Contacts of the helix formed by residues 248 - 261 (chain F) in PDB entry 5CEV
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 TYR 248 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243D ILE* 3.2 40.1 - - + +
244D GLY* 3.9 25.8 - - - -
230F LEU* 4.3 8.7 - - + -
234F ASP* 3.6 24.9 + - + +
247F THR* 1.3 75.3 - - - +
249F ARG* 1.3 63.5 + - + +
251F SER* 3.6 2.3 + - - -
252F HIS* 3.0 62.2 + + - -
285F VAL* 3.9 41.5 - - + -
288F ALA* 3.7 11.4 - - + +
289F LEU* 5.5 0.4 - - + -
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Residues in contact with ARG 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D MET* 3.4 19.7 - - - +
198D VAL* 3.9 7.7 - - - +
199D ASP* 2.8 42.6 + - - +
231D ASP* 5.8 0.2 - - - -
244D GLY* 4.0 19.1 - - - +
245D GLY 2.8 34.9 + - - -
247D THR* 3.6 14.7 - - - +
250D GLU* 2.9 40.4 + - - -
412D GAI 3.7 18.4 - - - +
247F THR* 3.3 7.6 + - - +
248F TYR* 1.3 78.9 - - + +
250F GLU* 1.3 65.8 + - + +
252F HIS* 3.1 2.9 + - - +
253F LEU* 2.9 19.9 + - - +
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Residues in contact with GLU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASP* 5.0 1.3 + - - +
249E ARG* 2.9 43.4 + - - -
121F TYR* 4.1 2.2 - - - -
198F VAL* 3.7 15.8 - - - +
202F GLY* 5.8 0.3 - - - -
203F MET* 3.7 32.2 + - + +
246F LEU* 3.4 8.3 - - + +
247F THR* 3.0 37.5 + - + +
249F ARG* 1.3 75.6 - - + +
251F SER* 1.3 57.3 + - - +
253F LEU* 3.3 8.4 + - - +
254F ALA* 2.9 27.9 + - - +
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Residues in contact with SER 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F TYR* 2.9 26.1 + - - -
230F LEU* 3.3 23.5 - - - +
246F LEU* 4.1 1.7 - - - +
247F THR 3.1 16.1 + - - -
248F TYR 3.8 5.2 - - - -
250F GLU* 1.3 75.3 - - - +
252F HIS* 1.3 64.7 + - - +
254F ALA* 3.4 2.5 + - - +
255F MET* 3.0 29.2 + - - +
289F LEU* 3.8 25.8 - - - -
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Residues in contact with HIS 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D GAI 3.5 29.3 + - - +
35F ARG* 5.5 1.8 - - - -
248F TYR* 3.0 66.0 + + - -
249F ARG 3.1 4.9 + - - +
251F SER* 1.3 72.6 - - - +
253F LEU* 1.3 61.2 + - - +
255F MET* 3.2 3.1 + - - +
256F GLU* 2.8 35.5 + - - +
288F ALA* 3.5 32.6 - - + +
289F LEU* 3.8 10.7 - - + +
292F SER* 2.8 26.5 + - - +
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Residues in contact with LEU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 3.7 41.1 - - + +
199D ASP* 3.7 24.5 - - + +
200D ARG* 3.9 10.8 - - + +
412D GAI 3.6 1.2 + - - -
203F MET* 4.3 11.2 - - + -
204F THR* 3.4 37.0 - - - +
249F ARG 2.9 12.7 + - - +
250F GLU* 3.5 9.0 - - - +
252F HIS* 1.3 76.0 - - - +
254F ALA* 1.3 53.4 + - - +
256F GLU* 3.1 8.9 + - - +
257F MET* 2.8 51.6 + - - +
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Residues in contact with ALA 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F TYR* 4.0 22.4 - - + +
203F MET* 4.6 2.7 - - - +
207F MET* 3.8 36.4 - - + +
250F GLU 2.9 14.9 + - - +
251F SER 3.5 9.2 - - - +
252F HIS 3.2 0.2 - - - -
253F LEU* 1.3 76.2 - - - +
255F MET* 1.3 63.5 + - + +
257F MET* 3.3 0.5 + - - -
