* 3.4 9.9 - - + +
265B LYS* 1.3 77.0 - - - +
267B ARG* 1.3 61.1 + - - +
269B ILE* 3.4 4.2 + - - +
270B ILE* 3.0 43.6 + - + +
294B VAL* 3.9 15.3 - - + -
308B ILE* 3.7 33.4 - - + -
310B LEU* 3.9 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 2.9 23.3 + - - +
264B SER* 3.5 8.5 - - - +
265B LYS 3.2 0.2 - - - -
266B PHE* 1.3 75.1 - - - +
268B LYS* 1.3 57.8 + - - +
270B ILE* 3.3 3.4 + - - +
271B LYS* 2.9 63.9 + - - +
284B VAL* 3.9 8.2 - - - +
285B GLU 2.3 32.9 + - - -
286B LYS* 3.9 0.8 - - - +
287B GLU* 3.0 44.1 - - - +
293B ALA 3.8 21.0 + - - -
294B VAL* 4.0 29.8 - - + +
295B THR 4.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ARG* 5.8 1.4 - - - +
264B SER 3.0 14.7 + - - +
265B LYS* 3.1 36.7 + - + +
267B ARG* 1.3 75.0 - - - +
269B ILE* 1.3 66.0 + - - +
271B LYS* 3.3 9.1 + - - +
272B GLU* 3.0 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ARG* 3.7 46.6 + - + +
182B MET* 3.9 22.9 - - + -
187B SER* 4.3 13.9 - - - -
188B GLU* 4.3 11.7 - - - +
189B PHE* 3.7 30.5 - - + -
265B LYS* 2.9 28.8 + - + +
266B PHE* 3.7 5.8 - - - +
268B LYS* 1.3 77.2 - - - +
270B ILE* 1.3 65.6 + - - +
272B GLU* 3.1 9.1 + - - +
273B GLU* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.8 25.5 - - + +
182B MET* 3.8 17.7 - - + -
266B PHE* 3.0 50.8 + - + +
267B ARG 3.7 4.3 - - - +
269B ILE* 1.3 76.0 - - - +
271B LYS* 1.3 58.9 + - - +
273B GLU* 3.4 2.6 + - - +
274B VAL* 2.9 35.3 + - + +
284B VAL* 4.5 2.2 - - + -
294B VAL* 4.0 26.9 - - + -
296B LEU* 4.1 10.3 - - + -
308B ILE* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 2.9 53.5 + - + +
268B LYS* 3.7 7.6 - - - +
270B ILE* 1.3 75.9 - - - +
272B GLU* 1.3 63.5 + - - +
274B VAL* 3.2 2.1 + - - +
275B LYS* 3.0 34.2 + - - +
284B VAL* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ARG* 3.4 23.4 + - - +
185B ARG* 4.1 13.8 + - - +
268B LYS* 3.0 44.8 + - + +
269B ILE* 3.1 10.1 + - - +
271B LYS* 1.3 79.2 - - - +
273B GLU* 1.3 63.2 + - - +
275B LYS* 3.3 23.4 + - + +
276B GLU* 3.7 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 2.4 55.6 + - + +
178B LEU* 4.4 10.5 - - + -
181B ARG* 3.4 38.9 + - + -
185B ARG* 3.1 27.2 + - - -
269B ILE 3.0 14.7 + - - +
270B ILE* 4.0 3.4 - - - +
272B GLU* 1.3 76.1 - - - +
274B VAL* 1.3 58.0 + - - +
276B GLU* 2.9 27.0 + - - +
277B ILE* 3.6 9.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 5.3 0.2 - - + -
178B LEU* 3.9 18.4 - - + -
270B ILE* 2.9 30.3 + - + +
271B LYS* 3.2 6.9 + - - +
273B GLU* 1.3 72.5 - - - +
275B LYS* 1.3 66.3 + - + +
276B GLU 3.3 0.5 + - - -
277B ILE* 3.3 29.5 + - + +
282B VAL* 3.6 36.5 - - + +
283B SER* 4.3 3.6 - - - -
284B VAL* 4.2 13.2 - - + -
296B LEU* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 3.0 22.5 + - - +
272B GLU* 3.4 16.3 - - + +
274B VAL* 1.3 78.5 - - + +
276B GLU* 1.3 60.5 + - - +
277B ILE 3.2 2.4 + - - +
278B LYS* 2.6 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 3.3 27.7 + - - +
185B ARG* 4.6 16.5 + - - +
272B GLU 3.7 13.4 - - - +
273B GLU* 2.9 13.9 + - - +
275B LYS* 1.3 87.0 - - - +
277B ILE* 1.3 62.0 + - - +
278B LYS* 3.5 22.3 + - - +
----------------------------------------------------------
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