Contacts of the helix formed by residues 261 - 279 (chain A) in PDB entry 3S5O
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 GLN 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A LEU* 2.8 39.0 + - + +
259A THR* 2.9 34.5 + - - -
260A GLY* 1.3 74.8 + - - +
262A TRP* 1.3 59.0 + - - +
263A GLU* 3.3 2.9 - - - -
264A ASP* 3.3 17.3 + - + +
265A ALA* 2.9 26.3 + - - +
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Residues in contact with TRP 262 (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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228A MET* 3.3 46.4 - - + +
231A TYR* 4.1 4.3 - - + -
232A ALA* 3.9 30.3 - - + -
257A CYS* 3.4 55.4 - - + -
260A GLY* 3.1 35.4 + - - -
261A GLN* 1.3 70.3 - - - +
263A GLU* 1.3 61.6 + - - +
265A ALA* 3.9 1.8 - - - -
266A GLN* 2.8 27.0 + - - +
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Residues in contact with GLU 263 (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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261A GLN 3.3 0.6 - - - -
262A TRP* 1.3 80.2 - - - +
264A ASP* 1.3 64.5 + - - +
266A GLN* 3.4 11.0 + - - +
267A LYS* 3.3 28.3 + - + +
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Residues in contact with ASP 264 (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 LEU* 3.8 22.4 - - + +
261A GLN* 3.3 21.9 + - + +
263A GLU* 1.3 77.0 - - - +
265A ALA* 1.3 68.1 + - - +
267A LYS* 3.3 24.5 + - - +
268A LEU* 3.1 22.9 + - - +
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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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228A MET* 3.8 8.7 - - + -
253A LEU* 3.7 16.2 - - + +
256A LEU* 3.8 24.3 - - + +
257A CYS* 4.0 15.3 - - - +
261A GLN 2.9 18.1 + - - +
262A TRP* 3.5 10.8 - - + +
264A ASP* 1.3 76.5 - - - +
266A GLN* 1.3 52.3 + - - +
268A LEU 3.3 0.2 + - - -
269A GLN* 2.7 37.2 + - - +
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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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228A MET* 3.6 19.9 - - + +
262A TRP 2.8 20.7 + - - +
263A GLU* 3.5 10.8 - - - +
264A ASP 3.2 0.2 - - - -
265A ALA* 1.3 72.9 - - - +
267A LYS* 1.3 61.5 + - - +
269A GLN* 3.3 1.1 + - - +
270A HIS* 2.8 67.1 + - + +
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Residues in contact with LYS 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 GLU* 3.3 21.0 + - + +
264A ASP* 3.3 28.1 + - - +
266A GLN* 1.3 83.1 - - + +
268A LEU* 1.3 61.5 + - - +
270A HIS* 3.4 9.2 + - - +
271A ARG* 3.3 29.8 + - - +
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Residues in contact with LEU 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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249A GLN* 3.4 27.6 - - + +
252A GLN* 3.6 19.3 - - + -
253A LEU* 3.6 22.0 - - + +
256A LEU* 4.1 6.5 - - + -
264A ASP 3.1 13.5 + - - +
265A ALA 3.8 2.7 - - - +
267A LYS* 1.3 76.5 - - - +
269A GLN* 1.3 67.1 + - - +
271A ARG* 3.0 18.3 + - - +
272A LEU* 3.1 27.1 + - + +
326A TRP* 3.8 31.2 - - + -
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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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224A ALA 2.8 21.7 + - - +
225A GLY* 3.5 18.9 + - - +
226A PHE* 3.8 1.0 - - - -
227A LEU* 3.2 10.7 + - - -
228A MET* 2.9 49.3 + - + +
229A ALA 4.6 0.3 + - - -
253A LEU* 3.9 13.8 - - + +
265A ALA 2.7 22.2 + - - +
266A GLN 3.7 3.8 - - - +
268A LEU* 1.3 73.5 - - - +
270A HIS* 1.3 66.9 + - + +
272A LEU* 3.0 17.1 + - - +
273A ILE* 3.4 14.4 + - + +
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Residues in contact with HIS 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 GLN* 2.8 57.7 + - + +
267A LYS* 3.5 10.5 - - - +
269A GLN* 1.3 77.6 - - + +
271A ARG* 1.3 63.9 + - + +
272A LEU 3.4 0.2 + - - -
273A ILE* 3.4 31.8 + - + +
274A GLU* 4.7 1.4 + - - +
