Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 3H60
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 PHE 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR 6.1 0.2 - - - -
201B GLN* 4.3 7.9 - - + -
245B GLY 3.1 20.1 + - - +
246B GLN* 5.0 2.2 - - - -
247B PHE* 3.5 17.7 - + + -
248B TYR* 3.8 31.6 - + - -
276B GLY* 5.8 0.2 - - - -
277B SER* 1.3 88.0 - - - +
279B SER* 1.3 62.1 + - - +
281B GLU* 3.2 26.1 + - + +
282B VAL* 3.0 21.3 + - - +
322B LYS* 5.4 1.1 - - - -
481B HIS* 3.8 21.5 - + - -
482B PRO* 3.7 34.3 - - + -
484B VAL* 4.0 29.8 - - + -
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLY* 3.6 14.7 - - - -
273B VAL* 3.8 10.2 - - - +
274B ASP* 3.0 21.0 + - - -
276B GLY 3.0 18.7 + - - -
278B PHE* 1.3 77.0 - - - +
280B VAL* 1.3 63.7 + - - +
282B VAL* 3.5 2.5 + - - +
283B ILE* 3.0 25.5 + - - +
314B GLY 5.9 0.2 - - - -
315B PHE* 3.5 25.0 - - - -
318B GLU* 3.0 14.4 + - - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR* 4.7 4.3 - - + +
279B SER* 1.3 77.5 - - - +
281B GLU* 1.3 68.1 + - - +
283B ILE* 3.4 8.5 - - - +
284B LEU* 3.3 43.0 + - + +
315B PHE* 4.0 3.8 - - + -
318B GLU* 2.9 32.0 + - + +
319B VAL* 3.8 29.8 - - + -
322B LYS* 4.0 14.1 - - + -
323B TYR* 3.9 20.9 - - + +
331B PHE* 5.0 3.6 - - + -
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR* 3.5 49.8 - - + +
201B GLN* 5.8 4.1 - - - -
202B LYS 4.6 7.8 - - - +
203B LYS* 5.9 0.7 - - - -
247B PHE* 3.7 20.6 - - + -
278B PHE* 3.2 29.1 + - + +
280B VAL* 1.3 75.8 - - - +
282B VAL* 1.3 63.2 + - - +
285B THR* 2.7 32.2 + - - -
318B GLU* 3.2 0.2 - - - +
322B LYS* 2.8 37.5 + - - +
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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
----------------------------------------------------------
243B THR* 3.9 12.3 - - - +
245B GLY* 3.5 20.2 - - - +
246B GLN 3.8 3.4 - - - +
247B PHE* 3.5 35.8 - - - +
250B LEU* 4.0 18.6 - - + -
272B PHE* 3.5 19.5 - - + +
278B PHE 3.0 7.8 + - - +
279B SER 3.8 7.2 - - - +
281B GLU* 1.3 77.7 - - - +
283B ILE* 1.3 58.4 + - - +
285B THR* 3.5 1.9 - - - -
286B LEU* 2.9 49.1 + - + +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.5 38.8 - - + -
273B VAL* 3.9 6.3 - - + -
279B SER 3.0 17.1 + - - +
280B VAL* 3.4 14.6 - - - +
281B GLU 3.3 0.2 - - - -
282B VAL* 1.3 79.5 - - - +
284B LEU* 1.3 59.5 + - - +
286B LEU* 3.3 6.5 + - + +
287B PHE* 2.8 55.4 + - + +
299B LEU* 5.9 0.2 - - + -
315B PHE* 4.1 7.4 - - + -
331B PHE* 3.5 26.5 - - + -
335B PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.2 8.0 - - + +
198B TYR* 3.4 27.1 - - + +
204B LEU* 4.2 8.5 - - + -
209B ALA* 3.9 36.8 - - + +
212B ILE* 4.2 24.9 - - + +
213B LEU* 4.4 5.2 - - + -
280B VAL* 3.3 26.7 + - + +
283B ILE* 1.3 73.0 - - - +
285B THR* 1.3 57.3 + - - +
287B PHE* 3.9 3.2 - - + +
288B GLY* 2.7 31.7 + - - -
323B TYR* 4.1 6.1 - - + +
331B PHE* 3.9 29.4 - - + -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B MET* 3.3 12.9 - - + +
194B LEU* 4.3 4.7 - - - +
195B MET* 4.1 21.0 - - + +
198B TYR* 3.6 11.4 - - - -
247B PHE* 3.5 16.4 - - + -
250B LEU* 4.4 9.2 - - + -
251B LEU* 5.6 0.4 - - + -
254B PHE* 4.4 10.1 - - + -
281B GLU 2.7 22.8 + - - -
282B VAL 3.5 3.8 - - - -
284B LEU* 1.3 78.2 - - - +
286B LEU* 1.4 62.3 + - - +
288B GLY 3.3 0.9 + - - -
289B PHE* 3.0 43.3 + - + -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 4.8 1.1 - - - +
