Contacts of the helix formed by residues 231 - 246 (chain X) in PDB entry 3FKS
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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X LEU* 5.5 2.6 - - - +
49X GLU* 3.2 40.4 + - - +
51X ALA* 5.8 4.6 - - - +
62X ILE* 5.2 14.5 - - - +
64X MET* 4.2 7.9 - - - -
98X VAL* 3.5 16.2 - - + -
117X ILE* 4.6 8.3 - - + +
118X HIS* 3.5 21.0 - - - -
227X GLY 3.7 13.5 - - - +
228X ALA 3.4 1.4 + - - -
230X ALA* 1.3 96.4 + - - +
232X VAL* 1.3 59.9 + - - +
233X ALA 3.1 2.9 - - - -
234X LEU* 2.8 40.5 + - + +
235X THR* 3.0 11.8 + - - -
261X PHE* 5.0 6.5 - - - -
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Residues in contact with VAL 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X VAL* 3.3 21.0 - - + +
185X THR* 3.4 7.4 - - + +
186X GLY 4.5 1.6 - - - +
187X VAL* 3.9 22.7 - - + -
218X VAL* 3.5 24.7 - - + -
219X PHE 4.0 4.5 - - - +
220X GLY* 3.9 37.0 - - - +
228X ALA 3.1 18.9 + - - +
229X ARG* 4.3 8.3 - - - -
231X ARG* 1.3 72.4 - - - +
233X ALA* 1.3 63.2 + - - +
234X LEU 3.0 5.8 - - - -
235X THR* 3.5 2.2 - - - -
236X GLY 3.2 18.0 + - - -
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Residues in contact with ALA 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185X THR* 4.2 10.5 - - - +
187X VAL* 4.1 17.9 - - + -
229X ARG 5.1 1.6 - - - +
230X ALA 5.4 0.2 - - - +
231X ARG 3.1 1.5 - - - +
232X VAL* 1.3 80.6 - - + +
234X LEU* 1.3 59.3 + - + +
237X LEU* 3.1 23.3 + - - +
255X ILE* 5.3 7.2 - - + -
258X ILE* 5.7 2.5 - - + -
261X PHE* 4.7 15.5 - - + -
292X LEU* 3.8 28.8 - - + +
296X ILE* 5.9 0.7 - - - +
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Residues in contact with LEU 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X ILE* 3.9 17.5 - - + +
118X HIS* 3.9 16.4 - - + +
230X ALA 3.8 4.5 - - - +
231X ARG* 2.8 55.1 + - + +
233X ALA* 1.3 81.5 - - + +
235X THR* 1.3 56.7 + - - +
236X GLY 3.4 0.4 - - - -
237X LEU* 3.7 5.0 - - - +
238X THR* 2.7 34.5 + - - -
261X PHE* 5.2 3.4 - - + -
291X LEU 5.0 3.1 - - - +
292X LEU* 3.4 26.2 - - + -
295X ARG* 3.3 28.9 - - - +
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Residues in contact with THR 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X VAL* 3.6 24.1 - - + +
96X ILE* 4.7 7.6 - - + -
97X ASN 3.3 24.9 - - - +
98X VAL* 2.7 34.9 + - - +
117X ILE* 3.9 10.5 - - - +
218X VAL* 4.1 10.8 - - + -
231X ARG 3.0 3.3 + - - -
232X VAL* 3.2 9.8 + - - -
234X LEU* 1.3 79.9 - - - +
236X GLY* 1.3 60.9 + - - +
238X THR* 3.8 7.1 + - - -
239X ILE* 3.5 16.5 + - - +
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Residues in contact with GLY 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X VAL* 3.5 12.6 - - - +
185X THR* 3.9 20.6 + - - -
218X VAL* 3.7 24.8 - - - +
232X VAL 3.2 7.9 + - - -
235X THR* 1.3 77.3 - - - +
237X LEU* 1.3 63.6 + - - +
238X THR 3.4 0.2 - - - -
239X ILE* 3.4 17.9 + - - +
240X ALA* 3.6 3.1 + - - +
253X LEU* 4.7 1.3 - - - +
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Residues in contact with LEU 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X THR* 4.7 0.4 + - - -
233X ALA 3.1 18.4 + - - +
234X LEU* 3.5 5.6 + - - +
235X THR 3.3 0.4 - - - -
236X GLY* 1.3 76.5 - - - +
238X THR* 1.3 64.4 + - - +
239X ILE 3.2 0.5 + - - -
240X ALA* 3.2 5.8 + - + -
241X GLU* 3.1 34.5 + - + +
253X LEU* 4.0 18.8 - - + -
292X LEU* 3.5 42.2 - - + +
295X ARG* 3.7 33.7 - - + +
296X ILE* 3.4 25.8 - - + -
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Residues in contact with THR 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X VAL* 4.0 6.5 - - + +
87X VAL* 3.7 20.2 - - + -
115X LYS* 3.9 15.7 - - + +
116X PRO 3.4 18.3 + - - +
117X ILE* 3.3 20.6 + - - -
234X LEU 2.7 20.6 + - - -
235X THR 3.9 6.5 + - - -
