Contacts of the helix formed by residues 248 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D LEU* 4.3 8.5 - - + -
234D ASP* 3.9 22.7 - - + +
247D THR* 1.3 72.8 - - - +
249D ARG* 1.3 61.5 + - + +
251D SER* 3.3 4.5 + - - -
252D HIS* 3.0 64.4 + + - -
285D VAL* 3.8 41.5 - - + -
288D ALA* 3.8 11.0 - - + +
243E ILE* 3.3 35.4 - - + +
244E GLY* 4.1 25.8 - - - -
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Residues in contact with ARG 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D THR* 3.3 6.8 + - - +
248D TYR* 1.3 79.3 - - + +
250D GLU* 1.3 59.8 + - + +
252D HIS* 3.2 1.6 + - - +
253D LEU* 2.9 26.0 + - - +
410D GAI 3.8 15.0 - - - +
195E MET* 3.1 24.0 - - - +
198E VAL* 3.8 12.3 + - - +
199E ASP* 2.8 46.0 + - - +
244E GLY* 4.3 16.8 - - - +
245E GLY 2.9 25.3 + - - -
246E LEU* 3.7 0.6 - - - +
247E THR* 3.9 11.2 - - - +
250E GLU* 2.8 42.4 + - - -
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Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 4.0 1.8 - - - -
198D VAL* 3.8 10.3 - - - +
203D MET* 3.6 34.0 + - + +
246D LEU* 3.3 14.0 - - + +
247D THR* 3.0 32.8 + - - +
249D ARG* 1.3 76.3 - - + +
251D SER* 1.3 58.1 + - - +
253D LEU* 3.5 4.5 + - - +
254D ALA* 3.0 28.9 + - - +
199E ASP* 5.5 1.3 - - - +
249F ARG* 2.9 43.7 + - - -
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Residues in contact with SER 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 2.9 24.1 + - - -
230D LEU* 3.3 25.0 - - - +
246D LEU* 4.3 1.7 - - - +
247D THR 3.0 18.3 + - - -
248D TYR 3.6 5.2 - - - -
250D GLU* 1.3 74.7 - - - +
252D HIS* 1.3 63.6 + - - +
254D ALA* 3.5 1.6 + - - +
255D MET* 3.0 29.3 + - - +
289D LEU* 3.6 25.8 - - - -
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Residues in contact with HIS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ARG* 5.5 1.6 - - - -
248D TYR* 3.0 70.1 + + - +
249D ARG 3.2 3.3 + - - +
251D SER* 1.3 73.0 - - - +
253D LEU* 1.3 55.9 + - - +
255D MET* 3.1 4.8 + - - +
256D GLU* 2.7 40.7 + - - +
288D ALA* 3.6 30.5 - - + +
289D LEU* 3.9 11.9 - - + +
292D SER* 3.0 24.8 + - - +
296D GLU* 6.1 0.2 - - - -
410D GAI 3.5 30.2 + - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D MET* 4.2 12.3 - - + -
204D THR* 3.4 35.9 - - - +
249D ARG 2.9 17.6 + - - +
250D GLU* 3.7 5.4 - - + +
252D HIS* 1.3 74.8 - - - +
254D ALA* 1.3 52.4 + - - +
256D GLU* 3.0 10.2 + - - +
257D MET* 2.8 46.1 + - - +
410D GAI 3.9 0.4 + - - -
196E HIS* 3.6 36.8 - - + +
199E ASP* 3.7 22.2 - - + +
200E ARG* 3.7 21.3 - - + +
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 4.1 14.6 - - + +
203D MET* 4.5 3.1 - - - +
207D MET* 3.7 35.5 - - + +
250D GLU 3.0 18.5 + - - +
251D SER 3.6 4.9 - - - +
252D HIS 3.2 0.2 - - - -
253D LEU* 1.3 75.8 - - - +
255D MET* 1.3 75.0 + - + +
257D MET* 3.3 2.8 + - - +
258D LEU* 3.1 27.8 + - - +
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Residues in contact with MET 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 4.5 8.5 - - + -
223D LEU* 3.8 24.7 - - + -
225D LEU* 3.7 26.9 - - + -
251D SER 3.0 17.6 + - - +
252D HIS 3.6 5.6 - - - +
254D ALA* 1.3 88.9 - - + +
256D GLU* 1.3 58.4 + - - +
258D LEU* 3.4 20.1 + - + +
259D ALA* 3.1 27.9 + - - +
269D PHE* 4.6 3.1 - - - -
289D LEU* 3.5 27.4 - - + +
292D SER* 3.6 21.7 - - - +
293D LEU* 3.7 19.7 - - - +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D HIS* 2.7 20.2 + - - +
253D LEU* 3.4 8.4 - - - +
255D MET* 1.3 71.9 - - - +
257D MET* 1.3 62.0 + - - +
259D ALA* 3.6 3.4 + - - +
260D GLU* 3.3 22.3 + - - +
292D SER* 4.0 21.7 + - - -
296D GLU 4.7 11.3 - - - +
297D LYS* 5.4 2.2 - - + -
298D LEU* 4.4 11.6 + - - +
410D GAI 2.8 43.1 + - - -
196E HIS* 2.8 44.3 + - + +
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Residues in contact with MET 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D THR* 3.7 25.1 - - + +
207D MET* 3.7 20.9 - - + -
208D GLU* 3.8 17.9 - - + +
211D ILE* 3.4 15.6 - - + +
253D LEU* 2.8 46.7 + - + +
254D ALA 3.3 4.2 + - - +
256D GLU* 1.3 74.4 - - - +
258D LEU* 1.3 60.5 + - - +
260D GLU* 3.5 12.0 - - - +
261D ALA* 3.1 26.3 + - - +
196E HIS* 4.4 0.4 - - + -
200E ARG* 3.7 41.7 - - - +
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 3.8 21.3 - - + -
207D MET* 3.7 23.1 - - + -
211D ILE* 3.9 14.1 - - + -
223D LEU* 4.2 20.0 - - + -
254D ALA 3.1 15.3 + - - +
255D MET* 3.7 31.2 - - + +
256D GLU 3.3 0.2 - - - -
257D MET* 1.3 76.4 - - - +
259D ALA* 1.3 64.8 + - - +
261D ALA* 3.0 5.6 + - - +
262D GLN* 3.0 20.1 + - - -
263D ILE* 4.0 10.5 + - + +
264D ILE* 4.1 30.4 + - + +
293D LEU* 4.1 5.6 - - + -
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D MET 3.1 8.8 + - - +
256D GLU* 3.7 6.3 - - - +
257D MET 3.4 0.2 - - - -
258D LEU* 1.3 75.7 - - - +
260D GLU* 1.3 62.4 + - - +
262D GLN* 3.2 22.7 + - - +
292D SER 3.4 16.8 - - - +
293D LEU* 3.2 27.1 + - - +
295D GLY* 4.0 13.9 - - - +
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Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D GLU 3.3 13.8 + - - +
257D MET* 3.5 11.6 - - - +
259D ALA* 1.3 81.3 - - - +
261D ALA* 1.3 61.4 + - - +
262D GLN* 3.3 12.4 + - - +
196E HIS* 5.1 0.6 + - - -
200E ARG* 3.0 43.6 + - - -
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ILE* 3.4 35.4 - - + -
215D LYS* 3.3 23.1 + - - +
257D MET 3.1 14.4 + - - +
258D LEU 3.0 6.1 + - - +
260D GLU* 1.3 79.6 - - - +
262D GLN* 1.3 69.2 + - - +
263D ILE* 3.3 9.3 + - + +
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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