Contacts of the helix formed by residues 271 - 290 (chain A) in PDB entry 6J95
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 THR 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 5.4 1.9 + - - +
264A PHE* 4.9 6.5 + - - +
269A ASN* 4.9 7.4 - - + -
270A ASP* 1.3 81.7 - - - +
272A GLY* 1.3 59.5 + - - +
273A VAL* 3.4 11.4 + - - +
274A ILE* 3.1 35.4 + - + +
275A GLU* 3.0 36.4 + - - +
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Residues in contact with GLY 272 (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 THR* 1.3 74.1 - - - +
273A VAL* 1.3 56.3 + - - +
275A GLU* 3.7 11.3 - - - +
276A ALA* 2.8 30.0 + - - +
316A LEU* 3.5 14.4 - - - +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.9 23.6 - - + +
264A PHE* 3.5 27.1 - - + -
271A THR* 3.2 10.4 + - - +
272A GLY* 1.3 76.6 - - - +
274A ILE* 1.3 62.9 + - - +
276A ALA* 3.2 4.6 + - - +
277A VAL* 3.0 25.6 + - + +
316A LEU* 3.9 17.0 - - + -
317A ILE* 5.2 7.9 - - + -
320A THR* 3.9 27.8 - - + +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 4.3 6.1 - - - +
252A LEU* 4.4 5.2 - - + -
264A PHE* 3.4 40.6 - - + +
266A SER* 3.6 13.7 - - - -
269A ASN 3.6 22.9 - - - +
270A ASP* 4.2 15.0 - - - +
271A THR* 3.1 30.8 + - + +
273A VAL* 1.3 76.2 - - - +
275A GLU* 1.3 65.1 + - + +
277A VAL* 3.1 8.8 + - - +
278A TYR* 3.1 47.0 + - + -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP* 4.3 18.8 - - + +
271A THR* 3.0 25.3 + - - +
272A GLY* 3.9 8.5 - - - +
274A ILE* 1.3 79.0 - - + +
276A ALA* 1.3 55.7 + - - +
278A TYR* 3.4 5.7 + - - +
279A THR* 2.8 35.7 + - - +
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Residues in contact with ALA 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 GLY 2.8 18.7 + - - +
273A VAL 3.4 5.8 - - - +
274A ILE 3.2 0.2 - - - -
275A GLU* 1.3 75.0 - - - +
277A VAL* 1.3 65.4 + - - +
279A THR 3.3 0.7 + - - -
280A VAL* 3.0 28.4 + - - +
313A SER* 3.6 40.8 - - - +
316A LEU* 4.2 10.5 - - + -
317A ILE* 3.7 9.4 - - + -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.1 22.7 - - + -
264A PHE* 4.1 26.0 - - + -
273A VAL* 3.0 15.2 + - + +
274A ILE* 3.1 8.7 + - - +
276A ALA* 1.3 75.1 - - - +
278A TYR* 1.3 58.1 + - + +
280A VAL* 3.2 4.9 + - + +
281A LEU* 2.8 48.9 + - + +
317A ILE* 3.8 22.7 - - + -
375A LEU* 4.7 17.9 - - + -
376A ILE* 5.5 2.2 - - + -
379A HIS* 4.8 0.9 - - + -
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Residues in contact with TYR 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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248A SER* 2.6 46.3 + - - -
249A ARG* 3.6 23.5 + - - -
252A LEU* 3.9 12.8 - - + +
274A ILE* 3.1 46.2 + - + +
275A GLU* 4.0 5.8 - - - +
277A VAL* 1.3 72.9 - - + +
279A THR* 1.3 59.9 + - - +
281A LEU* 3.6 13.2 - - + +
282A ARG* 2.9 30.5 + - - +
379A HIS* 3.7 15.6 + - - -
380A GLU* 5.4 1.8 - - - -
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Residues in contact with THR 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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275A GLU* 2.8 23.9 + - - +
276A ALA 3.6 0.7 - - - -
277A VAL 3.3 0.2 - - - -
278A TYR* 1.3 76.4 - - - +
280A VAL* 1.3 62.4 + - - +
282A ARG* 3.4 31.5 + - - +
283A GLU* 3.1 19.8 + - - +
309A LYS* 4.0 21.3 - - + +
310A VAL* 4.4 5.2 - - + -
313A SER* 3.5 24.7 + - - +
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Residues in contact with VAL 280 (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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183A PHE* 3.8 4.9 - - + -
184A VAL* 3.4 35.7 - - + -
276A ALA 3.0 19.7 + - - +
277A VAL* 3.6 5.4 - - + +
279A THR* 1.3 75.9 - - - +
281A LEU* 1.3 64.7 + - + +
283A GLU* 3.3 7.8 + - - +
284A ALA* 3.0 21.4 + - + +
310A VAL* 4.7 6.1 - - + +
313A SER* 4.0 11.0 - - - -
314A LEU* 3.6 28.5 - - + -
317A ILE* 4.0 14.8 - - + -
372A MET* 5.8 0.7 - - - -
376A ILE* 4.7 9.4 - - + -
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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
