Contacts of the helix formed by residues 281 - 293 (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 LYS 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A SER 2.9 21.7 + - - -
234A ASP* 3.4 23.4 + - - +
236A PRO* 3.8 17.3 - - + -
277A ASP* 3.1 8.3 + - - +
278A GLU* 3.3 28.3 + - - +
279A ARG 3.1 4.9 - - - -
280A ASN* 1.3 76.1 - - - +
282A THR* 1.3 59.0 + - - +
284A SER* 3.2 9.0 - - - -
285A VAL* 2.9 35.5 + - + +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.0 21.7 - - + +
235A ALA* 3.9 20.6 - - + +
236A PRO* 3.5 7.3 - - - +
237A GLY* 2.8 34.0 + - - +
238A VAL* 4.4 0.4 - - + -
272A VAL* 4.3 10.1 - - + -
277A ASP* 2.7 32.0 + - - -
281A LYS* 1.3 70.2 - - - +
283A ALA* 1.3 61.9 + - - -
285A VAL* 3.3 8.3 + - - +
286A ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.5 29.4 - - + +
27A MET* 3.9 10.7 - - + +
30A ALA* 3.9 3.1 - - + -
272A VAL* 3.9 13.6 - - + +
277A ASP* 3.9 1.0 + - - -
280A ASN* 3.1 30.1 + - - +
282A THR* 1.3 77.7 - - - +
284A SER* 1.3 57.6 + - - +
286A ALA* 3.2 3.4 + - - +
287A VAL* 2.9 32.9 + - - +
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Residues in contact with SER 284 (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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30A ALA* 4.0 15.3 - - - +
35A ARG* 5.5 0.3 + - - -
279A ARG 5.0 0.7 + - - -
280A ASN* 2.9 19.4 + - - +
281A LYS* 3.2 13.5 - - - -
283A ALA* 1.3 74.5 - - - +
285A VAL* 1.3 65.6 + - - +
287A VAL* 3.2 4.9 + - - +
288A ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.4 5.4 - - + -
230A LEU* 3.6 29.6 - - + -
234A ASP 3.7 21.3 - - - +
235A ALA* 5.3 1.3 - - + -
248A TYR* 4.1 25.4 - - + -
281A LYS* 2.9 21.7 + - + +
282A THR* 3.3 8.3 + - - +
284A SER* 1.3 75.6 - - - +
286A ALA* 1.3 58.6 + - - +
288A ALA* 3.2 7.9 + - - +
289A LEU* 2.9 45.7 + - + +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.6 25.4 - - - -
227A LEU* 3.8 26.2 - - + +
269A PHE* 3.9 7.2 - - + -
272A VAL* 4.3 0.4 - - + -
282A THR 3.0 13.0 + - - +
283A ALA* 3.4 9.2 - - - +
284A SER 3.2 0.2 - - - -
285A VAL* 1.3 77.2 - - - +
287A VAL* 1.3 56.4 + - - +
289A LEU* 3.3 5.1 + - - +
290A MET* 2.9 37.3 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.4 33.0 - - + +
30A ALA* 3.6 23.3 - - + +
31A GLY 3.9 15.0 - - - +
32A VAL* 3.9 17.0 - - + -
35A ARG* 4.0 23.1 - - + +
283A ALA 2.9 17.6 + - - +
284A SER* 3.2 7.4 + - - +
286A ALA* 1.3 72.3 - - - +
288A ALA* 1.3 61.3 + - - +
290A MET* 3.2 11.3 + - + +
291A GLY* 3.0 24.4 + - - -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.6 27.9 + - - +
248A TYR* 3.9 11.2 - - - +
252A HIS* 3.5 23.0 - - + +
284A SER 3.0 13.4 + - - +
285A VAL* 3.2 9.6 + - - +
287A VAL* 1.3 75.6 - - - +
289A LEU* 1.3 62.3 + - - +
291A GLY* 3.1 10.4 + - - -
292A SER* 3.2 16.1 + - - -
296A GLU* 4.3 0.9 - - - +
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Residues in contact with LEU 289 (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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225A LEU* 4.5 15.3 - - + -
227A LEU* 4.5 7.4 - - + -
230A LEU* 4.2 12.3 - - + -
248A TYR* 5.6 0.2 - - + -
251A SER* 3.5 48.5 - - - +
252A HIS* 3.7 23.3 - - + +
255A MET* 3.5 15.1 - - + +
269A PHE* 4.0 11.2 - - + -
285A VAL* 2.9 40.7 + - + +
286A ALA* 3.6 5.2 - - - +
288A ALA* 1.3 73.3 - - - +
290A MET* 1.3 60.3 - - - +
292A SER* 3.3 1.7 + - - -
293A LEU* 3.0 25.6 + - - +
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Residues in contact with MET 290 (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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27A MET* 3.7 28.0 - - + -
32A VAL* 3.6 26.7 - - + -
36A LEU* 4.5 6.1 - - + -
93A LEU* 4.0 12.3 - - + -
95A LEU* 3.9 20.2 - - + -
269A PHE* 3.5 32.8 - - + -
286A ALA* 2.9 32.9 + - + +
287A VAL* 3.2 16.6 + - + +
289A LEU* 1.3 75.8 - - - +
291A GLY* 1.3 63.8 + - - +
293A LEU* 3.3 3.3 + - - +
294A PHE* 2.9 38.3 + - + -
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Residues in contact with GLY 291 (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* 4.3 10.5 - - - -
36A LEU* 4.5 3.1 - - - +
39A LEU* 3.4 11.1 - - - +
287A VAL 3.0 13.4 + - - -
288A ALA 3.1 5.0 + - - -
290A MET* 1.3 76.7 - - - +
292A SER* 1.3 58.6 + - - +
294A PHE 3.3 6.4 + - - -
295A GLY 3.4 0.3 + - - -
296A GLU* 2.8 44.7 + - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 2.8 29.5 + - - -
255A MET* 3.5 22.6 - - - +
256A GLU* 4.1 19.9 + - - +
259A ALA* 3.3 13.3 - - - +
288A ALA 3.2 6.2 + - - -
289A LEU 3.6 3.6 - - - -
291A GLY* 1.3 73.2 - - - +
293A LEU* 1.3 67.3 + - - +
295A GLY* 3.0 12.6 + - - -
296A GLU* 3.9 16.2 + - - +
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Residues in contact with LEU 293 (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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223A LEU* 3.9 27.4 - - + -
255A MET* 3.6 16.3 - - - +
258A LEU* 4.3 13.5 - - + -
259A ALA* 3.3 18.1 - - - +
264A ILE* 4.0 33.4 - - + -
267A ALA* 4.1 9.2 - - + -
269A PHE* 4.0 16.8 - - + -
289A LEU 3.0 13.6 + - - +
290A MET* 3.5 7.9 - - - +
292A SER* 1.3 77.0 - - - +
294A PHE* 1.3 87.0 + - + +
295A GLY 3.2 4.3 + - - -
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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