Contacts of the helix formed by residues 236 - 255 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234L LEU 4.2 3.1 - - - +
235L ARG* 1.3 85.6 - - + +
237L GLU* 1.3 76.8 + - - +
239L ILE* 3.2 8.9 + - + +
240L ALA* 3.0 25.6 + - - +
433L GLU* 5.1 7.8 - - + +
436L VAL* 5.6 5.6 - - + -
437L LYS* 4.8 18.2 - - + +
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Residues in contact with GLU 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L ARG* 3.3 39.5 + - - +
236L PRO* 1.3 96.5 - - - +
238L ARG* 1.3 60.4 + - + +
240L ALA* 3.3 6.5 + - - +
241L GLU* 3.1 28.6 + - - +
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Residues in contact with ARG 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212L ILE* 3.4 42.9 - - + +
232L ASP* 3.6 13.3 + - - +
233L SER* 3.8 19.0 - - - +
235L ARG* 3.0 47.8 + - + +
237L GLU* 1.3 76.4 - - - +
239L ILE* 1.3 59.8 + - - +
240L ALA 3.4 0.2 - - - -
241L GLU* 2.6 41.7 + - - +
242L PHE* 3.5 10.9 + - - +
236S VAL* 3.1 30.1 + - - +
237S ASN* 3.6 22.2 - - - +
241S GLN* 4.0 8.7 + - - -
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Residues in contact with ILE 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213L PHE* 4.6 9.9 - - + -
233L SER 3.5 19.3 - - - +
234L LEU* 4.3 13.9 - - + +
235L ARG 3.1 9.7 + - - +
236L PRO* 4.0 6.1 - - + +
238L ARG* 1.3 74.9 - - - +
240L ALA* 1.3 60.8 + - - +
242L PHE* 3.6 6.1 + - - +
243L ARG* 2.9 47.0 + - - +
429L LEU* 4.1 13.2 - - + +
432L LEU* 3.6 34.1 - - + -
433L GLU* 3.7 39.9 - - + +
436L VAL* 5.3 2.7 - - + -
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Residues in contact with ALA 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L PRO 3.0 16.8 + - - +
237L GLU* 3.4 8.1 - - - +
239L ILE* 1.3 80.1 - - - +
241L GLU* 1.3 55.1 + - - +
243L ARG* 3.3 10.9 + - - +
244L LYS* 3.0 29.8 + - - +
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Residues in contact with GLU 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L ARG* 5.5 0.5 - - - -
212L ILE* 3.8 13.1 - - + +
237L GLU* 3.1 9.1 + - - +
238L ARG* 2.6 45.9 + - - +
240L ALA* 1.3 76.8 - - - +
242L PHE* 1.3 63.5 + - - +
244L LYS* 3.4 9.1 + - - +
245L LEU* 3.3 30.1 + - + +
236S VAL* 3.2 27.4 - - - +
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Residues in contact with PHE 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L LEU* 4.2 10.8 - - + -
102L ALA* 4.8 11.2 - - + -
209L ALA* 3.2 39.8 - - + +
210L MET* 5.0 0.2 - - - -
212L ILE* 3.8 16.4 - - + -
213L PHE* 3.1 33.0 - + + -
238L ARG 3.5 15.0 + - - +
239L ILE* 3.7 5.2 - - - +
240L ALA 3.3 0.2 - - - -
241L GLU* 1.3 76.2 - - - +
243L ARG* 1.3 69.3 + - - +
245L LEU* 3.4 5.1 + - - +
246L TYR* 2.9 38.4 + + + +
425L VAL* 3.9 28.9 - - + -
429L LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L ILE* 2.9 29.6 + - - +
240L ALA* 3.3 9.4 + - - +
242L PHE* 1.3 81.6 - - - +
244L LYS* 1.3 55.0 + - - +
246L TYR* 3.3 5.5 - - + +
247L LYS* 3.1 56.0 + - + +
426L GLU* 3.4 18.3 + - - +
429L LEU* 3.4 30.4 - - + +
430L ASP* 2.9 25.6 + - - -
433L GLU* 3.0 34.8 + - - +
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Residues in contact with LYS 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L ALA 3.0 12.9 + - - +
241L GLU* 3.4 11.9 - - - +
243L ARG* 1.3 71.4 - - - +
245L LEU* 1.3 77.6 + - - +
247L LYS* 3.4 7.1 + - - +
248L GLU* 2.4 59.5 + - - +
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Residues in contact with LEU 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L LYS* 4.0 34.1 - - + +
208L ARG* 3.7 39.0 - - + +
209L ALA* 4.0 17.3 - - + +
212L ILE* 3.9 17.3 - - + -
241L GLU* 3.3 20.2 + - + +
242L PHE 3.8 4.0 - - - +
244L LYS* 1.3 84.3 - - - +
246L TYR* 1.3 66.7 + - - +
248L GLU* 3.2 15.7 + - - +
249L VAL* 2.9 30.2 + - - +
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Residues in contact with TYR 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L MET* 4.0 23.8 - - + -