324A ASN* 4.4 4.3 - - - +
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Residues in contact with ARG 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 LYS* 3.3 16.3 + - - +
268A LEU* 3.0 13.8 + - - +
270A HIS* 1.3 78.2 - - + +
272A LEU* 1.3 57.8 + - - +
273A ILE 3.4 0.2 - - - -
275A PRO* 3.3 12.4 - - - +
324A ASN* 2.8 43.3 + - - +
325A GLY* 3.7 15.2 + - - -
326A TRP* 2.9 67.6 + - + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA* 4.8 6.1 - - + +
225A GLY* 5.5 0.2 - - - -
242A LEU* 3.9 12.9 - - + +
246A LEU* 3.8 23.8 - - + -
249A GLN* 4.2 20.9 - - + +
250A VAL* 4.7 10.3 - - + -
253A LEU* 3.9 25.6 - - + -
268A LEU* 3.4 24.9 - - + +
269A GLN* 3.0 15.8 + - - +
271A ARG* 1.3 77.4 - - - +
273A ILE* 1.3 58.8 + - - +
274A GLU 3.5 0.9 - - - -
275A PRO* 3.5 3.6 - - - -
276A ASN* 2.8 34.0 + - - +
326A TRP* 3.7 24.5 - - + -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 4.0 24.7 - - - +
269A GLN* 3.4 21.3 + - + +
270A HIS* 3.4 28.2 + - + +
271A ARG 3.4 1.8 - - - -
272A LEU* 1.3 78.7 - - - +
274A GLU* 1.3 66.1 + - + +
276A ASN* 3.5 5.5 + - - +
277A ALA* 2.9 30.7 + - + +
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Residues in contact with GLU 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 HIS 4.7 2.0 + - - +
273A ILE* 1.3 81.0 - - + +
275A PRO* 1.4 62.2 - - - +
277A ALA* 3.2 8.7 + - + +
278A ALA* 2.9 28.6 + - - +
320A ASP* 3.9 24.1 - - - +
323A SER* 4.0 7.8 + - - -
324A ASN* 2.9 32.0 + - - +
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Residues in contact with PRO 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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242A LEU* 4.2 8.5 - - + -
246A LEU* 4.5 2.5 - - + -
271A ARG 3.3 26.0 - - - +
272A LEU* 3.5 7.4 - - - +
274A GLU* 1.4 93.9 - - + +
276A ASN* 1.3 60.8 + - - +
278A ALA* 3.3 11.3 + - + +
279A VAL* 3.3 16.6 + - - +
320A ASP 3.6 13.4 - - - +
321A PHE* 3.7 39.7 - - + -
324A ASN* 3.8 2.0 - - - +
326A TRP* 3.5 21.5 - - + +
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Residues in contact with ASN 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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223A SER* 3.1 22.4 + - - -
224A ALA* 3.2 21.8 + - - +
225A GLY* 3.2 24.1 - - - +
241A ALA 5.6 0.5 + - - -
242A LEU* 3.8 20.1 + - + +
272A LEU 2.8 22.0 + - - +
273A ILE 3.5 4.0 + - - +
275A PRO* 1.3 74.5 - - - +
277A ALA* 1.3 60.2 + - - +
279A VAL* 3.4 5.2 + - - +
280A THR* 2.7 49.7 + - - +
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Residues in contact with ALA 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 ILE* 2.9 23.2 + - + +
274A GLU* 3.6 8.1 - - + +
276A ASN* 1.3 74.3 - - - +
278A ALA* 1.3 62.9 + - - +
280A THR* 3.2 12.0 + - - -
281A ARG* 3.3 36.5 + - + +
282A ARG* 2.8 30.9 + - + -
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Residues in contact with ALA 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 GLU 2.9 9.4 + - - +
275A PRO 3.5 9.9 - - - +
276A ASN 3.2 0.2 - - - -
277A ALA* 1.3 76.7 - - - +
279A VAL* 1.3 57.7 + - - +
280A THR 3.3 0.2 - - - -
282A ARG* 3.9 9.8 - - - +
283A PHE* 3.0 38.9 + - + +
287A GLY* 4.6 0.2 - - - -
317A LEU* 3.7 23.1 - - + +
320A ASP* 3.4 28.9 + - + +
321A PHE* 4.1 2.0 - - + -
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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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6A EDO 4.5 2.4 + - - -
78A ASN* 4.6 1.7 - - - +
241A ALA* 4.5 5.7 - - + +
242A LEU* 4.1 29.6 - - + +
275A PRO 3.3 12.8 + - - +
276A ASN* 3.6 11.7 - - - +
278A ALA* 1.3 77.7 - - - +
280A THR* 1.3 65.9 + - + +
284A GLY 3.4 23.1 - - - +
287A GLY 4.2 1.8 - - - -
288A LEU* 3.9 26.4 - - + +
291A ILE* 3.7 29.4 - - + -
317A LEU* 4.3 2.0 - - + -
321A PHE* 4.0 12.8 - - + -
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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