Contacts of the helix formed by residues 231 - 246 (chain F) in PDB entry 6CP3
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 ARG 231 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 4.9 6.5 - - - +
49F GLU* 2.4 39.4 + - - +
51F ALA* 5.9 1.4 - - - +
62F ILE* 3.8 26.2 - - - +
64F MET* 3.7 17.0 - - + -
83F ILE* 5.2 0.4 - - + -
98F VAL* 4.1 7.4 - - + -
117F ILE* 4.4 10.3 - - + +
118F HIS* 3.8 11.5 - - - -
227F GLY 3.6 15.9 - - - +
228F ALA 3.1 3.0 + - - +
229F ARG 3.2 0.2 - - - -
230F ALA* 1.3 119.2 + - - +
232F VAL* 1.3 61.5 + - - +
233F ALA* 3.2 2.7 - - - -
234F LEU* 2.9 41.1 + - - +
235F THR* 3.1 12.5 + - - -
261F PHE* 5.1 2.6 - - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL* 3.7 20.2 - - + -
185F THR* 3.9 5.9 - - + +
186F GLY 4.3 3.8 - - - +
187F VAL* 3.7 24.9 - - + -
218F VAL* 4.0 12.7 - - + +
219F PHE 3.3 33.4 - - - +
220F GLY* 4.2 6.3 - - - +
228F ALA 2.9 18.3 + - - +
229F ARG* 3.8 14.8 - - - +
231F ARG* 1.3 76.8 - - - +
233F ALA* 1.3 64.6 + - - +
235F THR* 3.1 6.2 + - - -
236F GLY 3.1 18.2 + - - -
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Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F THR* 4.2 7.0 - - + -
187F VAL* 4.0 19.3 - - + -
229F ARG 5.0 0.2 + - - -
231F ARG 3.2 0.4 - - - +
232F VAL* 1.3 82.0 - - - +
234F LEU* 1.3 57.7 + - - +
236F GLY 3.5 0.7 + - - -
237F LEU* 2.9 28.1 + - - +
255F ILE* 5.0 8.7 - - + +
258F ILE* 4.5 10.3 - - + -
261F PHE* 4.5 10.8 - - + -
292F LEU* 3.9 31.2 - - + +
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Residues in contact with LEU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 4.1 16.4 - - + -
118F HIS* 3.5 33.0 - - + +
230F ALA 4.1 7.2 - - - +
231F ARG* 2.9 30.3 + - - +
233F ALA* 1.3 75.6 - - - +
235F THR* 1.3 57.0 + - - +
237F LEU* 3.4 19.1 - - + +
238F THR* 2.9 33.6 + - - -
261F PHE* 4.8 8.7 - - + -
291F LEU* 5.2 2.9 - - + +
292F LEU* 3.7 28.0 - - + -
295F ARG* 4.0 10.8 - - - +
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Residues in contact with THR 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 3.7 30.8 - - + +
96F ILE* 4.8 1.8 - - + -
97F ASN 4.1 13.2 - - - +
98F VAL* 3.2 22.1 + - - +
117F ILE* 4.0 13.0 - - - +
218F VAL* 3.7 22.0 - - + -
231F ARG 3.1 10.1 + - - -
232F VAL* 3.1 10.6 + - - -
234F LEU* 1.3 76.8 - - - +
236F GLY* 1.3 62.3 + - - +
238F THR* 3.2 3.6 + - - -
239F ILE* 3.1 24.8 + - + +
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Residues in contact with GLY 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F VAL* 3.8 8.7 - - - +
185F THR* 3.5 25.4 - - - -
218F VAL* 3.8 14.9 - - - +
232F VAL 3.1 12.4 + - - -
233F ALA 3.9 1.8 - - - -
235F THR* 1.3 76.4 - - - +
237F LEU* 1.3 56.9 + - - +
239F ILE 3.5 0.7 + - - -
240F ALA* 2.9 28.6 + - - +
253F LEU* 4.1 4.4 - - - +
255F ILE* 6.2 0.4 - - - -
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ALA 2.9 18.6 + - - +
234F LEU* 3.4 19.7 - - + +
236F GLY* 1.3 78.3 - - - +
238F THR* 1.3 57.1 + - - +
240F ALA* 3.1 6.7 + - + +
241F GLU* 2.8 33.0 + - + +
253F LEU* 5.0 4.2 - - - +
255F ILE* 5.9 0.6 - - - +
291F LEU 4.6 0.2 - - - +
292F LEU* 4.2 11.9 - - + +
295F ARG* 3.4 74.5 - - + +
296F ILE* 3.6 22.9 - - + -
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Residues in contact with THR 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 5.0 6.5 - - + -
87F VAL* 4.7 7.9 - - + -
115F LYS* 4.1 25.8 - - + +
116F PRO 3.8 17.0 - - - +
117F ILE* 3.3 28.0 + - + -
234F LEU 2.9 17.6 + - - -
235F THR 3.2 4.5 + - - -
237F LEU* 1.3 76.3 - - - +
239F ILE* 1.3 58.2 + - - +
241F GLU* 3.8 13.2 - - + +
242F TYR* 2.9 29.7 + - - +
295F ARG* 4.0 2.9 + - - -
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Residues in contact with ILE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 4.0 12.6 - - + -
