Contacts of the helix formed by residues 248 - 261 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A LEU* 4.3 9.0 - - + -
234A ASP* 3.9 22.5 - - + +
247A THR* 1.3 73.1 - - - +
249A ARG* 1.3 65.2 + - + +
251A SER* 3.2 4.7 + - - -
252A HIS* 3.0 62.2 + + - -
285A VAL* 4.1 39.5 - - + -
288A ALA* 3.9 10.2 - - + +
289A LEU* 5.7 0.2 - - + -
407A GAI 5.9 0.9 - - - -
243B ILE* 3.3 36.0 - - + +
244B GLY* 4.0 28.3 - - - -
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR* 3.3 7.0 + - - +
248A TYR* 1.3 79.5 - - + +
250A GLU* 1.3 58.9 + - + +
252A HIS* 3.1 3.4 + - - +
253A LEU* 2.9 27.0 + - - +
407A GAI 3.6 13.9 - - - +
195B MET* 3.2 25.7 - - - +
198B VAL* 3.7 10.5 + - - +
199B ASP* 2.7 48.6 + - - +
244B GLY* 4.2 17.5 - - - +
245B GLY 2.9 26.4 + - - -
246B LEU* 3.8 0.2 - - - +
247B THR* 3.9 11.5 - - - +
250B GLU* 2.8 40.6 + - - -
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 4.0 2.0 - - - -
198A VAL* 3.8 10.2 - - - +
203A MET* 3.6 34.9 + - + +
246A LEU* 3.3 11.9 - - + +
247A THR* 2.9 33.6 + - - +
249A ARG* 1.3 76.4 - - + +
251A SER* 1.3 58.0 + - - +
253A LEU* 3.5 4.1 + - - +
254A ALA* 3.0 27.9 + - - +
199B ASP* 5.1 1.8 + - - +
249C ARG* 2.8 46.1 + - - -
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.0 22.8 + - - -
230A LEU* 3.2 23.6 - - - +
246A LEU* 4.3 1.4 - - - +
247A THR 2.9 15.1 + - - -
248A TYR 3.4 9.2 - - - -
250A GLU* 1.3 74.7 - - - +
252A HIS* 1.3 64.3 + - - +
254A ALA* 3.5 2.4 + - - +
255A MET* 3.1 29.3 + - - +
289A LEU* 3.5 26.2 - - - -
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Residues in contact with HIS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG* 5.5 1.6 - - - -
248A TYR* 3.0 69.4 + + - -
249A ARG* 3.1 6.5 + - - +
251A SER* 1.3 73.6 - - - +
253A LEU* 1.3 56.1 + - - +
255A MET* 3.2 3.8 + - - +
256A GLU* 2.7 41.1 + - - +
288A ALA* 3.5 31.2 - - + +
289A LEU* 3.9 11.1 - - + +
292A SER* 2.8 26.1 + - - +
296A GLU* 6.1 0.2 - - - -
407A GAI 3.5 25.7 + - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 4.4 10.8 - - + -
204A THR* 3.4 38.6 - - - +
249A ARG 2.9 16.7 + - - +
250A GLU* 3.7 5.8 - - - +
252A HIS* 1.3 75.3 - - - +
254A ALA* 1.3 54.0 + - - +
256A GLU* 3.2 8.4 + - - +
257A MET* 2.8 49.4 + - + +
407A GAI 4.1 0.6 + - - -
196B HIS* 3.4 47.6 - - + +
199B ASP* 3.7 23.1 - - + +
200B ARG* 3.9 7.2 - - + +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.0 15.0 - - + +
203A MET* 4.6 3.3 - - - +
207A MET* 3.9 34.5 - - + +
250A GLU 3.0 17.3 + - - +
251A SER 3.5 6.3 - - - +
253A LEU* 1.3 77.5 - - - +
255A MET* 1.3 75.1 + - + +
257A MET* 3.3 3.1 + - - +
258A LEU* 3.0 27.6 + - - +
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Residues in contact with MET 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.4 7.9 - - + -
223A LEU* 3.8 29.2 - - + -
225A LEU* 3.6 28.0 - - + -
251A SER 3.1 15.9 + - - +
252A HIS 3.6 0.4 - - - +
254A ALA* 1.3 93.1 - - + +
256A GLU* 1.3 57.1 + - - +
258A LEU* 3.3 14.5 + - + +
259A ALA* 2.9 28.9 + - - +
269A PHE* 4.6 4.0 - - - -
289A LEU* 3.5 30.1 - - + +
292A SER* 3.5 23.8 - - - +
293A LEU* 3.6 16.0 - - - +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A HIS* 2.7 22.9 + - - +
253A LEU* 3.4 8.5 - - - +
255A MET* 1.3 74.3 - - - +
257A MET* 1.3 56.0 + - - +
259A ALA* 3.3 8.7 + - - +
260A GLU* 3.1 28.3 + - - +
292A SER* 4.1 17.5 + - - -
296A GLU 4.8 11.2 - - - +
297A LYS* 5.4 2.7 - - + -
298A LEU* 4.3 12.0 + - - +
407A GAI 2.8 40.4 + - - -
196B HIS* 2.8 43.7 + - + +
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Residues in contact with MET 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A THR* 3.7 29.2 - - + +
207A MET* 3.8 22.0 - - + -
208A GLU* 3.7 18.4 - - + +
211A ILE* 3.5 20.8 - - + +
253A LEU* 2.8 39.7 + - + +
254A ALA 3.7 4.9 - - - +
256A GLU* 1.3 73.6 - - - +
258A LEU* 1.3 57.2 + - - +
260A GLU* 3.6 12.8 - - - +
261A ALA* 3.1 19.8 + - - +
196B HIS* 4.2 6.5 - - + -
200B ARG* 3.5 42.4 - - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 3.6 26.2 - - + -
207A MET* 3.6 24.0 - - + -
211A ILE* 3.7 15.7 - - + -
223A LEU* 4.1 12.8 - - + -
254A ALA 3.0 20.2 + - - +
255A MET* 3.7 25.6 - - + +
257A MET* 1.3 73.2 - - - +
259A ALA* 1.3 67.1 + - - +
261A ALA* 3.0 5.5 + - - +
262A GLN* 3.0 19.9 + - - -
263A ILE* 4.0 13.6 + - + +
264A ILE* 4.0 29.6 - - + +
293A LEU* 4.3 4.9 - - + -
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A MET 2.9 6.2 + - - +
256A GLU* 3.4 10.1 - - - +
258A LEU* 1.3 75.8 - - - +
260A GLU* 1.3 61.7 + - - +
262A GLN* 3.1 22.9 + - - +
292A SER 3.3 17.9 - - - +
293A LEU* 3.3 26.0 + - - +
295A GLY* 4.0 13.2 - - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLU 3.1 13.3 + - - +
257A MET* 3.6 11.7 - - - +
259A ALA* 1.3 79.6 - - - +
261A ALA* 1.3 61.8 + - - +
262A GLN* 3.3 12.7 + - - +
196B HIS* 4.9 1.5 + - - -
200B ARG* 3.0 43.1 + - - -
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.5 34.5 - - + -
215A LYS* 3.3 24.6 + - - +
257A MET 3.1 15.0 + - - +
258A LEU 3.0 8.8 + - - +
260A GLU* 1.3 75.1 - - - +
262A GLN* 1.3 71.9 + - - +
263A ILE* 3.3 11.5 + - + -
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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