Contacts of the helix formed by residues 283 - 304 (chain A) in PDB entry 3HW2
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 SER 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LEU* 3.3 32.7 + - - +
277A VAL* 5.7 0.7 - - - -
280A PRO* 3.5 33.0 - - - +
281A SER* 3.0 3.7 - - - +
282A THR* 1.3 81.0 - - - +
284A GLN* 1.3 63.5 + - - +
285A SER* 3.0 7.7 + - - -
286A MET* 3.7 5.9 + - - +
287A LEU 3.9 1.0 + - - -
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Residues in contact with GLN 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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276A LEU* 4.8 3.3 - - + +
283A SER* 1.3 78.6 + - - +
285A SER* 1.3 64.5 + - - +
287A LEU* 3.8 27.9 - - + +
288A ALA* 3.7 18.6 + - + +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 5.2 7.4 + - - -
281A SER 3.7 5.0 + - - -
282A THR* 3.2 28.2 + - - -
283A SER* 3.0 1.9 + - - -
284A GLN* 1.3 81.3 + - - +
286A MET* 1.3 63.0 + - - +
287A LEU 3.4 0.2 + - - -
288A ALA* 3.8 9.1 + - - +
289A GLU* 4.1 7.6 + - - +
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Residues in contact with MET 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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138A LEU* 3.7 22.4 - - + -
141A HIS* 4.0 31.6 - - + +
143A GLN* 5.7 0.7 - - - -
144A MET* 3.4 39.3 - - + -
166A LEU* 4.5 2.0 - - + -
275A PHE* 3.5 33.0 - - + -
276A LEU* 6.0 1.3 - - + -
282A THR* 3.9 32.3 - - + +
283A SER 3.7 3.8 + - - +
285A SER* 1.3 77.7 - - - +
287A LEU* 1.3 61.9 + - - +
288A ALA 3.6 0.2 - - - -
289A GLU* 3.5 6.8 + - - +
290A ILE* 3.3 24.7 + - + +
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Residues in contact with LEU 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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263A LYS* 5.6 4.5 - - + -
266A LEU* 5.4 1.3 - - + -
272A PHE* 4.9 22.0 - - + -
276A LEU* 3.9 31.6 - - + +
283A SER 3.9 1.6 + - - -
284A GLN* 3.8 37.0 - - + +
285A SER 3.3 0.8 - - - -
286A MET* 1.3 74.3 - - - +
288A ALA* 1.3 63.4 + - + +
289A GLU 3.1 1.9 + - - -
290A ILE* 3.2 8.3 + - + +
291A VAL* 2.9 48.2 + - + +
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Residues in contact with ALA 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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263A LYS* 6.6 0.2 - - - +
284A GLN* 3.7 12.0 + - + +
285A SER 3.8 4.7 + - - +
286A MET 3.6 0.6 - - - -
287A LEU* 1.3 81.0 - - + +
289A GLU* 1.3 57.2 + - - +
291A VAL* 4.4 6.3 - - - +
292A GLU* 3.1 27.1 + - - +
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Residues in contact with GLU 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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137A ILE 3.1 25.7 - - - +
138A LEU* 3.6 18.8 - - + +
139A LYS 3.9 4.5 + - - -
140A SER* 3.6 26.4 + - - -
141A HIS* 4.6 9.4 + - + +
285A SER 4.1 5.8 + - - +
286A MET* 3.5 12.0 + - - +
287A LEU 3.1 0.8 - - - -
288A ALA* 1.3 76.4 - - - +
290A ILE* 1.3 58.1 + - - +
292A GLU* 3.0 13.0 + - - +
293A ALA* 2.6 40.0 + - + +
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Residues in contact with ILE 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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137A ILE* 4.7 6.5 - - + +
138A LEU* 3.5 38.6 - - + -
146A ALA* 5.2 1.1 - - + -
164A LEU* 3.8 16.4 - - + -
166A LEU* 4.0 18.6 - - + -
266A LEU* 4.7 8.7 - - + -
272A PHE* 4.4 21.3 - - + -
275A PHE* 4.9 1.8 - - + -
286A MET* 3.3 19.4 + - + +
287A LEU* 3.2 9.7 + - + +
289A GLU* 1.3 75.6 - - - +
291A VAL* 1.3 66.8 + - + +
293A ALA* 3.4 4.1 + - - +
