Contacts of the helix formed by residues 278 - 299 (chain B) in PDB entry 2DOU
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 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LYS 3.3 7.1 - - - +
277B THR* 1.3 92.0 - - + +
279B LYS* 1.3 66.2 + - - +
280B GLU* 3.1 7.0 - - + +
281B VAL* 3.0 35.8 + - + +
282B VAL* 3.4 4.5 + - - +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR 3.2 5.3 + - - -
278B PRO* 1.3 71.6 - - - +
280B GLU* 1.3 56.9 + - - +
282B VAL* 3.3 8.8 + - - +
283B ARG* 2.8 42.1 + - + +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO* 3.1 7.5 - - + -
279B LYS* 1.3 78.0 - - - +
281B VAL* 1.3 58.9 + - + +
283B ARG* 3.3 8.3 + - - +
284B GLY* 2.9 24.1 + - - -
287B ARG* 3.7 10.2 + - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 4.7 7.2 - - + -
277B THR* 3.8 17.7 - - + -
278B PRO* 3.0 28.2 + - + +
280B GLU* 1.3 77.2 - - + +
282B VAL* 1.3 67.2 + - - +
284B GLY* 3.0 11.5 + - - -
285B TYR* 3.3 43.4 + - + +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASP* 3.5 44.4 - - + +
231B SER 4.2 9.6 - - - +
232B TYR* 3.7 31.0 - - + +
277B THR* 4.1 13.2 - - + +
278B PRO 3.4 10.3 + - - +
279B LYS* 3.3 9.1 + - - +
281B VAL* 1.3 77.6 - - - +
283B ARG* 1.3 67.9 + - - +
284B GLY 3.4 0.2 + - - -
285B TYR* 3.5 19.9 + - + +
286B ALA* 3.5 10.6 + - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 6.1 0.4 - - - +
202B ASP* 3.1 37.1 + - - +
204B VAL* 2.8 25.9 + - - +
205B TYR 4.1 9.9 + - - -
207B GLY 4.7 11.8 + - - +
279B LYS* 2.8 32.9 + - + +
280B GLU* 3.5 7.6 - - - +
281B VAL 3.1 0.2 - - - -
282B VAL* 1.3 80.4 + - - +
284B GLY* 1.3 65.7 + - - +
286B ALA* 3.2 15.8 + - - +
287B ARG* 2.9 36.5 + - - +
290B ARG* 5.7 2.6 - - - +
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU 2.9 15.2 + - - -
281B VAL* 3.0 5.7 + - - -
283B ARG* 1.3 75.2 - - - +
285B TYR* 1.3 64.2 + - - +
287B ARG* 2.9 31.1 + - - +
288B VAL* 3.0 18.2 + - - +
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 23.3 - - + -
38B PRO* 3.3 14.8 + - + -
39B PRO 3.8 0.5 - - - -
40B PRO* 3.3 28.5 - - + +
203B GLN* 6.0 2.0 - - + +
230B LYS 4.9 2.9 - - - +
231B SER 3.5 27.4 - - - -
232B TYR* 4.3 5.6 - + - -
233B ASN* 3.4 29.8 - - - +
281B VAL* 3.5 34.1 - - + +
282B VAL* 3.6 12.3 - - + +
283B ARG 3.3 0.2 - - - -
284B GLY* 1.3 73.8 - - - +
286B ALA* 1.3 63.8 + - - +
288B VAL* 3.1 20.4 + - + +
289B TYR* 3.2 22.2 + - + +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASP 3.6 23.3 - - - +
203B GLN* 4.2 8.7 - - - +
204B VAL 3.9 8.1 - - - +
205B TYR* 4.1 5.1 - - - -
282B VAL 3.5 2.7 + - - +
283B ARG* 3.2 30.2 + - - +
284B GLY 3.2 0.6 - - - -
285B TYR* 1.3 79.9 - - - +
287B ARG* 1.3 58.2 + - - +
289B TYR* 3.3 13.7 + - - +
290B ARG* 2.9 29.0 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 3.7 14.5 + - - +
283B ARG* 2.9 19.0 + - - +
284B GLY* 2.9 38.4 + - - +
286B ALA* 1.3 72.9 - - - +
288B VAL* 1.3 66.6 + - + +
290B ARG* 3.1 47.6 + - - +
291B GLU* 2.9 24.4 + - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.1 25.1 - - + -
284B GLY 3.0 18.6 + - - +
285B TYR* 3.2 9.4 - - + +
287B ARG* 1.3 76.9 - - + +
289B TYR* 1.3 65.2 + - + +
291B GLU* 2.9 42.0 + - - +
292B ARG* 2.9 43.6 + - - +
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.8 26.3 + - - -
36B ASP* 5.2 0.7 - - - -
37B LEU* 3.6 18.9 - - + +
203B GLN* 3.5 29.7 + - + -
205B TYR* 3.7 6.0 + - + -
230B LYS 5.7 0.2 - - - -
233B ASN* 4.2 5.9 + - - -
285B TYR* 3.2 29.5 + - + -
286B ALA* 3.3 9.4 + - - +
288B VAL* 1.3 78.3 - - + +
