Contacts of the helix formed by residues 275 - 291 (chain A) in PDB entry 6CJH
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 ARG 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE* 4.6 10.6 + - - +
272A TYR* 2.5 56.1 + - - +
274A LYS* 1.3 69.1 - - + +
276A CYS* 1.3 56.5 + - - +
277A ASP 2.8 2.0 - - - -
278A LEU* 2.5 39.5 + - + +
279A TRP 3.3 4.0 + - - -
353A ALA* 3.2 10.3 - - + +
354A LYS 2.8 29.7 + - - -
355A GLN 3.3 2.0 + - - -
356A ARG* 2.7 53.0 + - - +
357A LEU 3.9 13.2 - - - +
358A SER* 3.7 30.0 - - - +
359A ALA 5.3 0.2 - - - +
361A GLN* 3.9 9.9 + - - -
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Residues in contact with CYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ALA* 4.7 0.2 - - - -
204A ARG* 3.3 30.7 - - - +
272A TYR 4.2 0.2 + - - -
273A ASP* 3.1 26.2 + - - +
274A LYS* 3.8 5.2 - - - -
275A ARG* 1.3 74.6 - - - +
277A ASP* 1.3 86.1 + - - +
279A TRP* 3.2 14.6 + - - +
280A SER* 3.0 15.3 + - - -
353A ALA* 5.5 0.6 - - - +
356A ARG* 3.4 16.0 - - - +
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Residues in contact with ASP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.6 24.4 - - + +
197A HIS* 3.2 14.3 + - - +
202A ALA* 3.6 2.3 - - - -
203A HIS* 2.8 30.6 + - - +
204A ARG* 2.8 33.4 + - - +
206A LEU* 3.6 12.6 - - - +
274A LYS 3.3 11.2 - - - +
275A ARG 2.7 4.0 + - - -
276A CYS* 1.3 83.3 - - - +
278A LEU* 1.3 59.4 + - + +
280A SER* 3.3 8.9 - - - -
281A LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 5.9 0.4 - - + -
193A LEU* 5.0 6.1 - - + -
197A HIS* 3.7 28.3 - - + -
274A LYS 3.8 4.9 - - - +
275A ARG* 2.5 29.0 + - + +
277A ASP* 1.3 74.3 - - + +
279A TRP* 1.3 63.6 + - - +
280A SER 3.1 1.1 - - - -
281A LEU* 3.0 17.3 + - + +
282A GLY 3.0 18.5 + - - -
348A LEU* 3.3 24.2 - - + +
356A ARG* 4.1 5.8 - - - -
357A LEU 3.3 16.2 - - - +
359A ALA* 3.6 28.5 - - + +
362A VAL* 3.7 20.2 - - + -
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Residues in contact with TRP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG 3.3 3.8 + - - -
276A CYS* 3.2 11.1 + - - +
278A LEU* 1.3 73.5 - - - +
280A SER* 1.3 68.0 + - - +
282A GLY* 3.0 3.8 + - - -
283A VAL* 3.0 43.1 + - + +
295A PHE* 3.5 35.3 - + - -
322A ILE* 4.2 35.1 - - + +
325A GLY* 4.9 3.8 - - - -
327A TYR* 5.8 0.7 - + - -
348A LEU 3.9 11.2 - - - -
349A LEU* 3.7 38.4 - - + +
350A VAL 3.5 25.1 - - - -
351A ARG* 4.1 15.9 - - + -
356A ARG* 3.6 26.3 - - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG 4.2 10.4 + - - -
206A LEU* 3.8 29.8 - - - -
276A CYS 3.0 14.6 + - - -
277A ASP* 3.3 12.7 + - - -
278A LEU 3.1 0.4 - - - -
279A TRP* 1.3 84.3 - - - +
281A LEU* 1.3 57.0 + - - +
283A VAL* 3.3 6.8 + - - +
284A ILE* 2.9 34.7 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 6.5 0.2 - - + -
186A VAL* 3.9 38.6 - - + -
189A VAL* 4.0 23.6 - - + -
190A ALA* 4.4 11.7 - - + +
193A LEU* 4.1 19.5 - - + -
206A LEU* 4.0 8.5 - - + +
277A ASP 3.1 11.9 + - - +
278A LEU* 3.0 24.7 + - + +
280A SER* 1.3 77.9 - - - +
282A GLY* 1.3 51.4 + - - +
284A ILE* 3.3 15.4 + - + +
285A LEU* 2.7 36.3 + - + +
288A LEU* 6.2 0.2 - - + -
348A LEU* 4.8 6.1 - - + -
362A VAL* 4.5 6.1 - - + -
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU 3.0 10.8 + - - -
279A TRP 3.0 4.2 + - - -
281A LEU* 1.3 72.2 - - - +
283A VAL* 1.3 65.3 + - - +
285A LEU* 3.2 4.8 + - - +
286A TYR* 3.0 24.9 + - - +
345A ILE* 4.4 8.1 - - - +
348A LEU* 3.9 27.3 - - - +
349A LEU* 4.1 11.0 - - - -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP* 3.0 47.4 + - + +
