Contacts of the helix formed by residues 278 - 293 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 4.1 13.2 - - + -
245A GLY 3.0 20.6 + - - +
246A GLN* 5.0 2.2 - - - -
247A PHE* 3.5 18.4 - - + -
248A TYR* 3.8 38.4 - + - -
277A SER* 1.3 91.2 - - - +
279A SER* 1.3 57.4 + - - +
281A GLU* 3.1 25.2 - - + +
282A VAL* 2.9 26.3 + - - +
322A LYS* 5.2 1.8 - - - -
481A HIS* 4.1 19.5 - + + -
482A PRO* 3.9 23.1 - - + -
484A VAL* 4.0 30.5 - - + -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLY* 3.5 12.0 - - - -
273A VAL* 3.5 11.4 - - - +
274A ASP* 3.0 23.6 + - - -
276A GLY 3.1 14.4 + - - -
278A PHE* 1.3 78.3 - - - +
280A VAL* 1.3 58.4 + - - +
282A VAL* 3.2 2.3 + - - +
283A ILE* 2.9 32.9 + - - +
314A GLY 5.7 0.3 - - - -
315A PHE* 3.6 24.0 - - - +
318A GLU* 3.1 14.2 + - - -
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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
----------------------------------------------------------
198A TYR* 4.6 5.2 - - + +
203A LYS* 6.3 1.1 - - + -
279A SER* 1.3 76.8 - - - +
281A GLU* 1.3 69.4 + - - +
283A ILE* 3.5 7.9 - - - +
284A LEU* 3.1 45.1 + - + +
315A PHE* 4.0 2.9 - - + -
318A GLU* 3.1 32.9 + - + +
319A VAL* 3.8 30.1 - - + +
322A LYS* 4.1 16.6 - - + -
323A TYR* 4.1 17.0 - - + +
331A PHE* 5.2 3.1 - - + -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.4 47.4 - - + +
201A GLN* 5.9 3.7 - - - -
202A LYS 4.7 5.2 - - - +
203A LYS* 5.9 0.7 - - - -
247A PHE* 3.6 24.0 - - + -
278A PHE* 3.1 35.2 - - + +
280A VAL* 1.3 74.3 - - - +
282A VAL* 1.3 66.8 + - - +
285A THR* 2.9 28.9 + - - -
318A GLU* 3.3 1.0 - - - +
322A LYS* 3.0 33.0 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.9 11.7 - - - +
245A GLY* 3.6 14.4 - - - +
246A GLN 3.8 3.6 - - - +
247A PHE* 3.5 35.2 - - - +
250A LEU* 4.1 17.7 - - + +
272A PHE* 3.5 21.5 - - + +
278A PHE 2.9 13.8 + - - +
279A SER 3.2 5.8 + - - +
281A GLU* 1.3 77.1 - - - +
283A ILE* 1.3 64.0 + - - +
285A THR* 3.3 1.9 + - - -
286A LEU* 3.0 44.4 + - + +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 3.5 36.3 - - + -
273A VAL* 3.7 8.3 - - + -
279A SER 2.9 23.8 + - - +
280A VAL* 3.5 12.1 - - - +
282A VAL* 1.3 75.3 - - - +
284A LEU* 1.3 60.3 + - - +
286A LEU* 3.4 5.9 + - + +
287A PHE* 2.9 65.3 + - + -
299A LEU* 5.3 0.2 - - + -
315A PHE* 3.9 10.5 - - + -
331A PHE* 3.4 22.9 - - + -
335A PHE* 3.8 15.9 - - + -
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.1 9.8 - - + +
198A TYR* 3.3 28.0 - - + +
204A LEU* 4.5 5.6 - - + -
209A ALA* 4.0 29.4 - - + +
212A ILE* 4.4 19.7 - - + +
213A LEU* 4.3 17.0 - - + -
280A VAL* 3.1 29.1 + - + +
283A ILE* 1.3 76.0 - - - +
285A THR* 1.3 58.0 + - - +
287A PHE* 4.1 3.3 - - + +
288A GLY* 2.9 24.4 + - - -
323A TYR* 4.1 8.1 - - + +
331A PHE* 3.9 29.6 - - + -
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Residues in contact with THR 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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191A MET* 3.5 11.6 - - + +
194A LEU* 4.2 4.9 - - - +
195A MET* 4.0 17.2 - - + +
198A TYR* 3.6 11.6 - - - -
247A PHE* 3.5 14.0 - - + -
250A LEU* 4.1 20.0 - - + -
251A LEU* 5.5 0.4 - - + -
254A PHE* 4.2 4.7 - - + -
281A GLU 2.9 20.4 + - - -
282A VAL 3.7 3.1 - - - -
284A LEU* 1.3 77.9 - - - +
286A LEU* 1.3 63.2 + - - +
288A GLY 3.3 1.0 + - - -
289A PHE* 3.0 45.3 + - + -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 4.7 2.5 - - - +
250A LEU* 4.3 15.3 - - + -
254A PHE* 4.7 2.9 - - + -
268A PHE* 3.9 24.5 - - + -
272A PHE* 3.4 42.4 - - + -
