Contacts of the helix formed by residues 236 - 255 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234J LEU 3.9 3.3 - - - +
235J ARG* 1.3 85.3 - - + +
237J GLU* 1.3 76.7 + - - +
239J ILE* 3.2 7.7 + - + +
240J ALA* 3.0 24.8 + - - +
433J GLU* 5.1 8.5 - - + +
436J VAL* 5.6 5.6 - - + -
437J LYS* 4.8 17.9 - - - +
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Residues in contact with GLU 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J ARG* 3.3 39.0 + - - +
236J PRO* 1.3 94.8 - - - +
238J ARG* 1.3 59.9 + - + +
240J ALA* 3.3 6.9 + - - +
241J GLU* 3.1 28.7 + - - +
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Residues in contact with ARG 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I VAL* 3.1 29.9 + - - +
237I ASN* 3.6 22.8 - - - +
241I GLN* 4.0 9.0 + - - -
212J ILE* 3.4 43.1 - - + +
232J ASP* 3.6 13.3 + - - +
233J SER* 3.8 19.1 - - - +
235J ARG* 3.0 48.6 + - + +
237J GLU* 1.3 77.7 - - - +
239J ILE* 1.3 60.1 + - - +
241J GLU* 2.6 41.3 + - - +
242J PHE* 3.5 10.7 + - - +
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Residues in contact with ILE 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J PHE* 4.6 9.9 - - + -
233J SER 3.5 18.8 - - - +
234J LEU* 4.3 13.7 - - + +
235J ARG 3.1 10.4 + - - +
236J PRO* 3.2 6.0 + - + +
238J ARG* 1.3 74.2 - - - +
240J ALA* 1.3 59.7 + - - +
242J PHE* 3.6 6.3 + - - +
243J ARG* 2.9 47.1 + - - +
429J LEU* 4.1 14.1 - - + -
432J LEU* 3.6 34.5 - - + +
433J GLU* 3.7 39.3 - - + +
436J VAL* 5.3 2.5 - - + -
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Residues in contact with ALA 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236J PRO 3.0 16.5 + - - +
237J GLU* 3.4 7.9 - - - +
239J ILE* 1.3 77.8 - - - +
241J GLU* 1.3 55.0 + - - +
243J ARG* 3.3 10.5 + - - +
244J LYS* 3.0 30.6 + - - +
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Residues in contact with GLU 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I VAL* 3.2 27.4 - - - +
208J ARG* 5.5 0.5 - - - -
212J ILE* 3.8 11.5 - - + +
237J GLU* 3.1 9.2 + - - +
238J ARG* 2.6 47.1 + - - +
240J ALA* 1.3 75.5 - - - +
242J PHE* 1.3 64.0 - - - +
244J LYS* 3.4 8.7 + - - +
245J LEU* 3.3 30.1 + - + +
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Residues in contact with PHE 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J LEU* 4.2 11.2 - - + -
102J ALA* 4.8 10.8 - - + -
209J ALA* 3.2 39.2 - - + +
210J MET* 5.0 0.2 - - - -
212J ILE* 3.8 15.3 - - + -
213J PHE* 3.1 32.5 - + + -
238J ARG 3.5 14.8 + - - +
239J ILE* 3.7 5.6 - - - +
241J GLU* 1.3 76.3 - - - +
243J ARG* 1.3 68.4 + - - +
245J LEU* 3.4 4.7 + - - +
246J TYR* 2.9 39.0 + + + +
425J VAL* 3.9 29.8 - - + -
429J LEU* 3.9 24.7 - - + -
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Residues in contact with ARG 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LYS* 5.9 1.4 - - - +
239J ILE* 2.9 29.4 + - - +
240J ALA* 3.3 9.8 + - - +
242J PHE* 1.3 83.8 - - - +
244J LYS* 1.3 54.3 + - - +
246J TYR* 3.3 5.9 - - + +
247J LYS* 3.1 53.6 + - + +
426J GLU* 3.4 18.8 + - - +
429J LEU* 3.4 29.6 - - + +
430J ASP* 2.9 26.0 + - - -
433J GLU* 3.0 35.0 + - - +
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Residues in contact with LYS 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LYS* 5.9 0.2 - - - +
240J ALA 3.0 13.1 + - - +
241J GLU* 3.4 12.6 - - - +
242J PHE 3.3 0.2 - - - -
243J ARG* 1.3 71.2 - - - +
245J LEU* 1.3 76.6 + - - +
247J LYS* 3.4 7.8 + - - +
248J GLU* 2.4 58.9 + - - +
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Residues in contact with LEU 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LYS* 4.0 34.8 - - + +
208J ARG* 3.7 39.3 - - + +
209J ALA* 4.0 16.6 - - + +
212J ILE* 3.9 17.5 - - + -
241J GLU* 3.3 19.4 + - + +
242J PHE 3.8 4.7 - - - +
244J LYS* 1.3 83.8 - - - +
246J TYR* 1.3 66.5 + - - +
248J GLU* 3.2 16.3 + - - +
249J VAL* 2.9 30.0 + - - +
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Residues in contact with TYR 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J MET* 4.0 22.2 - - + -
