Contacts of the helix formed by residues 248 - 261 (chain B) in PDB entry 4CEV
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 4.1 9.0 - - + -
234B ASP* 3.9 22.9 + - + +
247B THR* 1.3 72.7 - - - +
249B ARG* 1.3 64.2 + - + +
251B SER* 3.2 4.9 + - - -
252B HIS* 3.0 60.3 + + - -
285B VAL* 3.8 40.6 - - + -
288B ALA* 3.8 11.5 - - + +
243C ILE* 3.3 36.4 - - + +
244C GLY* 4.0 28.0 - - - -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B THR* 3.3 7.4 + - - +
248B TYR* 1.3 79.9 - - + +
250B GLU* 1.3 60.5 + - + +
252B HIS* 3.1 2.4 + - - +
253B LEU* 2.9 26.5 + - - +
408B GAI 3.6 13.2 - - - +
195C MET* 3.1 24.6 - - - +
198C VAL* 3.9 8.5 + - - +
199C ASP* 2.9 46.6 + - - +
244C GLY* 4.0 19.5 - - - +
245C GLY 2.7 34.7 + - - -
246C LEU* 3.5 0.4 - - - +
247C THR* 3.9 9.1 - - - +
250C GLU* 2.7 42.2 + - - -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG* 2.8 37.7 + - - -
121B TYR* 4.1 1.8 - - - -
198B VAL* 3.7 9.9 - - - +
202B GLY* 6.0 0.2 - - - -
203B MET* 3.7 32.0 + - + +
246B LEU* 3.3 12.1 - - + +
247B THR* 2.8 42.6 + - - +
249B ARG* 1.3 76.0 - - + +
251B SER* 1.3 57.3 - - - +
253B LEU* 3.5 6.3 + - - +
254B ALA* 3.0 28.2 + - - +
199C ASP* 5.5 2.0 - - - +
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 2.9 25.0 + - - -
225B LEU* 5.9 0.2 - - - -
230B LEU* 3.2 24.4 - - - +
246B LEU* 4.3 1.2 - - - +
247B THR 3.0 14.3 + - - -
248B TYR 3.5 7.0 - - - -
250B GLU* 1.3 78.7 - - - +
252B HIS* 1.3 57.0 + - - +
254B ALA* 3.4 2.1 + - - +
255B MET* 3.0 33.8 + - - +
289B LEU* 3.5 27.6 - - - -
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.5 1.6 - - - -
248B TYR* 3.0 70.8 + + - +
249B ARG* 3.1 3.6 + - - +
251B SER* 1.3 72.7 - - - +
253B LEU* 1.3 61.2 + - - +
255B MET* 3.4 2.9 + - - +
256B GLU* 2.8 36.7 + - - +
288B ALA* 3.6 37.1 - - + +
289B LEU* 3.9 11.7 - - + +
292B SER* 2.9 19.4 + - - +
296B GLU* 6.1 0.2 - - - -
408B GAI 3.4 27.9 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B MET* 4.2 12.6 - - + -
204B THR* 3.5 38.4 - - - +
249B ARG 2.9 15.9 + - - +
250B GLU* 3.7 6.1 - - + +
252B HIS* 1.3 77.5 - - - +
254B ALA* 1.3 51.5 + - - +
256B GLU* 3.1 8.4 + - - +
257B MET* 2.8 44.6 + - - +
408B GAI 3.8 1.2 + - - -
196C HIS* 3.5 45.1 - - + +
199C ASP* 3.9 20.4 - - + +
200C ARG* 3.8 11.4 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 4.0 15.3 - - + +
203B MET* 4.5 2.5 - - + -
207B MET* 3.8 33.9 - - + +
250B GLU 3.0 18.1 + - - +
251B SER 3.6 5.2 - - - +
252B HIS 3.3 0.2 - - - -
253B LEU* 1.3 75.6 - - - +
255B MET* 1.3 70.7 + - + +
257B MET* 3.3 3.6 + - - +
258B LEU* 3.0 32.3 + - - +
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Residues in contact with MET 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 4.5 8.3 - - + -
223B LEU* 3.7 29.8 - - + -
225B LEU* 3.6 27.4 - - + -
251B SER 3.0 15.8 + - - +
252B HIS 3.7 0.7 - - - +
254B ALA* 1.3 92.1 - - + +
256B GLU* 1.3 58.1 + - - +
258B LEU* 3.3 13.4 + - + +
259B ALA* 3.0 28.9 + - - +
269B PHE* 4.6 3.4 - - - -
289B LEU* 3.5 31.2 - - + +
292B SER* 3.6 20.2 - - - -
293B LEU* 3.7 17.8 - - - +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B HIS* 2.8 26.0 + - - +
253B LEU* 3.5 4.4 - - - +
255B MET* 1.3 73.8 - - - +
257B MET* 1.3 60.6 + - - +
259B ALA* 3.5 7.4 + - - +
260B GLU* 3.1 22.3 + - - +
292B SER* 4.0 19.9 + - - -
296B GLU 4.7 11.0 - - - +
297B LYS* 5.4 1.8 - - + -
298B LEU* 4.3 15.2 + - - +
408B GAI 2.7 46.7 + - - -
196C HIS* 2.8 37.3 + - + +
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Residues in contact with MET 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR* 3.6 26.7 - - + +
207B MET* 3.9 20.9 - - + -
208B GLU* 3.7 17.9 - - + +
211B ILE* 3.5 21.0 - - + +
253B LEU* 2.8 44.6 + - - +
254B ALA 3.8 4.0 - - - +
256B GLU* 1.3 71.1 - - - +
258B LEU* 1.3 61.4 + - - +
260B GLU* 3.5 12.0 - - - +
261B ALA* 3.1 20.4 + - - +
196C HIS* 4.1 6.3 - - + -
200C ARG* 3.7 42.0 - - - +
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ILE* 3.6 21.8 - - + -
207B MET* 3.6 23.8 - - + -
211B ILE* 3.8 15.9 - - + -
223B LEU* 4.2 17.3 - - + -
254B ALA 3.0 19.0 + - - +
255B MET* 3.6 26.7 - - + +
257B MET* 1.3 75.6 - - - +
259B ALA* 1.3 66.2 + - - +
261B ALA* 3.1 4.1 + - - +
262B GLN* 3.0 19.8 + - - -
263B ILE* 4.0 13.9 + - + +
264B ILE* 4.0 29.3 + - + +
293B LEU* 4.3 4.7 - - + -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B MET 3.0 10.3 + - - +
256B GLU* 3.6 6.7 - - - +
258B LEU* 1.3 73.9 - - - +
260B GLU* 1.3 65.2 + - - +
262B GLN* 3.0 23.3 + - - +
292B SER 3.4 16.2 - - - +
293B LEU* 3.3 27.9 + - - +
295B GLY* 3.9 13.2 - - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ILE* 5.9 0.5 - - - +
256B GLU 3.1 14.2 + - - +
257B MET* 3.5 12.8 - - - +
259B ALA* 1.3 80.6 - - - +
261B ALA* 1.3 63.4 + - - +
262B GLN* 3.2 13.4 + - - +
196C HIS* 4.9 0.6 + - - -
200C ARG* 2.8 45.0 + - - -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ILE* 3.4 34.8 - - + -
215B LYS* 3.3 24.3 + - - +
257B MET 3.1 13.6 + - - +
258B LEU 3.1 5.6 + - - +
260B GLU* 1.3 78.2 - - - +
262B GLN* 1.3 72.2 + - - +
263B ILE* 3.3 9.5 + - + -
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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