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277A VAL* 2.8 34.8 + - + +
278A TYR* 3.6 18.8 - - + +
280A VAL* 1.3 76.8 - - + +
282A ARG* 1.3 57.6 + - - +
284A ALA* 3.1 9.8 + - + +
285A GLU* 2.9 31.2 + - - +
376A ILE* 3.5 44.2 - - + -
379A HIS* 3.5 31.0 - - + +
380A GLU* 3.7 26.4 - - + +
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR 2.9 15.4 + - - +
279A THR* 3.4 38.3 + - - +
280A VAL 3.3 0.2 - - - -
281A LEU* 1.3 76.4 - - - +
283A GLU* 1.3 65.7 + - - +
285A GLU* 3.2 9.7 + - + +
286A ASP* 2.9 57.5 + - - +
306A ARG* 5.1 15.5 + - - +
309A LYS* 5.7 1.4 - - - +
310A VAL* 4.2 13.1 - - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.5 26.2 - - + -
279A THR 3.1 13.2 + - - +
280A VAL* 3.6 7.6 - - - +
282A ARG* 1.3 82.9 + - - +
284A ALA* 1.3 57.2 + - - +
286A ASP* 3.2 15.9 + - - +
287A ARG* 2.9 64.9 + - - +
306A ARG* 5.9 2.6 - - - +
307A GLN* 6.0 1.2 - - - -
310A VAL* 3.9 28.6 - - + +
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Residues in contact with ALA 284 (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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180A ILE* 4.2 2.8 - - - +
181A LEU* 4.8 15.7 - - + -
183A PHE* 3.6 22.1 - - + -
184A VAL* 5.0 4.7 - - + -
280A VAL* 3.0 14.2 + - + +
281A LEU* 3.1 15.9 + - + +
283A GLU* 1.3 75.8 - - - +
285A GLU* 1.3 60.4 + - - +
287A ARG* 3.4 3.6 + - - +
288A SER* 3.0 32.4 + - - -
376A ILE* 5.7 4.7 - - + -
554A ALA* 5.9 2.2 - - + -
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Residues in contact with GLU 285 (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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281A LEU 2.9 19.3 + - - +
282A ARG* 3.2 11.9 + - + +
284A ALA* 1.3 77.4 - - - +
286A ASP* 1.3 66.1 + - - +
288A SER* 3.0 13.8 + - - -
289A VAL* 3.1 16.0 + - - +
380A GLU* 4.5 7.8 - - - +
552A THR 4.4 3.0 - - - +
553A GLY* 3.5 17.6 - - - -
554A ALA* 3.0 34.2 + - - +
555A THR 4.2 0.3 + - - -
557A HIS* 3.0 38.0 + - + -
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Residues in contact with ASP 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 ARG* 2.9 40.6 + - - +
283A GLU* 3.2 17.3 + - - +
285A GLU* 1.3 78.0 - - - +
287A ARG* 1.3 58.4 + - + +
289A VAL* 3.1 13.9 - - + +
290A SER* 3.1 28.5 + - - -
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Residues in contact with ARG 287 (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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179A GLU 4.6 11.2 + - - -
180A ILE* 3.6 39.6 - - + +
183A PHE* 3.6 39.6 - - + +
283A GLU* 2.9 47.4 + - - +
284A ALA 3.9 3.8 - - - +
286A ASP* 1.3 75.7 - - - +
288A SER* 1.3 62.1 + - - +
290A SER* 3.8 7.3 - - - -
291A PRO* 3.2 19.6 - - - +
310A VAL* 5.6 2.8 - - - +
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Residues in contact with SER 288 (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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180A ILE* 3.4 20.4 - - - +
181A LEU* 5.4 0.3 - - - +
284A ALA 3.0 14.7 + - - -
285A GLU 3.0 8.9 + - - -
287A ARG* 1.3 79.2 - - - +
289A VAL* 1.3 60.6 + - - +
291A PRO* 3.4 6.1 - - - +
292A ILE* 3.3 17.8 - - - +
552A THR* 5.6 1.1 - - - -
553A GLY* 4.3 5.4 - - - -
554A ALA* 3.9 24.3 - - - +
602A RET 3.4 31.4 - - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU 3.1 13.0 + - - +
286A ASP* 3.1 26.9 - - - +
288A SER* 1.3 76.9 - - - +
290A SER* 1.3 66.8 + - - +
292A ILE* 3.0 27.7 + - + +
552A THR* 4.6 28.5 - - + +
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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
----------------------------------------------------------
286A ASP 3.1 17.9 + - - -
287A ARG* 3.8 8.5 - - - -
289A VAL* 1.3 77.5 - - - +
291A PRO* 1.3 68.4 - - - +
292A ILE 3.3 3.5 + - - +
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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