Contacts of the helix formed by residues 234 - 250 (chain F) in PDB entry 2W3S
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 GLN 234 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83F GLU* 5.7 2.4 + - - -
179F GLN* 3.5 16.9 - - - +
230F GLY* 3.2 28.7 + - - +
233F SER* 1.3 105.8 + - - +
235F GLY* 1.3 61.1 + - - +
236F ASN 3.0 1.6 + - - -
237F HIS* 3.5 23.0 + - - +
238F LEU* 4.0 9.4 - - - +
257F TYR* 5.1 1.4 + - - -
265F ILE 4.9 0.2 - - - +
266F THR* 3.4 19.6 - - + +
267F GLY* 2.7 30.8 + - - +
302F ASP* 3.5 10.1 + - - -
337F SER 4.4 2.9 + - - +
339F THR* 4.1 17.7 + - + +
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Residues in contact with GLY 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F GLN* 3.3 13.5 + - - -
180F ALA 6.4 0.2 - - - -
181F ALA* 5.3 1.0 - - - +
194F CYS* 6.3 1.1 - - - -
195F SER 4.9 9.0 - - - -
196F SER* 4.9 5.6 - - - -
202F ILE* 3.6 13.7 - - - +
231F LYS* 4.6 6.3 + - - +
233F SER* 3.0 4.2 + - - +
234F GLN* 1.3 77.1 - - - +
236F ASN* 1.3 62.2 + - - +
237F HIS 3.4 0.2 - - - -
238F LEU* 3.3 9.4 + - - +
239F ALA* 3.2 23.2 + - - +
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Residues in contact with ASN 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ALA* 3.2 31.9 - - + +
201F GLU* 3.3 23.6 - - - +
202F ILE* 3.5 32.5 - - - +
205F LYS* 3.5 28.3 - - - +
233F SER* 2.8 20.4 + - - +
235F GLY* 1.3 76.9 - - - +
237F HIS* 1.3 56.3 + - - +
239F ALA* 3.4 2.2 + - - +
240F ILE* 2.9 38.3 + - + +
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Residues in contact with HIS 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 4.0 10.8 - - + -
76F ALA* 3.2 28.7 - - + +
83F GLU* 3.7 21.9 + - - +
84F PRO 3.9 11.3 + - - -
85F VAL* 4.0 29.7 - - + +
97F PRO* 4.7 13.1 - - + +
233F SER 4.7 2.0 + - - -
234F GLN* 4.0 19.3 + - - +
235F GLY 3.4 0.8 - - - -
236F ASN* 1.3 78.0 - - - +
238F LEU* 1.3 61.8 + - - +
240F ILE* 4.0 1.4 - - - +
241F ALA* 3.0 24.6 + - - +
257F TYR* 3.8 17.7 - - - +
265F ILE* 5.5 6.3 - - + -
299F TRP* 5.5 3.4 - - - -
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Residues in contact with LEU 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F GLN* 3.6 20.4 - - + +
180F ALA* 3.5 21.8 - - - +
181F ALA* 3.7 13.0 - - + -
234F GLN 4.0 12.1 - - - +
235F GLY* 3.3 6.2 + - - +
237F HIS* 1.3 77.7 - - - +
239F ALA* 1.3 58.5 + - - +
241F ALA* 3.3 1.9 + - - +
242F CYS* 2.9 34.7 + - - -
255F MET* 3.3 40.6 - - + +
256F ARG* 4.0 2.9 - - - -
257F TYR* 3.3 46.9 - - + +
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Residues in contact with ALA 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ALA* 3.8 11.8 - - + +
192F ILE* 4.2 11.7 - - + +
194F CYS* 5.4 0.9 - - + -
202F ILE* 3.8 33.2 - - + -
205F LYS* 6.5 0.2 - - + -
206F VAL* 3.8 10.8 - - + +
235F GLY 3.2 14.8 + - - +
236F ASN* 3.7 3.8 - - - +
238F LEU* 1.3 77.3 - - - +
240F ILE* 1.3 64.6 + - - +
242F CYS* 3.9 2.5 - - - +
243F ALA* 3.1 25.1 + - - +
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Residues in contact with ILE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU* 5.2 7.6 - - + -
73F ASP 5.3 2.9 - - - +
75F ASP 4.0 4.7 - - - +
76F ALA* 3.8 15.7 - - + -
85F VAL* 3.6 38.8 - - + -
205F LYS* 4.0 35.0 - - + +
206F VAL* 4.4 4.0 - - + +
209F ALA* 3.7 21.8 - - + -
236F ASN 2.9 28.5 + - - +
237F HIS 4.0 2.2 - - - +
239F ALA* 1.3 75.7 - - - +
241F ALA* 1.3 70.9 + - - +
243F ALA* 3.2 5.1 + - - +
244F VAL* 2.9 25.5 + - + +
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Residues in contact with ALA 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 3.8 5.8 - - + -
37F PHE* 4.2 9.2 - - + -
70F LEU* 6.5 0.4 - - - -
85F VAL* 4.9 2.2 - - + +
100F LEU* 3.7 25.7 - - + +
237F HIS 3.0 20.1 + - - +
238F LEU 3.4 4.3 - - - +
240F ILE* 1.3 82.3 - - - +
242F CYS* 1.3 64.1 + - - +
244F VAL* 2.9 11.7 + - - +
