Contacts of the helix formed by residues 236 - 255 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234D LEU 3.9 3.3 - - - +
235D ARG* 1.3 85.0 - - + +
237D GLU* 1.3 77.8 + - - +
239D ILE* 3.2 7.8 + - + +
240D ALA* 3.0 25.5 + - - +
433D GLU* 5.1 8.1 - - + +
436D VAL* 5.6 4.9 - - + -
437D LYS* 4.8 17.5 - - + +
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Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG* 3.3 38.7 + - - +
236D PRO* 1.3 95.2 - - - +
238D ARG* 1.3 59.1 + - + +
240D ALA* 3.3 6.0 + - - +
241D GLU* 3.1 28.5 + - - +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C VAL* 3.1 29.9 + - - +
237C ASN* 3.6 23.0 - - - +
241C GLN* 4.0 9.0 + - - -
212D ILE* 3.4 44.7 - - + +
232D ASP* 3.6 13.3 + - - +
233D SER* 3.8 19.1 - - - +
235D ARG* 3.0 49.4 + - + +
237D GLU* 1.3 76.6 - - - +
239D ILE* 1.3 61.8 + - - +
241D GLU* 2.6 39.8 + - - +
242D PHE* 3.5 10.4 + - - +
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D PHE* 4.6 10.5 - - + -
233D SER 3.5 19.1 - - - +
234D LEU* 4.3 13.5 - - - +
235D ARG 3.1 10.4 + - - +
236D PRO* 3.2 5.6 + - + +
238D ARG* 1.3 75.0 - - - +
240D ALA* 1.3 59.9 + - - +
242D PHE* 3.6 6.3 + - - +
243D ARG* 2.9 47.6 + - - +
429D LEU* 4.1 12.8 - - + -
432D LEU* 3.6 34.3 - - + +
433D GLU* 3.7 38.8 - - + +
436D VAL* 5.3 2.5 - - + -
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D PRO 3.0 17.8 + - - +
237D GLU* 3.4 8.1 - - - +
239D ILE* 1.3 78.2 - - - +
241D GLU* 1.3 55.9 + - - +
243D ARG* 3.3 10.3 + - - +
244D LYS* 3.0 30.2 + - - +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C VAL* 3.2 27.7 - - - +
208D ARG* 5.5 0.3 - - - -
212D ILE* 3.8 11.5 - - + +
237D GLU* 3.1 9.3 + - - +
238D ARG* 2.6 47.9 + - - +
240D ALA* 1.3 76.3 - - - +
242D PHE* 1.3 65.2 + - - +
244D LYS* 3.4 8.8 + - - +
245D LEU* 3.3 29.6 + - + +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.2 10.8 - - + -
102D ALA* 4.8 11.2 - - + -
209D ALA* 3.2 39.6 - - + +
212D ILE* 3.8 15.0 - - + -
213D PHE* 3.2 32.5 - + + -
238D ARG 3.5 15.0 + - - +
239D ILE* 3.7 5.6 - - - +
240D ALA 3.3 0.2 - - - -
241D GLU* 1.3 76.3 - - - +
243D ARG* 1.3 72.3 + - - +
245D LEU* 3.4 4.1 + - - +
246D TYR* 2.9 37.4 + + + +
425D VAL* 3.9 29.4 - - + -
429D LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ILE* 2.9 30.5 + - - +
240D ALA* 3.3 10.3 + - - +
242D PHE* 1.3 81.6 - - - +
244D LYS* 1.3 53.0 + - - +
246D TYR* 3.3 5.7 - - + +
247D LYS* 3.1 54.2 + - + +
426D GLU* 3.4 19.2 + - - +
429D LEU* 3.4 28.8 - - + +
430D ASP* 2.9 25.3 + - - -
433D GLU* 3.0 34.8 + - - +
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Residues in contact with LYS 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ALA 3.0 13.1 + - - +
241D GLU* 3.4 12.8 - - - +
242D PHE 3.3 0.2 - - - -
243D ARG* 1.3 70.7 - - - +
245D LEU* 1.3 76.8 + - - +
247D LYS* 3.4 8.2 + - - +
248D GLU* 2.4 58.8 + - - +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LYS* 4.0 33.7 - - + +
208D ARG* 3.7 40.4 - - + +
209D ALA* 4.0 17.5 - - + +
212D ILE* 3.9 17.0 - - + -
241D GLU* 3.3 19.8 + - + +
242D PHE 3.8 5.2 - - - +
244D LYS* 1.3 83.8 - - - +
246D TYR* 1.3 66.4 + - - +
248D GLU* 3.2 16.2 + - - +
249D VAL* 2.9 29.5 + - - +
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Residues in contact with TYR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 4.0 22.2 - - + -
209D ALA* 4.8 5.5 - - + +
242D PHE* 2.9 32.6 + + + +
243D ARG* 3.3 15.3 - - + +
245D LEU* 1.3 76.3 - - - +
