Contacts of the helix formed by residues 281 - 293 (chain E) 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 LYS 281 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233E SER 3.0 21.0 + - - -
234E ASP* 3.4 24.1 - - - +
236E PRO* 3.7 17.5 - - + -
277E ASP* 3.1 8.5 + - - +
278E GLU* 3.3 27.3 + - - +
279E ARG 3.1 4.3 + - - -
280E ASN* 1.3 77.3 - - - +
282E THR* 1.3 58.4 + - - +
284E SER* 3.3 8.4 - - - -
285E VAL* 3.0 34.2 + - + +
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Residues in contact with THR 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E LEU* 3.8 30.4 - - + +
235E ALA* 3.5 12.9 - - + +
236E PRO 3.5 8.1 - - - -
237E GLY* 2.7 44.8 + - - +
272E VAL* 4.2 9.0 - - + -
277E ASP* 2.8 20.2 + - - -
281E LYS* 1.3 68.4 - - - +
283E ALA* 1.3 65.1 + - - -
284E SER 3.1 1.3 - - - -
285E VAL* 3.1 8.8 + - - +
286E ALA* 3.0 21.7 + - - +
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ALA* 3.5 30.7 - - + +
27E MET* 3.8 11.0 - - + +
30E ALA* 3.8 2.2 - - + -
272E VAL* 3.9 12.8 - - + +
277E ASP* 3.9 1.4 + - - -
280E ASN* 3.3 29.7 + - - +
282E THR* 1.3 78.3 - - - +
284E SER* 1.3 62.0 + - - +
286E ALA* 3.4 3.5 + - - +
287E VAL* 3.0 27.9 + - - +
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Residues in contact with SER 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ALA* 3.9 16.0 - - - +
35E ARG* 5.6 0.3 + - - -
279E ARG 5.1 0.5 + - - -
280E ASN* 2.7 23.8 + - - +
281E LYS* 3.3 12.4 - - - -
282E THR 3.1 0.2 - - - -
283E ALA* 1.3 74.8 - - - +
285E VAL* 1.3 65.6 + - - +
287E VAL* 3.1 4.0 + - - +
288E ALA* 2.9 23.8 + - - +
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Residues in contact with VAL 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E LEU* 4.3 6.7 - - + -
230E LEU* 3.6 29.4 - - + -
234E ASP 3.6 22.0 - - - +
235E ALA* 5.1 0.7 - - - -
248E TYR* 4.0 26.2 - - + -
281E LYS* 3.0 23.4 + - + +
282E THR* 3.1 8.7 + - - +
284E SER* 1.3 74.3 - - - +
286E ALA* 1.3 58.5 + - - +
288E ALA* 3.1 7.9 + - - +
289E LEU* 2.8 44.3 + - + +
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Residues in contact with ALA 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 3.7 25.6 - - + -
227E LEU* 3.8 26.6 - - + +
269E PHE* 4.2 5.7 - - + -
272E VAL* 4.4 1.1 - - + -
282E THR 3.0 11.9 + - - +
283E ALA 3.6 8.7 - - - +
285E VAL* 1.3 76.6 - - - +
287E VAL* 1.3 57.5 + - - +
289E LEU* 3.2 7.1 + - - +
290E MET* 2.8 38.2 + - + +
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Residues in contact with VAL 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 3.3 33.0 - - + +
30E ALA* 3.6 21.8 - - + +
31E GLY 4.0 2.9 - - - -
32E VAL* 3.9 26.5 - - + +
35E ARG* 3.9 25.9 - - + +
283E ALA 3.0 15.6 + - - +
284E SER* 3.1 7.4 + - - +
286E ALA* 1.3 75.8 - - - +
288E ALA* 1.3 62.7 + - - +
290E MET* 3.3 10.5 + - + +
291E GLY* 3.0 18.9 + - - -
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Residues in contact with ALA 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 3.5 27.9 + - - +
248E TYR* 3.9 10.8 - - - +
252E HIS* 3.5 28.7 - - + +
284E SER 2.9 12.4 + - - +
285E VAL* 3.1 9.6 + - - +
287E VAL* 1.3 77.7 - - - +
289E LEU* 1.3 61.7 + - - +
291E GLY* 3.1 11.8 + - - -
292E SER* 3.2 9.5 + - - -
296E GLU* 4.3 0.9 - - - +
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Residues in contact with LEU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E LEU* 4.5 20.4 - - + -
227E LEU* 4.7 2.9 - - + -
230E LEU* 4.2 12.3 - - + -
248E TYR 4.5 0.2 - - - +
251E SER* 3.5 50.0 - - - +
252E HIS* 3.7 24.0 - - + +
255E MET* 3.6 12.8 - - + +
269E PHE* 4.1 8.3 - - + -
285E VAL* 2.8 38.2 + - + +
286E ALA* 3.6 4.7 - - - +
288E ALA* 1.3 71.0 - - - +
290E MET* 1.3 66.2 + - - +
292E SER 3.3 1.6 + - - -
293E LEU* 3.0 22.8 + - - +
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Residues in contact with MET 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 3.6 31.9 - - + -
32E VAL* 3.6 24.2 - - + -
36E LEU* 4.6 5.2 - - + -
93E LEU* 4.1 13.0 - - + -
95E LEU* 3.9 20.0 - - + -
269E PHE* 3.4 30.7 - - + -
286E ALA* 2.8 29.6 + - + +
287E VAL* 3.5 18.6 - - + +
288E ALA 3.2 0.2 - - - -
289E LEU* 1.3 76.9 - - - +
291E GLY* 1.3 62.5 + - - +
293E LEU* 3.1 6.8 + - - +
294E PHE* 2.9 37.8 + - + -
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Residues in contact with GLY 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ARG* 4.3 10.5 - - - +
36E LEU* 4.5 2.4 - - - +
39E LEU* 3.4 12.3 - - - +
287E VAL 3.0 13.8 + - - -
288E ALA 3.1 5.5 + - - -
290E MET* 1.3 77.1 - - - +
292E SER* 1.3 57.7 + - - +
294E PHE 3.3 5.4 + - - -
295E GLY 3.4 0.7 + - - -
296E GLU* 2.9 43.7 + - - +
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Residues in contact with SER 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E HIS* 3.0 28.6 + - - -
255E MET* 3.6 18.2 - - - +
256E GLU* 4.0 22.9 + - - +
259E ALA* 3.3 11.6 - - - +
288E ALA 3.2 5.0 + - - -
289E LEU 3.6 7.6 - - - -
290E MET 3.2 0.2 - - - -
291E GLY* 1.3 72.5 - - - +
293E LEU* 1.3 68.9 + - - +
295E GLY* 3.0 12.5 + - - -
296E GLU* 3.8 17.5 + - - +
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Residues in contact with LEU 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E LEU* 3.8 28.0 - - + -
255E MET* 3.7 15.0 - - - +
258E LEU* 4.2 15.5 - - + -
259E ALA* 3.1 21.2 - - - +
264E ILE* 4.0 33.2 - - + -
267E ALA* 4.0 19.5 - - + -
269E PHE* 4.1 11.9 - - + -
289E LEU 3.0 14.4 + - - +
290E MET* 3.4 7.6 - - - +
292E SER* 1.3 74.8 - - - +
294E PHE* 1.3 79.0 + - + +
295E GLY 3.1 5.2 + - - -
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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
------------------------------------------------------------
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