258F LEU* 3.0 31.9 + - - +
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Residues in contact with MET 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F TYR* 4.5 7.9 - - + -
223F LEU* 3.8 23.8 - - + -
225F LEU* 3.5 28.7 - - + -
251F SER 3.0 20.3 + - - +
252F HIS 3.7 0.2 - - - +
254F ALA* 1.3 86.1 - - + +
256F GLU* 1.3 57.9 + - - +
258F LEU* 3.3 21.3 + - + +
259F ALA* 3.0 29.5 + - - +
269F PHE* 4.5 4.0 - - - -
289F LEU* 3.6 25.6 - - + +
292F SER* 3.6 23.8 - - - +
293F LEU* 3.7 19.9 - - - +
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Residues in contact with GLU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 2.8 37.1 + - + +
412D GAI 3.0 40.1 + - - -
252F HIS 2.8 18.6 + - - +
253F LEU* 3.5 4.9 - - - +
255F MET* 1.3 76.3 - - - +
257F MET* 1.3 58.4 + - - +
259F ALA* 3.5 3.2 + - - +
260F GLU* 3.0 27.2 + - - +
292F SER* 4.0 23.0 + - - +
296F GLU 4.5 13.9 - - - +
297F LYS* 5.2 3.6 - - + -
298F LEU* 4.3 14.4 + - - +
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Residues in contact with MET 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 4.4 0.7 - - + -
200D ARG* 3.9 33.0 - - - +
204F THR* 3.6 34.5 - - + +
207F MET* 3.8 22.0 - - + -
208F GLU* 3.6 20.4 - - + +
211F ILE* 3.5 16.0 - - + +
253F LEU* 2.8 45.3 + - + +
254F ALA 3.9 4.0 - - - +
256F GLU* 1.3 74.5 - - - +
258F LEU* 1.3 60.7 + - - +
260F GLU* 3.4 9.1 + - - +
261F ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ILE* 3.7 22.0 - - + -
121F TYR* 6.4 0.2 - - + -
207F MET* 3.4 25.6 - - + -
211F ILE* 4.0 13.2 - - + -
223F LEU* 4.2 17.9 - - + -
254F ALA 3.0 20.6 + - - +
255F MET* 3.7 26.7 - - + +
256F GLU 3.3 0.2 - - - -
257F MET* 1.3 74.8 - - - +
259F ALA* 1.3 63.9 + - - +
261F ALA* 3.3 5.0 + - - +
262F GLN* 3.0 17.8 + - - -
263F ILE* 3.9 11.5 + - + +
264F ILE* 4.0 32.8 + - + +
293F LEU* 4.1 5.6 - - + -
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Residues in contact with ALA 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F MET 3.0 15.9 + - - +
256F GLU* 3.7 5.4 - - - +
257F MET 3.3 0.2 - - - -
258F LEU* 1.3 78.2 - - - +
260F GLU* 1.3 63.1 + - - +
262F GLN* 3.0 21.8 + - - +
292F SER 3.5 10.8 - - - +
293F LEU* 3.2 27.1 + - - +
295F GLY* 4.0 12.8 - - - +
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Residues in contact with GLU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D HIS* 4.5 4.2 + - - -
200D ARG* 2.9 44.4 + - - -
256F GLU 3.0 18.2 + - - +
257F MET* 3.6 7.2 - - - +
259F ALA* 1.3 77.9 - - - +
261F ALA* 1.3 61.8 + - - +
262F GLN* 3.3 10.7 + - - +
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Residues in contact with ALA 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F ILE* 3.6 35.2 - - + -
215F LYS* 3.4 22.4 + - - +
257F MET 3.0 17.6 + - - +
258F LEU 3.7 5.4 - - - +
259F ALA 3.2 0.2 - - - -
260F GLU* 1.3 74.0 + - - +
262F GLN* 1.3 71.2 + - - +
263F ILE* 3.2 10.9 + - + +
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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
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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