Contacts of the helix formed by residues 263 - 278 (chain A) in PDB entry 5JJA
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 TYR 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PHE* 3.6 28.7 - + - -
221A ILE* 3.7 19.1 - - + -
222A ALA* 3.8 26.5 - - + +
225A LEU* 3.7 15.4 - - + +
254A LEU* 2.8 30.6 + - + +
257A VAL* 3.5 19.1 - - - +
259A SER* 3.6 21.1 - - - -
260A LEU* 3.7 23.8 - - + -
262A VAL* 1.3 82.7 - - + +
264A HIS* 1.3 67.5 + - - +
265A PRO 3.4 2.9 - - - -
266A GLN* 3.1 14.3 + - - +
267A LEU* 3.0 27.8 + - + -
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 4.3 4.9 - + - -
260A LEU* 2.9 52.4 + - + +
261A SER* 3.9 2.2 + - - -
262A VAL 3.7 0.2 - - - -
263A TYR* 1.3 77.0 - - - +
265A PRO* 1.3 72.2 - - + +
267A LEU* 3.2 4.4 + - + +
268A ALA* 2.8 25.9 + - + +
303A MET* 3.1 58.3 + - + +
304A PHE* 4.4 4.6 + - - -
306A ASN* 5.7 0.8 - - + +
307A GLU* 2.9 36.5 + - + -
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Residues in contact with PRO 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER 4.2 9.6 - - - +
262A VAL 4.8 1.6 - - - +
263A TYR* 3.5 4.0 - - - -
264A HIS* 1.3 98.0 - - + +
266A GLN* 1.3 74.4 + - - +
268A ALA* 3.4 6.2 + - + +
269A TYR* 3.1 22.3 + - - +
303A MET* 6.2 0.2 - - + -
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Residues in contact with GLN 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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222A ALA* 3.5 29.9 - - - +
225A LEU* 3.7 21.8 - - + +
226A GLU* 4.4 22.4 + - + +
262A VAL 4.2 2.0 + - - +
263A TYR* 3.1 24.6 - - - +
265A PRO* 1.3 86.4 - - - +
267A LEU* 1.3 61.9 + - - +
269A TYR* 3.3 8.1 + - - +
270A CYS* 3.2 25.5 + - - -
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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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225A LEU* 3.7 13.1 - - + +
251A LEU* 3.4 42.4 - - + +
254A LEU* 3.9 24.5 - - + -
255A HIS* 3.5 42.6 - - + +
260A LEU* 3.8 20.0 - - + -
263A TYR* 3.0 15.8 + - + +
264A HIS* 3.2 8.7 + - + +
266A GLN* 1.3 74.3 - - - +
268A ALA* 1.3 64.2 + - - +
270A CYS* 3.2 4.6 + - - +
271A VAL* 3.1 26.4 + - + +
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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
----------------------------------------------------------
264A HIS* 2.8 25.2 + - + +
265A PRO* 3.7 6.5 - - + +
267A LEU* 1.3 73.0 - - - +
269A TYR* 1.3 63.1 + - - +
271A VAL* 3.2 2.1 + - - +
272A VAL* 3.0 30.5 + - + +
307A GLU* 3.8 41.9 + - + -
310A GLU* 4.0 15.0 - - - +
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Residues in contact with TYR 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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225A LEU 5.8 0.2 - - - -
226A GLU* 6.4 1.1 - - - -
229A GLY* 4.0 28.3 - - - -
230A SER* 5.6 0.6 - - - -
233A ASN* 4.4 10.9 + - - +
265A PRO 3.1 14.3 + - - +
266A GLN* 3.6 11.9 - - - +
267A LEU 3.2 0.2 - - - -
268A ALA* 1.3 77.2 - - - +
270A CYS* 1.3 63.7 + - - +
272A VAL* 3.3 7.8 + - + +
273A GLN* 3.0 65.6 + - + +
310A GLU* 5.4 0.9 + - - -
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Residues in contact with CYS 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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225A LEU* 3.3 41.1 - - - -
228A LEU* 4.2 2.9 - - - -
229A GLY* 3.7 15.0 - - - -
232A ILE* 3.6 21.1 - - + +
251A LEU* 3.8 15.9 - - + -
266A GLN 3.2 12.9 + - - -
267A LEU 3.2 8.4 + - - +
269A TYR* 1.3 81.0 - - - +
271A VAL* 1.3 62.9 + - - +