86F PRO 4.0 17.0 - - - +
87F VAL* 5.0 6.3 - - + -
91F THR* 4.4 7.9 - - - +
96F ILE* 3.8 24.9 - - + -
183F VAL* 3.9 21.1 - - + -
216F ALA* 4.2 12.3 - - + -
218F VAL* 3.7 25.8 - - + -
235F THR* 3.1 12.4 + - + +
236F GLY 3.9 4.3 - - - +
238F THR* 1.3 76.8 - - - +
240F ALA* 1.3 62.3 + - - +
242F TYR* 3.6 4.8 + - - +
243F PHE* 3.2 42.7 + - + -
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Residues in contact with ALA 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F VAL* 4.3 4.9 - - + +
236F GLY 2.9 17.8 + - - +
237F LEU* 3.1 6.7 + - + +
239F ILE* 1.3 77.0 - - - +
241F GLU* 1.3 59.1 + - - +
242F TYR 3.3 0.3 + - - -
243F PHE* 3.3 7.0 + - - +
244F ARG* 3.0 24.1 + - - +
251F VAL* 3.9 23.4 - - + +
253F LEU* 4.0 31.4 - - + -
304F VAL* 5.3 5.6 - - + -
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Residues in contact with GLU 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ALA* 4.2 11.7 - - - +
120F ASP 5.1 3.8 - - - +
122F PRO* 5.4 1.6 - - - +
237F LEU* 2.8 22.7 + - + +
238F THR* 3.8 12.7 + - + +
240F ALA* 1.3 71.3 - - - +
242F TYR* 1.3 62.4 + - - +
244F ARG* 3.3 35.5 + - - +
245F ASP* 2.9 35.8 + - - +
295F ARG* 3.5 44.4 + - - +
304F VAL* 5.5 1.3 - - - -
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Residues in contact with TYR 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F VAL* 3.5 26.4 - - + +
88F GLY* 3.4 37.4 - - - -
112F LYS* 6.1 0.5 - - - +
113F LEU* 3.6 17.9 - - + +
115F LYS* 3.6 42.2 - - + +
238F THR 2.9 19.6 + - - +
239F ILE 3.8 5.6 - - - +
240F ALA 3.2 0.2 - - - -
241F GLU* 1.3 77.0 - - - +
243F PHE* 1.3 63.2 + + - +
245F ASP* 2.9 3.0 + - - -
246F GLU* 2.4 77.7 + - + +
247F GLU* 5.2 4.3 - - + -
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Residues in contact with PHE 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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88F GLY* 3.3 39.9 - - - -
89F ARG* 4.1 12.8 - - + -
91F THR* 4.5 0.4 - - - -
92F LEU* 4.0 22.9 - - + -
181F PHE* 3.9 37.2 - + + -
183F VAL* 4.8 9.9 - - + -
239F ILE* 3.2 37.9 - - + -
240F ALA 3.3 6.7 + - - +
242F TYR* 1.3 82.2 - + - +
244F ARG* 1.3 62.6 + - - +
245F ASP 3.2 0.2 - - - -
246F GLU 4.2 0.2 - - - -
247F GLU* 3.7 24.4 + - + +
248F GLY 3.4 18.5 + - - -
249F GLN* 3.7 9.3 + - + +
251F VAL* 3.9 15.9 - - + +
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Residues in contact with ARG 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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122F PRO* 4.0 13.7 - - - +
240F ALA 3.0 14.3 + - - +
241F GLU* 3.3 40.5 + - - +
242F TYR 3.1 0.6 - - - -
243F PHE* 1.3 79.7 - - - +
245F ASP* 1.3 89.4 + - - +
248F GLY 4.1 3.2 + - - -
249F GLN 5.2 0.7 - - - +
251F VAL* 3.9 6.0 - - + +
295F ARG 3.6 9.9 + - - -
297F THR* 3.1 34.8 + - - +
299F THR* 3.3 37.6 + - - +
301F LYS* 3.5 20.4 - - - +
302F GLY* 3.8 22.5 + - - +
303F SER 4.6 0.7 - - - +
304F VAL* 3.7 22.5 - - + +
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Residues in contact with ASP 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LYS* 5.5 7.4 - - - +
241F GLU* 2.9 22.2 + - - +
242F TYR* 2.9 3.8 + - - +
244F ARG* 1.3 109.4 + - - +
246F GLU* 1.3 65.6 + - - +
247F GLU 3.5 0.2 - - - -
248F GLY 4.6 1.7 + - - -
299F THR* 4.2 2.3 + - - +
301F LYS* 3.3 40.0 + - + +
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Residues in contact with GLU 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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113F LEU* 5.1 4.4 - - - +
115F LYS* 4.2 8.8 + - - -
242F TYR* 2.4 78.2 + - + +
245F ASP* 1.3 72.1 - - - +
247F GLU* 1.3 73.4 + - + +
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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