209L ALA* 4.8 5.1 - - + +
242L PHE* 2.9 31.8 + + + +
243L ARG* 3.3 14.6 - - + +
245L LEU* 1.3 76.4 - - - +
247L LYS* 1.3 67.1 + - + +
249L VAL* 3.3 4.9 + - - +
250L ARG* 2.7 58.4 + - + +
422L ALA 2.6 29.5 + - - -
425L VAL* 3.7 23.6 - - + -
426L GLU* 2.9 45.2 + - - +
429L LEU* 4.9 3.8 - - + -
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Residues in contact with LYS 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243L ARG* 3.1 32.9 + - + +
244L LYS* 3.9 6.3 - - - +
245L LEU 3.3 0.2 - - - -
246L TYR* 1.3 82.6 - - + +
248L GLU* 1.3 66.6 - - - +
250L ARG* 3.1 6.8 + - - +
251L GLU* 3.0 40.9 + - - +
426L GLU* 3.9 26.7 + - - -
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Residues in contact with GLU 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L VAL* 5.1 1.2 - - - +
205L LYS* 2.7 45.1 + - + +
244L LYS* 2.4 54.2 + - - +
245L LEU* 3.6 8.5 - - - +
247L LYS* 1.3 76.8 - - - +
249L VAL* 1.3 67.1 + - + +
251L GLU* 3.6 10.9 + - - +
252L PHE* 3.3 19.9 + - - +
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Residues in contact with VAL 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L MET* 3.4 24.5 - - + -
109L LEU* 4.8 4.0 - - + -
202L VAL* 3.9 23.1 - - + -
205L LYS* 3.8 27.6 - - + -
206L ALA* 4.0 27.1 - - + +
209L ALA* 6.1 0.2 - - + -
245L LEU 2.9 19.1 + - - +
246L TYR* 3.9 3.8 - - - +
248L GLU* 1.3 78.3 - - + +
250L ARG* 1.3 64.1 + - - +
252L PHE* 3.2 4.3 + - - +
253L ILE* 3.1 29.8 + - + +
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Residues in contact with ARG 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L MET* 3.7 10.5 - - + +
246L TYR* 2.7 51.9 + - + +
247L LYS* 3.1 7.2 + - - +
249L VAL* 1.3 73.2 - - - +
251L GLU* 1.3 64.0 + - + +
253L ILE* 3.1 14.3 + - - +
254L GLU* 2.9 52.7 + - + +
422L ALA* 4.0 21.1 + - + +
423L GLN* 3.5 35.0 + - - +
426L GLU* 4.0 12.9 + - - +
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Residues in contact with GLU 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L LYS* 3.0 32.4 + - - +
248L GLU* 3.8 8.7 - - - +
250L ARG* 1.3 77.8 - - + +
252L PHE* 1.3 52.6 + - - +
254L GLU* 3.3 11.9 + - - +
255L GLN* 2.7 63.1 + - - +
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Residues in contact with PHE 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L LEU* 3.4 34.8 - - + -
113L TYR* 3.9 10.3 - + - -
144L LYS* 4.0 2.9 - - - +
195L HIS 4.2 5.8 - - - -
198L GLU* 3.7 29.2 - - + -
199L ALA* 4.1 20.4 - - + -
202L VAL* 3.7 32.1 - - + -
248L GLU 3.3 11.0 + - - +
249L VAL 3.2 8.9 + - - +
251L GLU* 1.3 80.5 - - - +
253L ILE* 1.3 57.3 + - - +
255L GLN* 5.0 0.2 - - - -
256L VAL* 3.0 63.2 + - + -
257L TYR 3.0 9.0 + - - -
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Residues in contact with ILE 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L MET* 3.4 42.4 - - + +
109L LEU* 4.3 18.2 - - + -
249L VAL* 3.1 21.2 + - + +
250L ARG* 3.1 6.7 + - - +
252L PHE* 1.3 77.1 - - + +
254L GLU* 1.3 53.6 + - - +
257L TYR* 3.8 13.5 - - + -
258L ILE* 2.8 56.2 + - + +
418L CYS* 4.0 33.7 - - - -
419L LEU* 4.5 18.2 - - + -
422L ALA* 4.7 3.6 - - + -
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Residues in contact with GLU 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L ARG* 2.9 57.7 + - + +
251L GLU* 3.6 12.1 - - - +
253L ILE* 1.3 81.2 - - + +
255L GLN* 1.3 66.3 + - + +
258L ILE* 4.1 10.7 - - - +
259L THR* 3.6 14.9 - - - +
419L LEU* 3.5 26.8 - - + +
423L GLN* 4.6 1.4 - - - +
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Residues in contact with GLN 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142L SER* 3.0 24.0 + - - -
143L PRO* 4.0 27.8 - - + +
144L LYS* 3.6 26.4 - - + +
195L HIS* 5.9 0.2 - - - -
251L GLU* 2.7 44.3 + - - +
254L GLU* 1.3 83.0 + - + +
256L VAL* 1.3 62.9 + - + +
259L THR* 2.9 16.9 + - - +
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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