237X LEU* 1.3 77.6 - - - +
239X ILE* 1.3 64.8 + - - +
241X GLU* 3.0 32.6 + - + +
242X TYR* 3.2 6.9 + - - +
295X ARG* 3.9 0.9 + - - +
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Residues in contact with ILE 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X VAL* 5.1 3.1 - - + -
86X PRO 3.3 26.5 - - - +
87X VAL* 4.0 14.6 - - + -
88X GLY 5.3 1.3 - - - +
91X THR* 4.1 15.5 - - + +
96X ILE* 4.3 13.2 - - + -
183X VAL* 3.8 16.2 - - + -
216X ALA* 4.5 7.4 - - + -
218X VAL* 4.6 9.6 - - + -
235X THR 3.5 18.4 - - - +
236X GLY* 3.4 13.9 - - - +
237X LEU 3.2 0.4 - - - -
238X THR* 1.3 75.6 - - - +
240X ALA* 1.3 59.2 + - - +
242X TYR* 3.0 17.9 + - - +
243X PHE* 3.0 40.1 - - + -
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Residues in contact with ALA 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183X VAL* 3.9 20.2 - - + -
236X GLY 3.6 3.5 + - - +
237X LEU* 3.2 10.5 + - + +
239X ILE* 1.3 78.7 - - - +
241X GLU* 1.3 57.5 + - - +
242X TYR 3.4 0.2 - - - -
243X PHE* 3.7 7.0 + - - +
244X ARG* 3.1 25.1 + - - +
251X VAL* 3.7 24.7 - - + +
253X LEU* 4.6 18.4 - - + -
304X VAL* 4.6 6.2 - - + +
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Residues in contact with GLU 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X ALA* 4.6 9.1 - - - +
237X LEU* 3.1 27.5 - - + +
238X THR* 3.0 23.8 + - + +
240X ALA* 1.3 77.9 - - - +
242X TYR* 1.3 63.3 + - - +
244X ARG* 3.4 31.7 + - - +
245X ASP* 3.1 27.6 + - - +
246X GLU* 5.4 0.3 - - - +
295X ARG* 2.8 49.3 + - - +
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Residues in contact with TYR 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X VAL* 3.5 40.5 + - + -
88X GLY* 3.7 27.8 - - - +
89X ARG* 5.1 2.2 - - + -
112X LYS* 4.9 15.8 - - - +
113X LEU* 4.7 16.0 - - + +
115X LYS* 4.2 19.1 - - + +
238X THR 3.2 2.9 + - - +
239X ILE 3.0 11.1 + - - +
241X GLU* 1.3 78.5 - - - +
243X PHE* 1.3 63.7 + + + +
246X GLU* 3.0 41.8 + - + +
247X GLU* 2.9 40.1 + - + -
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Residues in contact with PHE 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X GLY* 3.5 26.2 - - - -
89X ARG* 4.5 11.4 - - + -
91X THR* 4.7 0.4 - - - -
92X LEU* 4.0 22.4 - - + -
181X PHE* 3.4 48.5 - + + -
183X VAL* 4.5 8.5 - - + -
239X ILE* 3.0 47.7 + - + -
240X ALA* 4.0 5.6 - - - +
241X GLU 3.3 0.4 - - - -
242X TYR* 1.3 81.2 - + + +
244X ARG* 1.3 58.6 + - - +
247X GLU* 3.5 15.5 - - + +
248X GLY 3.2 3.3 + - - -
249X GLN* 3.1 29.4 + - + +
251X VAL* 3.6 21.0 - - + +
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Residues in contact with ARG 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X ASP 5.8 0.8 + - - -
122X PRO* 3.8 31.2 - - - +
240X ALA 3.1 18.1 + - - +
241X GLU* 3.4 29.9 + - - +
242X TYR 3.1 1.2 - - - -
243X PHE* 1.3 76.9 - - - +
245X ASP* 1.3 89.3 + - - +
248X GLY* 3.3 15.9 - - - -
251X VAL* 4.2 4.7 - - - -
295X ARG* 3.4 23.1 + - - +
297X THR* 3.8 23.0 + - - +
299X THR* 3.9 9.4 - - - +
301X LYS 3.8 0.2 - - - -
302X GLY* 3.1 46.7 + - - +
304X VAL* 3.9 11.4 - - + -
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Residues in contact with ASP 245 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241X GLU* 3.1 9.1 + - - +
244X ARG* 1.3 114.1 + - - +
246X GLU* 1.3 75.4 + - + +
248X GLY* 3.9 4.9 + - - -
299X THR* 3.5 7.8 + - - +
301X LYS* 3.1 44.2 + - + +
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Residues in contact with GLU 246 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X LYS* 3.9 26.6 + - - +
241X GLU 5.4 0.2 - - - +
242X TYR* 3.0 37.1 + - + +
245X ASP* 1.3 85.9 - - + +
247X GLU* 1.3 64.0 + - - +
248X GLY* 3.5 0.3 + - - -
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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