Contacts of the helix formed by residues 236 - 255 (chain B) in PDB entry 2FRV
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 PRO 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B LEU 3.9 3.6 - - - +
235B ARG* 1.3 84.8 - - + +
237B GLU* 1.3 75.9 + - - +
239B ILE* 3.2 7.8 + - + +
240B ALA* 3.0 24.9 + - - +
433B GLU* 5.1 8.1 - - + +
436B VAL* 5.6 5.2 - - + -
437B LYS* 4.8 18.6 - - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ARG* 3.3 39.4 + - - +
236B PRO* 1.3 93.9 - - - +
238B ARG* 1.3 59.9 + - + +
240B ALA* 3.3 6.9 + - - +
241B GLU* 3.1 28.7 + - - +
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.1 29.5 + - - +
237A ASN* 3.6 23.6 - - - +
241A GLN* 4.0 9.2 + - - -
212B ILE* 3.4 43.7 - - + +
232B ASP* 3.6 13.9 + - - +
233B SER* 3.8 18.9 - - - +
235B ARG* 3.0 47.4 + - + +
237B GLU* 1.3 76.2 - - - +
239B ILE* 1.3 59.9 + - - +
241B GLU* 2.6 40.0 + - - +
242B PHE* 3.5 10.2 + - - +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 4.6 9.9 - - + -
233B SER 3.5 19.3 - - - +
234B LEU* 4.3 13.2 - - + +
235B ARG 3.1 10.4 + - - +
236B PRO* 3.2 6.0 + - + +
238B ARG* 1.3 73.5 - - - +
240B ALA* 1.3 59.7 + - - +
242B PHE* 3.6 5.9 + - - +
243B ARG* 2.9 47.1 + - - +
429B LEU* 4.1 13.0 - - + +
432B LEU* 3.6 33.9 - - + -
433B GLU* 3.7 38.4 - - + +
436B VAL* 5.3 2.7 - - + -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PRO 3.0 17.1 + - - +
237B GLU* 3.4 7.9 - - - +
239B ILE* 1.3 78.5 - - - +
241B GLU* 1.3 56.3 + - - +
243B ARG* 3.3 10.4 + - - +
244B LYS* 3.0 30.6 + - - +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.2 27.7 - - - +
208B ARG* 5.5 0.7 - - - -
212B ILE* 3.8 11.8 - - + +
237B GLU* 3.1 9.9 + - - +
238B ARG* 2.6 46.2 + - - +
240B ALA* 1.3 75.3 - - - +
242B PHE* 1.3 63.7 + - - +
244B LYS* 3.4 8.3 + - - +
245B LEU* 3.3 29.2 + - + +
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.2 10.5 - - + -
102B ALA* 4.8 11.7 - - + -
209B ALA* 3.2 39.1 - - + +
210B MET 4.7 0.4 - - - -
212B ILE* 3.8 15.0 - - + -
213B PHE* 3.1 33.2 - + + -
238B ARG 3.5 15.7 + - - +
239B ILE* 3.7 5.4 - - - +
241B GLU* 1.3 75.7 - - - +
243B ARG* 1.3 69.7 + - - +
245B LEU* 3.4 4.9 + - - +
246B TYR* 2.9 38.4 + + + +
425B VAL* 3.9 28.9 - - + -
429B LEU* 3.9 25.1 - - + -
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Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ILE* 2.9 28.6 + - - +
240B ALA* 3.5 9.4 - - - +
242B PHE* 1.3 83.1 - - - +
244B LYS* 1.3 53.6 + - - +
246B TYR* 3.3 5.4 - - + +
247B LYS* 3.1 54.2 + - + +
426B GLU* 3.4 19.8 + - - +
429B LEU* 3.4 28.3 - - + +
430B ASP* 2.9 26.4 + - - -
433B GLU* 3.0 35.2 + - - +
165E LYS* 5.9 1.0 - - - +
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Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ALA 3.0 12.4 + - - +
241B GLU* 3.4 12.3 - - - +
242B PHE 3.3 0.4 - - - -
243B ARG* 1.3 71.8 - - - +
245B LEU* 1.3 77.1 + - - +
247B LYS* 3.4 7.6 + - - +
248B GLU* 2.4 59.5 + - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LYS* 4.0 33.7 - - + +
208B ARG* 3.7 40.4 - - + +
209B ALA* 4.0 17.5 - - + +
212B ILE* 3.9 17.5 - - + -
241B GLU* 3.3 18.7 + - + +
242B PHE 3.8 4.5 - - - +
244B LYS* 1.3 83.0 - - - +
246B TYR* 1.3 67.3 + - - +
248B GLU* 3.2 16.2 + - - +
249B VAL* 2.9 29.4 + - - +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 4.0 22.9 - - + -