294A ILE* 2.9 46.5 + - + +
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Residues in contact with VAL 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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259A GLU* 3.8 15.0 - - + +
262A VAL* 4.1 12.6 - - + +
263A LYS* 3.7 43.5 - - + +
266A LEU* 4.2 17.7 - - + -
287A LEU* 2.9 39.2 + - + +
288A ALA* 4.4 5.2 - - - +
290A ILE* 1.3 74.6 - - + +
292A GLU* 1.3 66.0 + - - +
294A ILE* 3.0 6.4 + - - +
295A SER* 2.9 28.0 + - - +
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Residues in contact with GLU 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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205A TYR* 5.2 2.0 - - - +
209A LYS* 2.6 30.5 + - - +
288A ALA 3.1 20.5 + - - +
289A GLU* 3.0 13.7 + - - +
291A VAL* 1.3 78.0 - - - +
293A ALA* 1.3 69.7 + - - +
295A SER* 2.9 21.8 + - - -
296A ASP* 3.0 26.8 + - - +
308A GLN* 3.7 8.4 + - - -
311A GLN* 5.0 1.4 - - - +
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Residues in contact with ALA 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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137A ILE* 4.0 38.8 - - + +
148A ILE* 4.4 5.0 - - - +
289A GLU* 2.6 24.0 + - + +
290A ILE 3.8 3.4 - - - +
292A GLU* 1.3 77.2 + - - +
294A ILE* 1.3 63.5 + - - +
296A ASP* 3.9 10.6 - - - +
297A GLN* 3.8 19.2 + - - +
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Residues in contact with ILE 294 (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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137A ILE* 5.0 2.0 - - + -
148A ILE* 4.2 22.4 - - + -
161A PRO* 4.4 9.4 - - + -
164A LEU* 4.2 15.0 - - + -
178A LEU* 4.8 12.8 - - + -
181A ILE* 4.2 10.5 - - + -
262A VAL* 3.8 30.1 - - + -
266A LEU* 4.5 4.7 - - + -
290A ILE* 2.9 38.4 + - + +
291A VAL 3.4 5.6 - - - +
293A ALA* 1.3 74.5 - - - +
295A SER* 1.3 68.2 + - - +
297A GLN* 2.9 16.7 + - - +
298A VAL* 3.1 29.2 + - + +
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Residues in contact with SER 295 (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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205A TYR* 3.4 25.1 - - - -
258A ILE* 4.4 18.3 - - - +
259A GLU* 3.8 22.1 - - - +
262A VAL* 4.2 6.4 - - - +
291A VAL* 2.9 18.7 + - - +
292A GLU* 2.9 12.6 + - - -
294A ILE* 1.3 71.4 - - - +
296A ASP* 1.3 52.6 + - - -
298A VAL* 3.1 4.4 + - - +
299A PHE* 2.6 36.9 + - - +
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Residues in contact with ASP 296 (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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205A TYR* 2.9 22.6 + - - -
209A LYS* 3.3 21.6 - - - -
292A GLU* 3.0 35.8 + - - +
293A ALA* 3.9 9.2 - - - +
294A ILE 3.1 0.2 + - - -
295A SER* 1.3 78.4 - - - +
297A GLN* 1.3 53.6 + - + +
299A PHE* 3.3 2.3 + - - +
300A HIS* 2.6 37.5 + - - +
306A ASP* 6.1 0.2 - - - +
307A PRO* 3.4 22.1 - - + +
308A GLN* 3.8 14.3 + - + -
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Residues in contact with GLN 297 (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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63A GLU* 4.4 15.6 - - - +
137A ILE* 4.7 8.5 - - - +
148A ILE* 3.7 29.2 - - - +
150A ARG* 2.9 44.5 + - - +
158A TYR* 5.8 0.2 - - - -
161A PRO* 3.8 13.6 - - + +
293A ALA 4.1 7.9 + - - +
294A ILE* 2.9 12.9 + - - +
296A ASP* 1.3 77.3 - - + +
298A VAL* 1.3 53.9 + - - +
300A HIS* 3.6 8.7 + - - +
301A ALA* 2.7 34.9 + - - +
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Residues in contact with VAL 298 (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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160A LEU* 3.9 15.5 - - + -
