Contacts of the helix formed by residues 256 - 275 (chain C) in PDB entry 3H90
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 PRO 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASP 4.7 1.6 - - - +
254A SER* 4.4 12.3 - - - +
255A LEU 3.3 9.6 - - - +
256A PRO* 4.3 1.3 - - + -
254C SER 3.5 5.8 - - - +
255C LEU* 1.3 88.4 - - + +
257C LEU* 1.3 60.1 + - - +
258C VAL* 4.4 7.9 - - + +
259C GLN* 3.3 44.2 + - + +
260C ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A MET* 3.6 34.8 - - + +
252A GLU 3.8 11.0 - - - +
253A ASP 3.7 6.6 + - - +
255A LEU 2.6 18.2 + - - +
257A LEU* 5.1 5.6 - - + +
260A ALA* 3.9 20.4 - - + -
284A GLN* 3.9 29.8 - - + +
285A ASP 3.8 11.7 - - - +
286A PRO* 4.0 15.3 - - + -
255C LEU 3.8 0.9 + - - -
256C PRO* 1.3 73.5 - - - +
258C VAL* 1.3 54.0 + - - +
260C ALA* 3.1 7.2 + - + -
261C HIS* 2.7 38.2 + - + +
284C GLN* 5.0 2.9 - - + +
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASP* 3.2 47.0 + - - +
254A SER* 5.7 1.1 - - - -
286A PRO* 3.8 15.9 - - + -
256C PRO* 4.5 7.2 - - + -
257C LEU* 1.3 77.8 - - - +
259C GLN* 1.3 71.7 + - + +
261C HIS* 3.7 3.3 + - - +
262C MET* 3.2 24.6 + - - +
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Residues in contact with GLN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 4.4 16.4 - - + +
256C PRO* 3.3 39.6 + - + +
257C LEU 3.1 0.2 - - - -
258C VAL* 1.3 88.5 - - + +
260C ALA* 1.3 67.1 + - - +
262C MET* 2.9 21.9 + - - +
263C VAL* 3.3 9.7 + - - +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.9 24.2 - - + -
251C MET* 3.4 24.8 - - - +
255C LEU* 3.9 13.5 - - + +
256C PRO 2.9 17.3 + - - +
257C LEU* 3.5 9.2 - - + +
259C GLN* 1.3 72.4 - - - +
261C HIS* 1.3 63.4 + - - +
263C VAL* 3.2 5.2 - - - +
264C ALA* 3.0 19.2 + - - +
284C GLN* 3.6 8.7 - - + +
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Residues in contact with HIS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A HIS* 3.2 20.2 - + - -
284A GLN 3.6 6.1 - - - -
285A ASP* 3.0 10.1 - - - -
286A PRO* 3.6 25.0 - - + +
288A SER* 4.6 9.5 + - - -
291A ZN 1.8 39.2 - - - -
257C LEU* 2.7 25.4 + - + +
258C VAL 3.9 5.1 + - - +
260C ALA* 1.3 73.9 - - - +
262C MET* 1.3 51.2 + - - +
264C ALA* 3.5 2.0 - - + -
265C ASP* 2.6 56.4 + - + +
284C GLN* 3.4 8.9 - - - +
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Residues in contact with MET 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C VAL 3.2 14.1 + - - +
259C GLN* 2.9 14.3 + - - +
261C HIS* 1.3 71.8 + - - +
263C VAL* 1.3 67.8 + - - +
265C ASP* 2.8 24.3 + - + -
266C GLN* 2.9 41.1 + - + +
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Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TRP* 4.7 1.3 - - + -
227C GLY* 3.7 32.5 - - - +
228C VAL* 3.9 21.8 - - + +
251C MET* 3.8 23.3 - - + -
255C LEU* 4.5 6.3 - - + -
259C GLN 3.4 9.9 - - - +
260C ALA* 3.2 17.5 - - - +
262C MET* 1.3 74.4 - - - +
264C ALA* 1.3 62.7 + - - +
266C GLN* 3.2 17.5 + - - +
267C VAL* 3.0 25.5 + - + +
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A HIS* 5.4 1.8 - - + -
249C LEU* 3.8 22.9 - - + -
251C MET* 4.3 2.9 - - + -
260C ALA 3.0 8.4 + - - +
261C HIS* 3.6 6.3 - - + +
263C VAL* 1.3 77.5 - - - +
265C ASP* 1.3 57.9 + - - +
267C VAL* 3.5 1.7 + - - +
268C GLU* 3.0 28.6 + - - +
282C ILE* 4.0 16.4 - - + +
284C GLN* 3.4 33.0 - - - +
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Residues in contact with ASP 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A HIS* 6.4 0.4 - - - -
261C HIS* 2.6 45.7 + - + +
262C MET* 2.8 18.5 + - + +
264C ALA* 1.3 68.7 - - - +