209B ALA* 4.8 4.6 - - + +
242B PHE* 2.9 31.4 + + + +
243B ARG* 3.3 15.3 - - + +
245B LEU* 1.3 77.8 - - - +
247B LYS* 1.3 66.2 + - + +
249B VAL* 3.3 5.4 + - - +
250B ARG* 2.7 54.7 + - + +
422B ALA 2.6 29.7 + - - -
425B VAL* 3.7 24.0 - - + -
426B GLU* 2.9 45.1 + - - +
429B LEU* 4.9 3.8 - - + -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ARG* 3.1 32.0 + - + +
244B LYS* 3.9 5.8 - - - +
245B LEU 3.3 0.2 - - - -
246B TYR* 1.3 83.1 - - + +
248B GLU* 1.3 66.4 + - - +
250B ARG* 3.1 6.4 + - - +
251B GLU* 3.0 41.5 + - - +
426B GLU* 3.9 25.6 - - - -
164E THR* 5.0 8.5 + - - -
165E LYS* 4.3 17.6 - - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL* 5.1 1.2 - - + +
205B LYS* 2.7 44.9 + - + +
244B LYS* 2.4 55.8 + - - +
245B LEU* 3.2 10.0 + - - +
247B LYS* 1.3 75.1 - - - +
249B VAL* 1.3 65.5 + - + +
251B GLU* 3.6 11.1 + - - +
252B PHE* 3.3 20.1 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 3.4 23.6 - - + -
109B LEU* 4.8 3.8 - - + -
202B VAL* 3.9 23.1 - - + -
205B LYS* 3.8 27.4 - - + -
206B ALA* 4.0 28.0 - - + +
209B ALA* 6.1 0.2 - - + -
245B LEU 2.9 18.6 + - - +
246B TYR* 3.9 4.0 - - - +
248B GLU* 1.3 77.9 - - + +
250B ARG* 1.3 66.1 + - - +
252B PHE* 3.2 4.5 + - - +
253B ILE* 3.1 29.6 + - + +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 3.7 10.7 - - + +
246B TYR* 2.7 51.1 + - + +
247B LYS* 3.1 7.2 + - - +
249B VAL* 1.3 72.8 - - - +
251B GLU* 1.3 62.3 + - + +
253B ILE* 3.1 13.8 + - - +
254B GLU* 2.9 52.2 + - + +
422B ALA* 4.0 21.0 + - + +
423B GLN* 3.5 34.4 + - - +
426B GLU* 4.0 5.3 + - - +
164E THR 5.7 0.2 + - - -
165E LYS* 3.2 28.5 + - - +
166E GLY* 4.6 7.7 - - - -
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LYS* 3.0 32.8 + - - +
248B GLU* 3.8 8.4 - - - +
250B ARG* 1.3 77.9 - - + +
252B PHE* 1.3 53.3 + - - +
254B GLU* 3.3 10.4 + - - +
255B GLN* 2.7 63.7 + - - +
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Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.4 34.8 - - + -
113B TYR* 3.9 10.8 - + - -
144B LYS* 4.0 3.4 - - - +
195B HIS 4.2 5.2 - - - -
198B GLU* 3.7 28.9 - - + -
199B ALA* 4.1 20.6 - - + -
202B VAL* 3.7 32.8 - - + -
248B GLU 3.3 9.9 + - - +
249B VAL 3.2 8.6 + - - +
251B GLU* 1.3 79.5 - - - +
253B ILE* 1.3 57.3 + - + +
255B GLN* 5.0 0.2 - - - -
256B VAL* 3.0 62.4 + - + -
257B TYR 3.0 9.7 + - - -
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 3.4 41.7 - - + +
109B LEU* 4.3 17.5 - - + -
249B VAL* 3.1 22.6 + - + +
250B ARG* 3.1 6.7 + - - +
252B PHE* 1.3 76.3 - - + +
254B GLU* 1.3 53.4 + - - +
257B TYR* 3.8 13.9 - - + -
258B ILE* 2.8 55.8 + - + +
418B CYS* 4.0 33.0 - - - -
419B LEU* 4.5 18.6 - - + -
422B ALA* 4.7 4.7 - - + -
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PRO* 5.8 0.3 - - - +
250B ARG* 2.9 56.9 + - + +
251B GLU* 3.6 11.5 - - - +
253B ILE* 1.3 80.2 - - + +
255B GLN* 1.3 66.3 + - + +
258B ILE* 4.1 10.3 - - - +
259B THR* 3.6 14.9 - - - +
419B LEU* 3.5 28.4 - - + +
423B GLN* 4.6 1.6 - - - +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B SER* 3.0 23.4 + - - -
143B PRO* 4.0 29.0 - - + +
144B LYS* 3.6 25.7 - - + +
251B GLU* 2.7 45.1 + - - +
252B PHE* 5.0 0.2 - - - -
254B GLU* 1.3 83.4 + - + +
256B VAL* 1.3 63.1 + - + +
259B THR* 2.9 17.0 + - - -
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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