280A SER* 3.6 7.4 - - - +
282A GLY* 1.3 74.0 - - - +
284A ILE* 1.3 69.5 + - + +
286A TYR* 3.2 8.0 + - - +
287A ILE* 3.1 25.2 + - + +
293A PRO* 5.2 2.7 - - + -
294A PRO* 3.5 31.4 - - + -
295A PHE* 4.6 6.1 - - + -
349A LEU* 3.6 9.6 - - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 6.0 1.6 - - + -
189A VAL* 6.5 0.4 - - + -
206A LEU* 3.9 26.2 - - + +
207A LYS* 3.8 24.5 - - - -
208A PRO* 4.2 20.4 - - + -
211A ILE* 4.1 21.1 - - + -
280A SER 2.9 18.3 + - - +
281A LEU* 3.4 17.9 - - + +
283A VAL* 1.3 75.8 - - + +
285A LEU* 1.3 57.8 + - - +
287A ILE* 2.8 32.8 + - + +
288A LEU* 3.1 33.1 + - + +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 4.4 1.8 - - + -
186A VAL* 4.0 24.9 - - + -
281A LEU* 2.7 21.1 + - + +
282A GLY* 3.2 6.9 + - - +
284A ILE* 1.3 72.7 - - - +
286A TYR* 1.3 54.7 - - - +
288A LEU* 2.7 37.6 + - + +
289A LEU* 3.1 28.7 + - + +
341A ALA* 5.6 1.3 - - - +
344A LEU* 3.7 31.2 - - + -
345A ILE* 4.0 19.5 - - + -
348A LEU* 5.1 4.9 - - + -
367A TRP* 4.1 18.6 - - + -
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Residues in contact with TYR 286 (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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282A GLY 3.0 12.6 + - - +
283A VAL 3.5 9.0 - - - +
285A LEU* 1.3 75.1 - - - +
287A ILE* 1.3 53.7 + - - +
288A LEU 3.2 0.2 + - - -
289A LEU 3.3 0.7 + - - -
290A SER* 2.3 55.6 + - - -
292A TYR* 3.2 49.1 - + - -
294A PRO* 3.7 39.9 + - + +
327A TYR* 4.6 6.1 - + + -
328A GLU 2.7 30.4 + - - -
329A PHE* 3.6 23.6 - + - -
330A PRO* 3.7 6.6 - - - +
334A TRP* 3.6 15.7 - + - -
345A ILE* 3.7 22.8 - - + +
349A LEU* 4.8 1.3 - - + -
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 5.0 19.6 - - + +
175A ARG 4.6 1.0 - - - +
176A HIS* 4.2 2.3 - - - +
208A PRO* 5.4 11.0 - - + -
283A VAL* 3.1 25.1 - - + +
284A ILE* 2.8 19.2 + - + +
286A TYR* 1.3 76.0 - - - +
288A LEU* 1.3 60.7 + - + +
290A SER* 3.8 0.2 - - - -
291A GLY* 3.0 28.5 + - - +
292A TYR* 3.3 30.1 - - - +
293A PRO* 3.8 24.0 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 5.1 9.4 - - + -
171A ILE* 4.5 17.7 - - + -
176A HIS* 3.3 4.0 - - - +
177A PHE* 3.0 57.7 + - + +
182A ALA* 4.2 16.2 - - + -
185A VAL* 4.2 22.7 - - + -
186A VAL* 4.7 5.8 - - + -
219A VAL* 6.1 0.4 - - + -
284A ILE* 3.1 34.9 + - + +
285A LEU* 2.7 30.1 + - + +
287A ILE* 1.3 82.0 - - + +
289A LEU* 1.3 56.3 + - - -
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Residues in contact with LEU 289 (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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176A HIS* 2.7 29.2 + - - -
177A PHE 4.1 9.0 - - - +
178A ASN* 5.0 0.2 - - - -
179A GLU* 4.2 26.9 - - + +
182A ALA* 4.2 20.9 - - + -
285A LEU* 3.1 33.7 + - + +
288A LEU* 1.3 80.2 - - - +
290A SER* 1.3 57.4 + - - +
334A TRP* 4.0 20.0 - - + -
337A ILE* 4.4 19.7 - - + +
341A ALA* 4.3 18.8 - - + -
345A ILE* 4.3 13.9 - - + -
367A TRP* 4.5 4.5 - - + -
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 5.3 1.6 - - - +
176A HIS* 4.0 12.7 - - - -
286A TYR* 2.3 30.0 + - - -
289A LEU* 1.3 79.6 - - - +
291A GLY* 1.3 56.8 + - - +
292A TYR* 2.9 43.2 + - - -
333A ASP* 4.2 10.1 - - - +
334A TRP* 3.3 31.9 - - - +
337A ILE* 5.5 1.6 - - - -
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 5.5 2.3 - - - +
175A ARG* 3.3 43.6 + - - +
176A HIS* 3.7 2.3 - - - +
287A ILE* 3.0 22.2 + - - +
290A SER* 1.3 77.7 - - - +
292A TYR* 1.3 60.4 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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