266C GLN* 1.3 56.5 + - - +
268C GLU* 3.2 13.9 + - - +
269C GLN* 2.7 42.8 + - - +
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Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TRP* 2.7 48.0 + - + +
226C PRO* 5.7 1.4 - - - +
227C GLY 5.6 0.3 + - - -
262C MET* 2.9 38.3 + - + +
263C VAL* 3.4 13.3 - - - +
265C ASP* 1.3 73.6 - - - +
267C VAL* 1.3 56.6 + - - +
269C GLN* 2.9 8.2 + - - +
270C ALA* 2.7 35.5 + - - +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 5.0 2.9 - - + +
222C VAL* 3.6 36.1 - - + -
225C TRP* 3.6 29.4 - - + -
228C VAL* 3.8 20.6 - - + -
249C LEU* 3.9 18.6 - - + -
263C VAL 3.0 16.1 + - - +
264C ALA 3.9 3.8 - - - +
266C GLN* 1.3 75.7 - - - +
268C GLU* 1.3 62.4 + - - +
270C ALA* 3.4 6.0 + - - +
271C ILE* 2.8 33.8 + - + +
282C ILE* 4.6 3.1 - - + -
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A HIS* 5.5 6.4 + - - -
264C ALA 3.0 16.0 + - - +
265C ASP* 3.4 17.6 - - - +
267C VAL* 1.3 76.2 - - - +
269C GLN* 1.3 68.4 + - + +
271C ILE* 3.2 9.2 + - - +
272C LEU* 3.0 37.8 + - + +
280C VAL* 3.5 41.1 + - + +
281C ILE* 4.6 1.9 - - - -
282C ILE* 4.0 14.2 + - + +
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Residues in contact with GLN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ASP* 2.7 29.4 + - - +
266C GLN* 3.4 8.7 - - - +
268C GLU* 1.3 77.5 - - - +
270C ALA* 1.3 62.2 + - - +
272C LEU* 3.3 21.6 + - - +
273C ARG* 3.0 43.7 + - + +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 3.7 15.7 - - + -
225C TRP* 3.3 37.2 - - + -
266C GLN 2.7 10.9 + - - +
267C VAL 3.5 9.0 - - - +
269C GLN* 1.3 68.0 - - - +
271C ILE* 1.3 64.7 + - - +
272C LEU 2.9 3.6 - - - -
273C ARG* 2.8 22.2 + - - +
274C ARG* 3.2 11.8 + - - +
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C ILE* 4.4 18.4 - - + -
221C ILE* 4.1 23.3 - - + +
222C VAL* 4.1 10.5 - - + -
245C ILE* 3.6 34.1 - - + -
247C ILE* 5.6 1.3 - - + -
267C VAL* 2.8 44.2 + - + +
268C GLU* 3.6 8.5 - - - +
270C ALA* 1.3 77.5 - - - +
272C LEU* 1.3 56.7 + - - +
275C PHE* 3.1 36.4 + - + +
278C SER* 5.0 0.6 - - - -
280C VAL* 3.6 15.0 - - + -
282C ILE* 4.7 8.7 - - + -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C GLU* 3.0 26.8 + - + +
269C GLN* 3.5 24.0 - - - +
270C ALA 2.8 0.6 + - - -
271C ILE* 1.3 77.3 - - - +
273C ARG* 1.3 61.4 + - - +
275C PHE 3.5 14.5 - - - +
276C PRO* 3.5 10.6 - - - +
277C GLY 6.2 0.4 - - - +
278C SER* 4.0 24.7 - - - +
279C ASP* 4.7 0.2 - - - -
280C VAL* 3.5 40.4 - - + +
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Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C GLN* 3.0 35.0 - - + +
270C ALA* 2.8 10.6 + - - +
272C LEU* 1.3 77.3 - - - +
274C ARG* 1.3 63.9 + - + +
276C PRO* 3.4 15.3 - - - +
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Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLU* 2.7 53.6 + - - +
220C ASP* 5.6 2.6 - - - +
221C ILE* 3.8 38.5 - - + +
270C ALA 3.2 6.8 + - - +
271C ILE 4.0 4.0 - - - +
273C ARG* 1.3 81.6 - - + +
275C PHE* 1.3 70.3 + - + +
276C PRO* 3.3 7.3 - - - +
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Residues in contact with PHE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C LEU* 5.6 0.2 - - + -
214C GLU* 3.1 61.2 - - + -
217C GLU* 3.9 27.4 - - + -
218C ILE* 3.6 23.8 - - + -
221C ILE* 4.6 2.7 - - + -
243C ARG* 3.7 19.1 - - - +
245C ILE* 4.5 2.7 - - + -
271C ILE* 3.1 27.2 + - + +
272C LEU 3.5 7.6 - - - +
274C ARG* 1.3 90.7 - - + +
276C PRO* 1.3 67.8 - - - +
278C SER* 3.0 33.3 + - - +
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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