282A VAL* 3.0 35.2 + - + +
283A ILE* 3.8 5.8 - - + +
285A THR* 1.3 78.9 - - - +
287A PHE* 1.3 57.1 + - - +
289A PHE* 3.4 1.1 + - + -
290A LYS* 3.0 24.8 + - - +
297A PHE* 3.4 33.4 - - + -
299A LEU* 4.0 15.7 - - + +
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.6 18.6 - - + -
213A LEU* 3.4 34.5 - - + -
216A VAL* 3.9 18.0 - - + +
220A LEU* 4.7 1.8 - - + -
272A PHE* 5.6 0.2 - + - -
283A ILE* 2.9 43.4 + - + +
284A LEU* 4.1 6.3 - - + +
286A LEU* 1.3 72.3 - - - +
288A GLY* 1.3 58.3 + - - +
290A LYS* 3.2 6.1 + - - +
291A LEU* 2.9 33.1 + - - +
299A LEU* 3.6 24.2 - - + -
331A PHE* 4.2 4.7 - + - -
334A VAL* 3.6 24.7 - - + -
335A PHE* 3.7 22.9 - + - -
338A LEU* 4.5 12.3 - - + -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 3.6 19.3 - - - +
191A MET* 3.6 23.8 - - - -
212A ILE* 4.1 8.5 - - - +
284A LEU 2.9 15.3 + - - -
285A THR 3.6 2.5 - - - -
287A PHE* 1.3 75.7 - - - +
289A PHE* 1.3 57.4 + - - +
291A LEU* 3.3 6.2 + - - +
292A LEU 3.0 21.8 + - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 5.7 3.6 - - + -
191A MET* 3.8 28.0 - - + +
195A MET* 3.8 20.6 - - + -
254A PHE* 3.7 26.7 - + - -
259A LEU* 3.9 24.9 - - + -
260A PRO* 3.6 26.5 - - + -
285A THR* 3.0 31.2 + - + +
288A GLY* 1.3 72.6 - - - +
290A LYS* 1.3 60.4 + - - +
292A LEU* 3.8 4.0 - - + +
293A TYR* 2.8 53.5 + + - +
297A PHE* 3.7 30.7 - + + +
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Residues in contact with LYS 290 (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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216A VAL* 3.8 20.9 - - + -
219A VAL* 4.2 16.4 - - + +
220A LEU* 4.1 23.8 - - + -
223A LEU* 4.3 15.3 - - - +
286A LEU 3.0 14.4 + - - +
287A PHE* 3.2 11.0 + - - +
289A PHE* 1.3 74.7 - - - +
291A LEU* 1.3 61.9 + - - +
294A PRO* 2.9 44.1 + - + +
297A PHE* 2.7 38.4 + - + +
298A HIS* 4.1 14.8 - - - +
299A LEU* 4.2 14.4 - - + +
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Residues in contact with LEU 291 (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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186A VAL* 3.8 28.3 - - + +
212A ILE* 3.7 39.9 - - + +
215A GLN* 3.7 46.2 - - + +
216A VAL* 3.8 11.2 - - + -
219A VAL* 3.8 15.3 - - + -
287A PHE 2.9 13.0 + - - +
288A GLY 3.5 7.2 - - - +
290A LYS* 1.3 76.6 - - - +
292A LEU* 1.3 61.2 + - - +
294A PRO* 3.6 12.3 - - - +
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Residues in contact with LEU 292 (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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185A LYS* 5.5 3.1 - - - -
186A VAL* 3.9 14.3 - - + +
187A THR* 3.7 26.5 - - - -
188A ILE* 3.8 24.2 - - + +
191A MET* 3.9 16.4 - - + -
288A GLY 3.0 15.5 + - - +
289A PHE* 3.2 10.3 + - + +
291A LEU* 1.3 77.7 - - - +
293A TYR* 1.3 103.1 + - + +
294A PRO* 3.5 6.0 - - - +
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Residues in contact with TYR 293 (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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188A ILE* 4.1 15.6 - - - +
260A PRO* 3.3 40.0 + - + -
261A SER* 3.8 9.2 - - - +
262A GLU* 3.6 43.6 + - + -
289A PHE* 2.8 28.5 + + + +
290A LYS 3.5 2.7 - - - -
292A LEU* 1.3 114.8 - - + +
294A PRO* 1.3 60.4 - - - +
295A ASP 3.2 2.5 - - - -
296A HIS* 2.9 30.3 + - + +
297A PHE* 2.9 19.4 + - + +
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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
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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