245F ALA* 2.9 12.3 + - - +
255F MET* 3.9 20.2 - - - -
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Residues in contact with CYS 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 3.7 8.9 - - - +
181F ALA* 3.7 13.9 - - + -
182F LEU 4.5 1.3 - - - +
183F ALA* 3.6 12.6 - - + +
192F ILE* 5.3 0.4 - - + -
238F LEU 2.9 22.4 + - - +
239F ALA* 3.9 5.4 - - - +
241F ALA* 1.3 71.7 - - - +
243F ALA* 1.3 53.7 + - - +
245F ALA 3.3 0.2 + - - -
246F ALA* 2.8 37.1 + - - +
253F CYS* 3.2 29.7 - - - +
254F LYS 3.6 1.6 - - - -
255F MET* 3.3 35.4 - - - -
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Residues in contact with ALA 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ALA* 3.6 11.3 - - - +
190F VAL* 4.8 4.0 - - + +
192F ILE* 4.2 6.5 - - + -
206F VAL* 3.9 26.5 - - + -
209F ALA* 5.8 0.4 - - + -
210F LEU* 3.8 18.5 - - + +
239F ALA 3.1 19.0 + - - +
240F ILE* 3.4 5.4 - - - +
242F CYS* 1.3 73.4 - - - +
244F VAL* 1.3 58.5 + - + +
246F ALA* 3.1 2.8 + - - +
247F ARG* 2.8 30.7 + - - +
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Residues in contact with VAL 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 4.2 21.5 - - + -
69F ASP 4.9 0.9 - - - +
70F LEU* 3.9 31.2 - - + -
71F PRO* 4.2 17.9 - - + -
100F LEU* 5.5 3.4 - - + -
209F ALA* 4.1 23.6 - - + +
210F LEU* 4.1 19.1 - - + -
240F ILE* 2.9 22.3 + - + +
241F ALA* 2.9 4.0 + - - +
243F ALA* 1.3 73.0 - - - +
245F ALA* 1.3 63.0 + - - +
247F ARG* 3.3 3.4 + - - +
248F ALA* 2.9 23.7 + - + +
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Residues in contact with ALA 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 3.7 27.1 - - + -
65F PHE* 3.9 27.4 - - + -
100F LEU* 4.9 1.5 - - + +
102F ALA* 4.5 3.8 - - + -
241F ALA 2.9 7.2 + - - +
242F CYS 3.8 0.9 - - - +
244F VAL* 1.3 76.0 - - - +
246F ALA* 1.3 51.5 + - - +
248F ALA* 3.3 0.7 + - - -
249F THR* 2.6 43.9 + - + +
253F CYS* 3.4 19.1 - - - -
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Residues in contact with ALA 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ALA* 4.0 10.1 - - + -
185F PRO* 3.7 25.9 - - + +
190F VAL* 5.1 2.7 - - + -
242F CYS 2.8 18.4 + - - +
243F ALA* 3.6 3.6 - - - +
245F ALA* 1.3 74.7 - - - +
247F ARG* 1.3 64.9 + - - +
250F GLY* 2.9 26.2 + - - -
251F ARG 3.3 23.7 + - - +
253F CYS* 3.4 7.1 - - + -
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Residues in contact with ARG 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F PRO* 3.6 35.5 - - + +
72F HIS* 4.7 6.9 - - - -
185F PRO* 6.0 1.6 - - - -
190F VAL* 6.1 0.6 - - - +
210F LEU* 3.6 42.2 + - + -
243F ALA 2.8 16.1 + - - +
244F VAL* 3.4 8.4 + - - +
246F ALA* 1.3 74.8 - - - +
248F ALA* 1.3 71.5 + - - +
250F GLY* 3.6 6.1 + - - -
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Residues in contact with ALA 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F PHE* 3.6 30.3 - - + -
244F VAL* 2.9 17.3 + - + +
247F ARG* 1.3 89.5 - - - +
249F THR* 1.3 60.4 + - + +
250F GLY 3.6 0.3 + - - -
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Residues in contact with THR 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.7 20.9 - - + -
62F ILE* 4.1 16.2 - - + -
63F ALA* 4.3 16.8 - - + -
65F PHE* 5.0 1.8 - - + -
102F ALA* 5.0 3.4 - - + -
245F ALA 2.6 30.9 + - - +
248F ALA* 1.3 75.3 - - + +
250F GLY* 1.3 56.1 + - - +
251F ARG* 2.9 42.9 + - - +
253F CYS* 3.9 2.9 - - - -
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ASN* 5.3 1.6 + - - -
185F PRO* 4.0 14.6 - - - +
246F ALA 2.9 13.5 + - - -
247F ARG 3.6 4.9 + - - -
248F ALA 3.4 3.6 + - - -
249F THR* 1.3 74.6 - - - +
251F ARG* 1.3 57.9 + - - +
252F PRO* 4.4 2.1 - - - +
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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
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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