Contacts of the helix formed by residues 248 - 261 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ILE* 3.2 35.3 - - + +
244A GLY* 4.0 27.4 - - - -
230C LEU* 4.2 8.3 - - + -
234C ASP* 3.7 22.5 + - + +
247C THR* 1.3 73.2 - - - +
249C ARG* 1.3 60.7 + - + +
251C SER* 3.2 4.9 + - - -
252C HIS* 3.0 65.8 + + - -
285C VAL* 3.9 41.1 - - + -
288C ALA* 3.8 11.7 - - + +
289C LEU* 5.5 0.2 - - + -
409C GAI 6.1 1.1 - - - -
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Residues in contact with ARG 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 3.2 21.7 - - - +
198A VAL* 3.8 9.7 + - - +
199A ASP* 2.8 43.5 + - - +
244A GLY* 4.2 17.7 - - - +
245A GLY 2.7 35.6 + - - -
246A LEU* 3.7 0.6 - - - +
247A THR* 3.8 12.4 - - - +
250A GLU* 2.8 42.8 + - - -
247C THR* 3.3 7.4 + - - +
248C TYR* 1.3 79.3 - - + +
250C GLU* 1.3 59.5 + - + +
252C HIS* 3.2 2.6 + - - +
253C LEU* 2.9 29.8 + - - +
409C GAI 3.9 13.2 - - - +
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASP* 5.6 1.3 - - - +
249B ARG* 2.7 36.5 + - - -
121C TYR* 4.0 1.8 - - - -
198C VAL* 3.9 10.2 - - - +
203C MET* 3.7 33.5 + - + +
246C LEU* 3.2 11.7 - - + +
247C THR* 2.9 41.6 + - - +
248C TYR 3.4 0.2 - - - -
249C ARG* 1.3 75.3 - - + +
251C SER* 1.3 57.8 + - - +
253C LEU* 3.5 4.8 + - + +
254C ALA* 3.0 29.5 + - - +
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Residues in contact with SER 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 2.9 23.5 + - - -
230C LEU* 3.2 22.7 - - - +
246C LEU* 4.3 1.7 - - - +
247C THR 2.9 15.3 + - - -
248C TYR 3.2 9.8 + - - -
250C GLU* 1.3 73.7 - - - +
252C HIS* 1.3 63.4 + - - +
254C ALA* 3.4 2.4 + - - +
255C MET* 3.1 28.9 + - - +
289C LEU* 3.5 26.0 - - - -
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Residues in contact with HIS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 5.5 1.1 - - - -
248C TYR* 3.0 70.8 + + - -
249C ARG* 3.2 3.8 + - - +
251C SER* 1.3 73.7 - - - +
253C LEU* 1.3 60.4 + - - +
255C MET* 3.2 3.8 + - - +
256C GLU* 2.8 35.5 + - - +
288C ALA* 3.5 38.7 - - + +
289C LEU* 3.8 11.7 - - + +
292C SER* 2.9 20.0 + - - +
409C GAI 3.4 28.9 + - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 3.6 36.1 - - + +
199A ASP* 3.7 21.5 - - + +
200A ARG* 3.8 20.0 - - + +
203C MET* 4.2 13.0 - - + -
204C THR* 3.4 38.4 - - - +
249C ARG 2.9 16.1 + - - +
250C GLU* 3.7 5.2 - - - +
252C HIS* 1.3 75.1 - - - +
254C ALA* 1.3 57.8 + - - +
256C GLU* 3.2 9.5 + - - +
257C MET* 2.8 46.5 + - + +
409C GAI 3.7 0.6 + - - -
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Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 4.0 13.9 - - + -
203C MET* 4.5 2.9 - - - +
207C MET* 3.9 35.8 - - + +
250C GLU 3.0 18.3 + - - +
251C SER 3.5 4.9 - - - +
253C LEU* 1.3 75.6 - - - +
255C MET* 1.3 77.1 + - + +
257C MET* 3.2 3.6 + - - +
258C LEU* 3.0 26.8 + - - +
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Residues in contact with MET 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 4.5 9.9 - - + -
223C LEU* 3.8 27.4 - - + -
225C LEU* 3.6 27.8 - - + -
251C SER* 3.1 16.9 + - - +
252C HIS 3.7 0.2 - - - +
254C ALA* 1.3 92.8 - - + +
256C GLU* 1.3 57.2 + - - +
258C LEU* 3.2 14.7 + - + +
259C ALA* 2.9 30.5 + - - +
269C PHE* 4.6 3.4 - - - -
289C LEU* 3.4 29.2 - - + +
292C SER* 3.6 23.6 - - - +
293C LEU* 3.7 17.1 - - - +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 2.9 41.1 + - + +
252C HIS* 2.8 19.5 + - - +
253C LEU* 3.4 7.9 - - - +
255C MET* 1.3 77.0 - - - +
257C MET* 1.3 57.3 + - - +
259C ALA* 3.6 3.0 + - - +
260C GLU* 3.2 25.6 + - - +
292C SER* 4.0 22.2 + - - -
296C GLU 4.8 10.8 - - - +
297C LYS* 5.4 2.2 - - + -
298C LEU* 4.3 11.8 + - - +
409C GAI 2.7 46.2 + - - -
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Residues in contact with MET 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 4.3 0.4 - - + -
200A ARG* 3.6 42.2 - - - +
204C THR* 3.8 28.9 - - + +
207C MET* 3.7 22.0 - - + -
208C GLU* 3.8 17.0 - - + +
211C ILE* 3.5 15.1 - - + +
253C LEU* 2.8 43.0 + - + +
254C ALA 3.8 4.0 - - - +
256C GLU* 1.3 75.4 - - - +
258C LEU* 1.3 59.8 + - - +
260C GLU* 3.5 12.8 - - - +
261C ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 3.7 24.9 - - + -
207C MET* 3.6 23.3 - - + -
211C ILE* 3.8 15.7 - - + -
223C LEU* 4.3 13.5 - - + -
254C ALA 3.0 14.5 + - - +
255C MET* 3.2 31.4 + - + +
257C MET* 1.3 75.0 - - - +
259C ALA* 1.3 66.4 + - - +
260C GLU 3.1 0.2 - - - -
261C ALA* 3.0 5.9 + - - +
262C GLN* 3.0 19.8 + - - -
263C ILE* 4.0 14.3 + - + +
264C ILE* 3.8 30.6 + - + +
293C LEU* 4.3 4.9 - - + -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C MET 2.9 9.8 + - - +
256C GLU* 3.7 6.1 - - - +
258C LEU* 1.3 75.6 - - - +
260C GLU* 1.3 64.9 + - - +
262C GLN* 3.1 22.3 + - - +
292C SER 3.4 16.4 - - - +
293C LEU* 3.2 26.4 + - - +
295C GLY* 3.9 13.2 - - - +
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Residues in contact with GLU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 5.0 0.5 + - - -
200A ARG* 2.9 43.2 + - - -
256C GLU 3.2 15.3 + - - +
257C MET* 3.5 11.0 - - - +
258C LEU 3.1 0.2 - - - -
259C ALA* 1.3 81.0 - - - +
261C ALA* 1.3 59.7 + - - +
262C GLN* 3.3 13.2 + - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ILE* 3.5 33.7 - - + -
215C LYS* 3.3 23.0 + - - +
257C MET 3.1 14.5 + - - +
258C LEU 3.0 9.3 + - - +
260C GLU* 1.3 73.6 - - - +
262C GLN* 1.3 72.6 + - - +
263C ILE* 3.3 11.7 + - + -
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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