209J ALA* 4.8 4.9 - - + +
242J PHE* 2.9 31.6 + + + +
243J ARG* 3.3 15.0 - - + +
245J LEU* 1.3 76.4 - - - +
247J LYS* 1.3 66.6 + - + +
249J VAL* 3.3 5.4 + - - +
250J ARG* 2.7 57.3 + - + +
422J ALA 2.6 29.8 + - - -
425J VAL* 3.7 24.9 - - + -
426J GLU* 2.9 45.8 + - - +
429J LEU* 4.9 3.6 - - + -
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Residues in contact with LYS 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G THR* 4.9 8.9 + - - -
165G LYS* 4.2 17.9 - - - +
243J ARG* 3.1 31.7 + - + +
244J LYS* 3.9 6.5 - - - +
245J LEU 3.3 0.2 - - - -
246J TYR* 1.3 83.8 - - + +
248J GLU* 1.3 66.3 + - - +
250J ARG* 3.1 6.3 + - - +
251J GLU* 3.0 41.2 + - - +
426J GLU* 3.9 26.0 - - - -
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Residues in contact with GLU 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J VAL* 5.1 0.6 - - - +
205J LYS* 2.7 45.7 + - + +
244J LYS* 2.4 55.7 + - - +
245J LEU* 3.6 9.9 - - - +
247J LYS* 1.3 75.7 - - - +
249J VAL* 1.3 65.8 + - + +
251J GLU* 3.8 10.7 + - - +
252J PHE* 3.3 20.1 + - - +
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Residues in contact with VAL 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J MET* 3.4 24.2 - - + -
109J LEU* 4.8 3.8 - - + -
202J VAL* 3.9 22.0 - - + -
205J LYS* 3.8 26.9 - - + -
206J ALA* 4.0 28.5 - - + +
209J ALA* 6.1 0.2 - - + -
245J LEU 2.9 18.6 + - - +
246J TYR* 3.9 3.8 - - - +
248J GLU* 1.3 79.0 - - + +
250J ARG* 1.3 65.0 + - - +
252J PHE* 3.2 4.3 + - - +
253J ILE* 3.1 29.8 + - + +
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Residues in contact with ARG 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LYS* 3.2 27.3 + - - +
166G GLY* 4.6 7.7 - - - -
105J MET* 3.7 10.2 - - + +
246J TYR* 2.7 51.3 + - + +
247J LYS* 3.1 7.6 + - - +
249J VAL* 1.3 73.2 - - - +
251J GLU* 1.3 63.0 + - + +
253J ILE* 3.1 14.1 + - - +
254J GLU* 2.9 52.9 + - + +
422J ALA* 4.0 21.6 + - + +
423J GLN* 3.5 34.2 + - - +
426J GLU* 4.0 6.0 + - - -
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Residues in contact with GLU 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247J LYS* 3.0 33.0 + - - +
248J GLU* 3.8 8.7 + - - +
250J ARG* 1.3 77.3 - - + +
252J PHE* 1.3 51.7 + - - +
254J GLU* 3.3 10.4 + - - +
255J GLN* 2.7 64.3 + - - +
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Residues in contact with PHE 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J LEU* 3.4 35.2 - - + -
113J TYR* 3.9 11.0 - + - -
144J LYS* 4.0 2.9 - - - +
195J HIS 4.2 5.8 - - - -
198J GLU* 3.7 29.6 - - + -
199J ALA* 4.1 20.0 - - + -
202J VAL* 3.7 32.8 - - + -
248J GLU 3.3 10.8 + - - +
249J VAL 3.2 9.1 + - - +
251J GLU* 1.3 79.5 - - - +
253J ILE* 1.3 56.0 + - - +
255J GLN* 5.0 0.2 - - - -
256J VAL* 3.0 63.0 + - + -
257J TYR 3.0 9.2 + - - -
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Residues in contact with ILE 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J MET* 3.4 42.0 - - + +
109J LEU* 4.3 17.3 - - + -
249J VAL* 3.1 21.8 + - + +
250J ARG* 3.1 6.3 + - - +
252J PHE* 1.3 75.8 - - + +
254J GLU* 1.3 54.5 + - + +
255J GLN 3.4 0.2 - - - -
257J TYR* 3.8 13.5 - - + -
258J ILE* 2.8 55.5 + - + +
418J CYS* 4.0 33.4 - - - -
419J LEU* 4.5 18.6 - - + -
422J ALA* 4.7 4.7 - - + -
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Residues in contact with GLU 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250J ARG* 2.9 57.0 + - + +
251J GLU* 3.6 12.6 - - - +
253J ILE* 1.3 79.1 - - - +
255J GLN* 1.3 67.1 + - + +
258J ILE* 4.1 10.8 - - - +
259J THR* 3.6 14.6 - - - +
419J LEU* 3.5 28.5 - - + +
423J GLN* 4.6 1.6 - - - +
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Residues in contact with GLN 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J SER* 3.0 23.5 + - - -
143J PRO* 4.0 29.4 - - + +
144J LYS* 3.6 26.4 - - + +
195J HIS* 5.9 0.3 - - - -
251J GLU* 2.7 45.3 + - - +
254J GLU* 1.3 84.0 + - + +
256J VAL* 1.3 63.1 + - + +
259J THR* 2.9 16.8 + - - +
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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