290B ARG* 1.3 53.0 + - - +
292B ARG* 3.8 11.8 - - - +
293B ALA* 2.7 37.4 + - - +
312B THR 3.8 17.3 - - - +
313B MET* 2.9 40.7 - - + +
357B LEU* 3.9 24.6 - - + +
358B VAL* 5.5 0.4 - - - -
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.7 48.2 + - + +
206B GLU* 3.4 25.8 + - - -
283B ARG* 5.7 2.4 - - - +
286B ALA 2.9 14.9 + - - +
287B ARG* 3.1 52.5 + - - +
289B TYR* 1.3 76.7 - - - +
291B GLU* 1.3 63.1 + - - +
293B ALA* 3.8 0.5 - - - +
294B LEU* 3.0 48.9 + - + +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG 2.9 10.9 + - - +
288B VAL* 2.9 37.9 - - - +
290B ARG* 1.3 78.3 - - - +
292B ARG* 1.3 74.0 + - + +
294B LEU* 3.9 3.7 - - - +
295B GLY* 2.9 27.7 + - - -
361B LEU* 4.3 24.0 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 2.7 41.8 + - - -
37B LEU* 4.1 5.3 - - - +
288B VAL* 2.9 35.9 + - - +
289B TYR* 3.8 8.9 - - - +
291B GLU* 1.3 96.1 + - + +
293B ALA* 1.3 66.8 + - - +
294B LEU 3.3 0.2 + - - -
296B MET* 3.1 27.9 + - - +
357B LEU* 3.1 36.2 + - + -
359B ARG 3.3 25.0 + - - +
360B PRO* 3.8 17.2 - - - +
361B LEU* 4.4 10.1 - - - +
364B LEU* 3.5 18.3 - - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.2 32.3 - - + +
289B TYR 2.7 23.0 + - - +
290B ARG 3.8 0.4 - - - +
292B ARG* 1.3 73.0 - - - +
294B LEU* 1.3 58.5 + - - +
297B ALA* 3.0 31.2 + - - +
309B PRO* 3.8 11.4 - - + +
315B LEU* 3.8 10.1 - - + +
357B LEU* 3.4 19.4 - - + +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B TYR* 5.5 1.8 - - + -
206B GLU* 6.2 0.2 - - - +
290B ARG* 3.0 41.2 + - + +
291B GLU* 4.1 3.6 - - - +
293B ALA* 1.3 75.2 - - + +
295B GLY* 1.3 67.8 + - - +
297B ALA* 3.4 4.9 + - + +
298B GLU* 3.3 20.6 + - - +
309B PRO* 4.3 31.2 - - + +
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLU 2.9 17.8 + - - -
292B ARG 3.9 0.2 - - - -
294B LEU* 1.3 78.3 - - - +
296B MET* 1.3 62.7 + - - +
298B GLU* 3.4 12.2 + - - +
299B ALA* 3.4 8.0 + - - +
361B LEU* 4.1 14.6 - - - -
365B LEU* 4.0 15.1 - - - +
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Residues in contact with MET 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.8 3.8 - - + -
292B ARG 3.1 16.9 + - - +
293B ALA 4.3 1.3 - - - +
295B GLY* 1.3 72.6 - - - +
297B ALA* 1.3 63.6 + - - +
298B GLU 3.3 0.2 - - - -
299B ALA* 3.3 7.0 + - - +
300B LEU* 3.0 46.6 + - + +
315B LEU* 4.3 5.4 - - + -
355B ILE* 3.2 47.1 - - + -
357B LEU* 4.2 8.3 - - + -
361B LEU* 4.2 3.0 - - - +
364B LEU* 3.7 52.5 - - + +
365B LEU* 4.6 3.4 - - - -
367B ALA 5.3 0.2 - - - -
368B ALA* 3.9 8.7 - - + +
371B ILE* 4.3 9.0 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 3.0 21.0 + - - +
294B LEU* 3.8 5.6 - - + +
295B GLY 3.3 0.4 - - - -
296B MET* 1.3 75.3 - - - +
298B GLU* 1.3 65.8 - - - +
300B LEU* 3.1 11.5 + - - +
301B LYS* 3.1 12.6 + - - -
306B LEU* 3.8 26.5 - - + +
309B PRO* 4.1 19.7 - - + -
315B LEU* 4.5 3.1 - - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU 3.3 10.2 + - - +
295B GLY* 3.7 9.2 - - - +
296B MET 3.3 0.2 - - - -
297B ALA* 1.3 78.3 - - - +
299B ALA* 1.3 61.2 + - - +
300B LEU 3.2 1.1 + - - -
301B LYS* 3.6 10.4 + - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY 3.4 8.6 + - - +
296B MET 3.3 9.1 + - - +
297B ALA 3.2 0.4 - - - -
298B GLU* 1.3 80.5 - - - +
300B LEU* 1.3 62.1 + - - +
301B LYS 3.6 1.6 - - - +
303B VAL* 4.2 7.6 - - - +
365B LEU* 4.2 17.5 - - + +
368B ALA* 3.9 23.9 - - + +
372B ARG* 5.3 2.3 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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