Contacts of the helix formed by residues 236 - 255 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H LEU 3.9 3.6 - - - +
235H ARG* 1.3 84.1 - - + +
237H GLU* 1.3 77.1 + - - +
239H ILE* 3.2 8.1 + - + +
240H ALA* 3.0 26.1 + - - +
433H GLU* 5.1 7.8 - - + +
436H VAL* 5.6 5.6 - - + -
437H LYS* 4.8 17.7 - - - +
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Residues in contact with GLU 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H ARG* 3.3 39.5 + - - +
236H PRO* 1.3 96.1 - - - +
238H ARG* 1.3 59.7 + - + +
240H ALA* 3.3 7.3 + - - +
241H GLU* 3.1 29.1 + - - +
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Residues in contact with ARG 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G VAL* 3.1 30.5 + - - +
237G ASN* 3.6 23.0 - - - +
241G GLN* 4.0 9.0 + - - -
212H ILE* 3.4 43.5 - - + +
232H ASP* 3.6 12.7 + - - +
233H SER* 3.8 20.0 - - - +
235H ARG* 3.0 47.9 + - + +
237H GLU* 1.3 76.1 - - - +
239H ILE* 1.3 60.2 + - - +
241H GLU* 2.6 40.5 + - - +
242H PHE* 3.5 10.7 + - - +
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Residues in contact with ILE 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H PHE* 4.6 9.9 - - + -
233H SER 3.5 18.8 - - - +
234H LEU* 4.3 13.5 - - - +
235H ARG 3.1 9.7 + - - +
236H PRO* 4.0 5.2 - - + +
238H ARG* 1.3 75.1 - - - +
240H ALA* 1.3 61.8 + - - +
242H PHE* 3.7 6.2 - - - +
243H ARG* 2.9 46.7 + - - +
429H LEU* 4.1 13.6 - - + +
432H LEU* 3.6 34.8 - - + -
433H GLU* 3.7 40.2 - - + +
436H VAL* 5.3 2.0 - - + -
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PRO 3.0 16.6 + - - +
237H GLU* 3.4 7.9 - - - +
239H ILE* 1.3 79.2 - - - +
241H GLU* 1.3 56.0 + - - +
243H ARG* 3.3 10.7 + - - +
244H LYS* 3.0 29.3 + - - +
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Residues in contact with GLU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G VAL* 3.2 27.2 - - - +
208H ARG* 5.5 0.5 - - - -
212H ILE* 3.8 12.2 - - + +
237H GLU* 3.1 10.7 + - - +
238H ARG* 2.6 45.6 + - - +
240H ALA* 1.3 75.1 - - - +
242H PHE* 1.3 64.0 + - - +
244H LYS* 3.4 8.9 + - - +
245H LEU* 3.3 30.2 + - + +
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Residues in contact with PHE 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 4.2 11.0 - - + -
102H ALA* 4.8 10.8 - - + -
209H ALA* 3.2 39.2 - - + +
210H MET* 4.7 0.7 - - - -
212H ILE* 3.8 15.5 - - + -
213H PHE* 3.2 34.1 - + + -
238H ARG 3.5 16.0 + - - +
239H ILE* 3.7 5.4 - - - +
241H GLU* 1.3 75.5 - - - +
243H ARG* 1.3 69.1 + - - +
244H LYS 3.4 0.2 + - - -
245H LEU* 3.4 4.8 + - - +
246H TYR* 2.9 37.7 + + + +
425H VAL* 3.9 29.6 - - + -
429H LEU* 3.9 24.2 - - + -
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Residues in contact with ARG 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H ILE* 2.9 29.2 + - - +
240H ALA* 3.5 9.8 - - - +
242H PHE* 1.3 83.2 - - - +
244H LYS* 1.3 55.4 + - - +
246H TYR* 3.3 5.4 - - + +
247H LYS* 3.1 55.0 + - + +
426H GLU* 3.4 19.0 + - - +
429H LEU* 3.4 29.8 - - + +
430H ASP* 2.9 26.2 + - - -
433H GLU* 3.0 35.0 + - - +
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Residues in contact with LYS 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H ALA 3.0 13.3 + - - +
241H GLU* 3.4 12.6 - - - +
243H ARG* 1.3 71.5 - - - +
245H LEU* 1.3 76.9 + - - +
247H LYS* 3.4 7.1 + - - +
248H GLU* 2.4 59.8 + - - +
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Residues in contact with LEU 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H LYS* 4.0 34.1 - - + +
208H ARG* 3.7 39.5 - - + +
209H ALA* 4.0 17.7 - - + +
212H ILE* 3.9 17.3 - - + -
241H GLU* 3.3 19.6 + - + +
242H PHE 3.8 4.9 - - - +
244H LYS* 1.3 82.7 - - - +
246H TYR* 1.3 66.0 + - - +
248H GLU* 3.2 16.3 + - - +
249H VAL* 2.9 30.0 + - - +
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Residues in contact with TYR 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H MET* 4.0 22.2 - - + -
209H ALA* 4.8 5.3 - - + +