161A PRO* 3.6 24.5 - - + -
181A ILE* 4.2 23.1 - - + +
185A LEU* 5.6 4.7 - - + -
258A ILE* 3.9 22.4 - - + -
261A MET* 5.6 1.1 - - + -
262A VAL* 4.9 0.2 - - + -
294A ILE* 3.3 27.8 - - + +
295A SER* 3.1 5.8 + - - +
297A GLN* 1.3 71.8 - - - +
299A PHE* 1.3 65.9 + - - +
301A ALA* 3.3 9.0 - - - +
302A ILE* 3.2 31.1 + - + +
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Residues in contact with PHE 299 (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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201A GLU* 4.8 0.2 - - + -
202A LYS* 4.1 8.1 - - - -
205A TYR* 3.5 42.0 - + + -
206A LEU* 3.7 26.2 - - + -
258A ILE* 4.0 16.9 - - + +
295A SER 2.6 21.7 + - - +
296A ASP* 3.4 5.8 - - - +
298A VAL* 1.3 71.3 - - - +
300A HIS* 1.3 60.9 + - - +
302A ILE* 2.7 24.4 + - - +
303A PHE* 3.0 51.8 + + + -
305A ILE* 3.7 26.9 - - + -
307A PRO* 3.7 19.3 - - + -
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Residues in contact with HIS 300 (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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63A GLU* 3.9 26.6 + - + +
67A GLU* 2.6 33.1 + - + +
158A TYR* 3.6 31.9 - + - -
296A ASP 2.6 20.6 + - - +
297A GLN* 3.3 9.0 + - - +
299A PHE* 1.3 74.7 - - - +
301A ALA* 1.3 59.2 + - - +
304A ARG* 2.8 33.6 + - + +
305A ILE 3.2 43.1 - - - +
306A ASP* 4.0 6.9 - - + +
307A PRO* 4.3 3.4 - - + -
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Residues in contact with ALA 301 (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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156A VAL* 2.8 21.5 - - + +
158A TYR* 3.7 14.6 - - + +
159A PRO 3.5 23.3 - - - +
160A LEU* 3.7 18.8 - - + -
297A GLN 2.7 20.9 + - - +
298A VAL 3.3 9.0 - - - +
299A PHE 3.1 0.2 - - - -
300A HIS* 1.3 74.9 + - - +
302A ILE* 1.3 59.8 + - - +
304A ARG* 3.7 14.7 + - - -
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Residues in contact with ILE 302 (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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156A VAL* 3.6 25.2 - - + +
160A LEU* 5.6 0.9 - - + -
185A LEU* 3.8 24.5 - - + -
197A TRP* 3.8 25.1 - - + -
198A LYS* 3.8 33.3 + - + +
258A ILE* 4.6 9.2 - - + -
261A MET* 6.3 0.4 - - + -
298A VAL* 3.2 18.4 + - + +
299A PHE 2.7 15.0 + - - +
301A ALA* 1.3 76.6 - - + +
303A PHE* 1.3 82.8 + - + +
304A ARG* 5.2 1.9 + - - +
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Residues in contact with PHE 303 (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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197A TRP* 4.7 2.2 - + - -
198A LYS* 3.3 44.4 - - + +
201A GLU* 4.3 11.7 - - + -
202A LYS* 3.4 37.9 - - + -
258A ILE* 5.0 0.2 - - + -
299A PHE* 3.0 50.5 + + + -
302A ILE* 1.3 96.6 - - + +
304A ARG* 1.3 70.1 + - - +
305A ILE* 3.6 25.7 + - + +
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Residues in contact with ARG 304 (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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67A GLU* 4.4 13.8 - - + +
70A PHE* 3.5 28.0 + - - +
74A GLU* 6.4 0.2 - - - +
156A VAL 2.9 14.1 + - - -
157A ASP* 2.5 33.3 + - - +
158A TYR* 2.8 40.2 - - + +
300A HIS* 2.8 43.3 + - + +
301A ALA 3.7 6.5 + - - +
302A ILE 5.2 1.9 + - - +
303A PHE* 1.3 81.3 - - - +
305A ILE* 1.3 60.1 + - - +
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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
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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