250B LEU* 4.1 17.3 - - + -
254B PHE* 4.7 3.8 - - + -
268B PHE* 4.1 22.9 - - + -
272B PHE* 3.4 42.6 - - + -
282B VAL* 2.9 35.0 + - + +
283B ILE* 3.7 7.9 - - + +
285B THR* 1.4 75.3 - - - +
287B PHE* 1.3 58.6 + - - +
289B PHE 3.3 1.4 + - - -
290B LYS* 2.9 25.3 + - - +
297B PHE* 3.3 34.0 - - + -
299B LEU* 4.1 15.9 - - + -
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 3.7 18.4 - - + -
213B LEU* 3.5 33.4 - - + -
216B VAL* 3.9 22.1 - - + +
220B LEU* 4.5 8.1 - - + -
272B PHE* 5.8 0.2 - + - -
283B ILE* 2.8 44.1 + - + +
284B LEU* 3.9 4.5 - - + +
286B LEU* 1.3 71.0 - - - +
288B GLY* 1.3 68.1 + - - +
290B LYS* 3.1 5.4 + - - +
291B LEU* 3.0 27.5 + - - +
299B LEU* 3.9 20.6 - - + -
331B PHE* 4.1 8.3 - + - -
334B VAL* 3.7 20.2 - - + -
335B PHE* 3.7 23.1 - + - -
338B LEU* 4.6 6.7 - - + -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.6 21.6 - - - +
191B MET* 3.6 22.2 - - - -
212B ILE* 4.3 8.2 - - - +
284B LEU 2.7 22.4 + - - -
285B THR 3.7 0.2 - - - -
287B PHE* 1.3 74.6 - - - +
289B PHE* 1.3 56.1 + - - +
291B LEU* 3.3 1.0 + - - +
292B LEU* 2.9 23.2 + - - +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 5.8 3.1 - - + -
191B MET* 3.9 27.5 - - + +
195B MET* 4.0 17.9 - - + -
254B PHE* 3.8 26.2 - + - -
259B LEU* 3.9 17.9 - - + -
260B PRO* 3.6 33.7 - - + -
285B THR* 3.0 27.5 + - + -
286B LEU 3.8 0.7 - - - +
288B GLY* 1.3 75.0 - - - +
290B LYS* 1.3 58.2 + - - +
292B LEU* 3.8 12.7 - - + +
293B TYR* 2.9 44.8 + + - +
297B PHE* 3.7 32.6 - + + +
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Residues in contact with LYS 290 (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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216B VAL* 3.7 20.0 - - + -
219B VAL* 3.9 21.6 - - + +
220B LEU* 4.0 17.3 - - + -
223B LEU* 4.3 16.1 - - - +
286B LEU 2.9 14.4 + - - +
287B PHE 3.1 8.3 + - - +
289B PHE* 1.3 76.2 - - - +
291B LEU* 1.3 57.6 + - - +
294B PRO* 2.8 58.6 + - + +
297B PHE* 2.9 28.2 + - + +
298B HIS* 4.2 13.5 - - - +
299B LEU* 3.8 23.6 - - + +
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Residues in contact with LEU 291 (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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186B VAL* 3.9 28.5 - - + -
212B ILE* 3.7 39.0 - - + +
215B GLN* 3.7 24.5 - - + +
216B VAL* 3.5 31.9 - - + +
219B VAL* 3.7 17.5 - - + -
287B PHE 3.0 12.5 + - - +
288B GLY 3.7 5.8 - - - +
290B LYS* 1.3 75.3 - - - +
292B LEU* 1.3 63.3 + - - +
294B PRO* 3.4 13.5 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.8 26.8 - - + +
187B THR* 3.8 2.0 - - - -
188B ILE* 3.8 35.4 - - + +
191B MET* 4.0 15.9 - - + -
288B GLY 2.9 16.0 + - - +
289B PHE* 3.8 10.5 - - + +
290B LYS 3.3 0.2 - - - -
291B LEU* 1.3 78.5 - - - +
293B TYR* 1.3 99.4 + - + +
294B PRO* 3.3 7.3 - - - +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 4.1 14.9 - - - +
260B PRO* 3.3 33.2 + - + -
261B SER* 3.7 12.2 - - - -
262B GLU* 3.5 45.1 - - + -
289B PHE* 2.9 27.3 + + - +
290B LYS 3.5 3.1 - - - -
292B LEU* 1.3 113.6 - - + +
294B PRO* 1.3 65.8 - - - +
295B ASP 3.2 2.2 - - - -
296B HIS* 3.1 16.2 + - + +
297B PHE* 3.0 27.7 + - + +
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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
------------------------------------------------------------
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