242H PHE* 2.9 32.2 + + + +
243H ARG* 3.3 15.3 - - + +
245H LEU* 1.3 76.0 - - - +
247H LYS* 1.3 67.1 + - + +
249H VAL* 3.3 5.4 + - - +
250H ARG* 2.7 54.2 + - + +
422H ALA 2.6 29.6 + - - -
425H VAL* 3.7 23.6 - - + -
426H GLU* 2.9 45.3 + - - +
429H LEU* 4.9 4.0 - - + -
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Residues in contact with LYS 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H ARG* 3.1 31.6 + - + +
244H LYS* 3.9 7.0 - - - +
245H LEU 3.3 0.2 - - - -
246H TYR* 1.3 82.4 - - + +
248H GLU* 1.3 65.2 + - - +
250H ARG* 3.1 6.7 + - + +
251H GLU* 3.0 41.3 + - - +
426H GLU* 3.9 26.1 + - - -
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Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H VAL* 5.1 1.3 - - - +
205H LYS* 2.7 44.4 + - + +
244H LYS* 2.4 54.3 + - - +
245H LEU* 3.2 9.2 + - - +
247H LYS* 1.3 75.3 - - - +
249H VAL* 1.3 66.7 + - + +
251H GLU* 3.6 11.0 + - - +
252H PHE* 3.3 20.3 + - - +
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Residues in contact with VAL 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H MET* 3.4 23.3 - - + -
109H LEU* 4.8 4.0 - - + -
202H VAL* 3.9 23.3 - - + -
205H LYS* 3.8 26.5 - - + -
206H ALA* 4.0 28.5 - - + +
209H ALA* 6.1 0.4 - - + -
245H LEU 2.9 18.2 + - - +
246H TYR* 3.9 4.0 - - - +
248H GLU* 1.3 77.7 - - + +
250H ARG* 1.3 63.7 + - - +
252H PHE* 3.2 4.0 + - - +
253H ILE* 3.1 29.8 + - + +
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Residues in contact with ARG 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H MET* 3.7 10.7 - - + +
246H TYR* 2.7 51.9 + - + +
247H LYS* 3.6 7.2 - - - +
249H VAL* 1.3 72.6 - - - +
251H GLU* 1.3 63.0 + - + +
253H ILE* 3.1 13.5 + - - +
254H GLU* 2.9 52.0 + - + +
422H ALA* 4.0 21.5 + - + +
423H GLN* 3.5 34.9 + - - +
426H GLU* 4.0 13.5 + - - +
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Residues in contact with GLU 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H LYS* 3.0 32.0 + - - +
248H GLU* 3.8 8.5 - - - +
250H ARG* 1.3 77.3 - - + +
252H PHE* 1.3 52.4 + - - +
254H GLU* 3.3 12.1 + - - +
255H GLN* 2.7 63.1 + - - +
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Residues in contact with PHE 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H LEU* 3.4 34.5 - - + -
113H TYR* 3.9 9.9 - + - -
144H LYS* 4.0 2.9 - - - +
195H HIS 4.2 5.4 - - - -
198H GLU* 3.7 29.6 - - - -
199H ALA* 4.1 20.4 - - + -
202H VAL* 3.7 32.5 - - + -
248H GLU 3.3 10.1 + - - +
249H VAL 3.2 8.2 + - - +
251H GLU* 1.3 79.3 - - - +
253H ILE* 1.3 55.9 + - - +
256H VAL* 3.0 62.8 + - + -
257H TYR 3.0 9.6 + - - -
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Residues in contact with ILE 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H MET* 3.4 42.6 - - + +
109H LEU* 4.3 17.7 - - + -
249H VAL* 3.1 21.6 + - + +
250H ARG* 3.1 6.0 + - - +
252H PHE* 1.3 77.4 - - + +
254H GLU* 1.3 53.8 + - - +
257H TYR* 3.8 14.1 - - + -
258H ILE* 2.8 54.9 + - + +
418H CYS* 4.0 32.1 - - - -
419H LEU* 4.5 18.6 - - + -
422H ALA* 4.7 4.7 - - + -
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Residues in contact with GLU 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H PRO* 5.8 0.2 - - - +
250H ARG* 2.9 57.0 + - + +
251H GLU* 3.6 12.8 - - - +
253H ILE* 1.3 81.1 - - + +
255H GLN* 1.3 65.9 + - + +
258H ILE* 4.1 10.9 - - - +
259H THR* 3.6 15.2 - - - +
419H LEU* 3.5 26.4 - - + +
423H GLN* 4.6 1.7 - - - +
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Residues in contact with GLN 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H SER* 3.0 23.9 + - - -
143H PRO* 4.0 28.1 - - + +
144H LYS* 3.6 27.4 - - + +
251H GLU* 2.7 44.0 + - - +
254H GLU* 1.3 81.9 + - + +
256H VAL* 1.3 63.4 + - + +
259H THR* 2.9 17.2 + - - -
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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
------------------------------------------------------------
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