247D LYS* 1.3 64.7 + - + +
249D VAL* 3.3 4.5 + - - +
250D ARG* 2.7 59.1 + - + +
422D ALA 2.6 28.8 + - - -
425D VAL* 3.7 24.7 - - + -
426D GLU* 2.9 45.5 + - - -
429D LEU* 4.9 4.0 - - + -
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Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ARG* 3.1 31.4 + - + +
244D LYS* 3.9 6.7 - - - +
245D LEU 3.3 0.4 - - - -
246D TYR* 1.3 82.6 - - + +
248D GLU* 1.3 66.2 + - - +
250D ARG* 3.1 7.1 + - - +
251D GLU* 3.0 41.9 + - - +
426D GLU* 3.9 26.8 + - - -
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D VAL* 5.1 0.8 - - - +
205D LYS* 2.7 45.6 + - + +
244D LYS* 2.4 55.5 + - - +
245D LEU* 3.2 9.8 + - - +
247D LYS* 1.3 75.3 - - - +
249D VAL* 1.3 66.8 + - + +
251D GLU* 3.6 11.5 + - - +
252D PHE* 3.3 19.9 + - - +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 3.4 22.9 - - + +
109D LEU* 4.8 4.0 - - + -
202D VAL* 3.9 23.3 - - + -
205D LYS* 3.8 26.9 - - + -
206D ALA* 4.0 27.4 - - + +
209D ALA* 6.1 0.2 - - + -
245D LEU 2.9 18.7 + - - +
246D TYR* 3.9 4.3 - - - +
248D GLU* 1.3 78.4 - - + +
250D ARG* 1.3 64.4 + - - +
252D PHE* 3.2 4.3 + - - +
253D ILE* 3.1 30.0 + - + +
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Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 3.7 9.8 - - + +
246D TYR* 2.7 51.3 + - + +
247D LYS* 3.1 7.8 + - - +
249D VAL* 1.3 73.7 - - - +
251D GLU* 1.3 64.2 + - + +
253D ILE* 3.1 14.4 + - + +
254D GLU* 2.9 52.5 + - + +
422D ALA* 4.0 21.1 + - + +
423D GLN* 3.5 35.4 + - - +
426D GLU* 4.0 12.5 + - - +
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Residues in contact with GLU 251 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D LYS* 3.0 33.5 + - - +
248D GLU* 3.8 9.0 - - - +
250D ARG* 1.3 77.3 - - + +
252D PHE* 1.3 50.8 + - - +
254D GLU* 3.3 11.0 + - - +
255D GLN* 2.7 63.7 + - - +
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Residues in contact with PHE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 3.4 34.1 - - + -
113D TYR* 3.9 10.8 - + - -
144D LYS* 4.0 2.9 - - - +
195D HIS 4.2 4.9 - - - -
198D GLU* 3.7 29.8 - - + -
199D ALA* 4.1 20.9 - - + -
202D VAL* 3.7 33.4 - - + -
248D GLU 3.3 10.6 + - - +
249D VAL 3.2 8.4 + - - +
251D GLU* 1.3 80.2 - - - +
253D ILE* 1.3 56.2 + - - +
255D GLN* 5.0 0.2 - - - -
256D VAL* 3.0 62.1 + - + -
257D TYR 3.0 9.7 + - - -
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Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 3.4 42.4 - - + +
109D LEU* 4.3 18.2 - - + -
249D VAL* 3.1 22.2 + - + +
250D ARG* 3.1 6.7 + - - +
252D PHE* 1.3 76.5 - - + +
254D GLU* 1.3 54.3 + - + +
257D TYR* 3.8 13.0 - - + -
258D ILE* 2.8 55.0 + - + +
418D CYS* 4.0 32.8 - - - -
419D LEU* 4.5 19.1 - - + -
422D ALA* 4.7 4.3 - - + -
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ARG* 2.9 56.0 + - + +
251D GLU* 3.6 12.5 - - - +
253D ILE* 1.3 80.6 - - + +
255D GLN* 1.3 66.1 + - + +
258D ILE* 4.1 11.1 - - - +
259D THR* 3.6 14.9 - - - +
419D LEU* 3.5 28.8 - - + +
423D GLN* 4.6 1.7 - - - +
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Residues in contact with GLN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D SER* 3.0 23.6 + - - -
143D PRO* 4.0 29.0 - - + +
144D LYS* 3.6 26.3 - - + +
195D HIS* 5.9 0.2 - - - -
251D GLU* 2.7 44.3 + - - +
252D PHE* 5.0 0.2 - - - -
254D GLU* 1.3 82.5 + - + +
256D VAL* 1.3 63.5 + - + +
259D THR* 2.9 17.1 + - - +
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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