273A GLN* 3.4 4.8 + - - +
274A PHE* 3.2 28.3 + - - -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.6 14.4 - - + -
251A LEU* 4.7 4.7 - - + -
252A LEU* 4.7 4.0 - - + -
255A HIS* 3.9 17.9 - - + -
267A LEU* 3.1 20.4 + - + +
268A ALA 3.2 6.5 + - - +
270A CYS* 1.3 75.5 - - - +
272A VAL* 1.3 63.6 + - + +
274A PHE* 3.3 16.4 + - - +
275A LEU* 3.4 12.5 + - + +
285A VAL* 3.5 36.3 - - + -
307A GLU* 3.7 21.1 - - - +
311A ILE* 4.4 10.8 - - + -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA* 3.0 22.9 + - + +
269A TYR* 3.8 9.0 - - + +
271A VAL* 1.3 77.7 - - + +
273A GLN* 1.3 65.2 + - - +
275A LEU* 3.1 9.6 + - - +
276A GLU* 3.1 35.7 + - - +
307A GLU* 4.6 2.2 - - + +
310A GLU* 3.9 45.1 - - + +
311A ILE* 4.2 14.1 - - + +
314A VAL* 4.4 11.2 - - + -
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Residues in contact with GLN 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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229A GLY 4.6 4.7 - - - +
232A ILE* 3.6 22.7 - - + -
233A ASN* 2.7 35.4 + - - +
269A TYR* 3.0 61.0 + - + +
270A CYS* 3.7 2.7 - - - +
272A VAL* 1.3 79.3 - - - +
274A PHE* 1.3 62.5 + - - +
276A GLU* 3.3 30.3 + - - +
277A LYS* 3.1 28.2 + - - +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.7 22.9 - - + -
235A PHE* 3.9 17.5 - + - -
239A LEU* 4.1 21.0 - - + +
243A HIS* 3.2 39.0 - - + -
244A LYS* 4.4 2.0 - - - -
246A PHE* 3.9 12.3 - + - -
247A LEU* 3.9 32.5 - - + -
251A LEU* 3.7 25.8 - - + -
270A CYS 3.2 21.0 + - - -
271A VAL 3.4 9.2 - - - +
272A VAL 3.2 0.4 - - - -
273A GLN* 1.3 77.8 - - - +
275A LEU* 1.3 59.8 + - + +
277A LYS* 3.3 5.9 + - + +
278A ASP* 3.0 28.8 + - - +
281A LEU* 4.1 4.0 - - + +
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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 VAL 3.4 10.9 + - - +
272A VAL* 3.1 8.9 + - - +
274A PHE* 1.3 76.7 - - + +
276A GLU* 1.3 63.0 + - - +
278A ASP 3.7 16.2 - - - +
279A SER* 3.7 9.2 + - - -
281A LEU* 3.6 42.6 - - + +
282A THR* 3.7 19.3 - - + +
285A VAL* 4.1 21.8 - - + -
311A ILE* 3.7 42.0 - - + -
314A VAL* 4.4 19.1 - - + +
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Residues in contact with GLU 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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272A VAL* 3.1 20.6 + - - +
273A GLN* 3.3 30.8 + - - +
275A LEU* 1.3 77.9 - - - +
277A LYS* 1.3 63.0 + - + +
314A VAL* 3.9 32.9 - - + +
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Residues in contact with LYS 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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232A ILE* 3.5 19.1 - - + +
233A ASN* 2.7 33.7 + - - +
234A GLY 4.1 1.0 - - - -
235A PHE* 2.8 30.0 + - + +
237A LEU* 3.4 39.6 - - + +
239A LEU* 4.0 20.6 - - + -
273A GLN* 3.1 19.3 + - - +
274A PHE* 3.5 9.2 - - + +
275A LEU 3.3 0.2 - - - -
276A GLU* 1.3 81.9 - - - +
278A ASP* 1.3 57.2 + - - +
279A SER 4.3 0.2 - - - -
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Residues in contact with ASP 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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237A LEU* 5.5 0.7 - - + -
239A LEU* 3.6 25.2 + - + +
244A LYS* 4.3 17.8 + - - +
274A PHE 3.0 13.7 + - - +
275A LEU* 3.7 7.8 - - - +
276A GLU 3.5 0.2 - - - -
277A LYS* 1.3 79.4 - - - +
279A SER* 1.3 62.1 + - - +
280A THR* 2.6 36.5 + - - +
281A LEU* 3.4 24.7 + - + +
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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