Contacts of the helix formed by residues 281 - 293 (chain C) in PDB entry 1CEV
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A SER* 6.4 0.2 - - - -
243A ILE* 6.1 5.4 - - + -
233C SER 2.9 24.9 + - - -
234C ASP* 3.4 24.6 + - - +
236C PRO* 4.2 12.7 - - + +
277C ASP* 3.4 6.3 + - - +
278C GLU* 3.1 21.0 + - + +
279C ARG 3.0 4.6 + - - +
280C ASN* 1.3 77.1 - - - +
282C THR* 1.3 58.0 + - - +
284C SER* 3.1 8.9 + - - -
285C VAL* 2.9 32.7 + - + +
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Residues in contact with THR 282 (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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227C LEU* 4.2 17.9 - - + +
235C ALA* 3.6 25.1 - - + +
236C PRO* 3.3 11.1 - - - +
237C GLY 2.9 33.6 + - - +
238C VAL* 4.2 2.5 - - + -
272C VAL* 4.5 6.5 - - + -
277C ASP* 2.9 26.7 + - - -
281C LYS* 1.3 68.6 - - - +
283C ALA* 1.3 66.0 + - - +
285C VAL* 3.2 8.9 + - + +
286C ALA* 2.9 22.3 + - - +
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Residues in contact with ALA 283 (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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26C ALA* 3.5 31.6 - - + +
27C MET* 3.9 11.1 - - + +
30C ALA* 3.7 2.9 - - + -
272C VAL* 4.3 6.8 - - + +
277C ASP* 3.5 2.8 + - - +
280C ASN* 3.2 30.6 + - - +
282C THR* 1.3 78.5 - - - +
284C SER* 1.3 61.3 + - - +
286C ALA* 3.2 4.9 + - - +
287C VAL* 3.1 27.0 + - - +
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Residues in contact with SER 284 (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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243A ILE* 5.5 2.6 - - - +
30C ALA* 3.8 18.4 + - - +
35C ARG* 5.3 1.6 + - - -
279C ARG 5.1 0.5 + - - -
280C ASN* 2.9 19.9 + - - +
281C LYS* 3.3 11.4 - - - -
283C ALA* 1.3 75.5 - - - +
285C VAL* 1.3 60.1 + - - +
287C VAL* 3.3 4.6 + - - +
288C ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 285 (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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243A ILE* 4.7 11.2 - - + -
227C LEU* 4.4 5.6 - - + -
230C LEU* 3.7 22.2 - - + -
234C ASP* 3.8 20.2 - - - +
235C ALA* 5.3 1.1 - - + -
248C TYR* 3.6 31.2 - - + -
281C LYS* 2.9 25.0 + - + +
282C THR* 3.4 11.0 - - - +
284C SER* 1.3 73.0 - - - +
286C ALA* 1.3 59.6 + - - +
288C ALA* 3.2 8.2 + - - +
289C LEU* 2.9 39.7 + - + +
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Residues in contact with ALA 286 (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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27C MET* 3.7 28.0 - - + -
227C LEU* 4.1 24.4 - - + +
269C PHE* 4.0 3.7 - - + -
272C VAL* 4.6 0.4 - - + -
282C THR 2.9 12.3 + - - +
283C ALA* 3.3 11.4 - - - +
285C VAL* 1.3 77.5 - - - +
287C VAL* 1.3 58.1 + - - +
289C LEU* 3.3 7.9 + - - +
290C MET* 2.9 36.3 + - + +
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Residues in contact with VAL 287 (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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27C MET* 3.5 25.8 - - - +
30C ALA* 3.7 21.8 - - + +
32C VAL* 3.9 20.4 - - + +
35C ARG* 3.7 37.6 - - + +
283C ALA 3.1 15.1 + - - +
284C SER 3.7 7.4 - - - +
285C VAL 3.3 0.2 - - - -
286C ALA* 1.3 75.4 - - - +
288C ALA* 1.3 59.5 + - - +
290C MET* 3.3 12.4 + - + +
291C GLY* 2.8 26.3 + - - -
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Residues in contact with ALA 288 (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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243A ILE* 4.5 6.7 - - + -
35C ARG* 3.4 28.8 + - - +
248C TYR* 3.2 28.1 + - + +
252C HIS* 4.7 0.7 - - - -
284C SER 3.0 14.5 + - - +
285C VAL* 3.2 8.5 + - - +
287C VAL* 1.3 76.3 - - - +
289C LEU* 1.3 58.6 + - - +
291C GLY* 3.2 2.3 + - - -
292C SER* 3.0 29.1 + - - -
296C GLU* 4.3 0.5 - - - +
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Residues in contact with LEU 289 (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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225C LEU* 4.5 16.4 - - + -
227C LEU* 4.4 10.8 - - + -
230C LEU* 4.3 15.3 - - + -
248C TYR* 4.0 13.9 - - + -
251C SER* 3.8 44.6 - - - +
252C HIS* 3.8 11.9 - - + +
255C MET* 3.6 11.6 - - + +
269C PHE* 3.8 10.8 - - + -
285C VAL* 2.9 28.0 + - + +
286C ALA 3.5 7.4 - - - +
288C ALA* 1.3 75.3 - - - +
290C MET* 1.3 60.1 + - - +
292C SER* 3.2 3.5 + - - +
293C LEU* 2.9 28.9 + - - +
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Residues in contact with MET 290 (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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27C MET* 3.9 25.1 - - - -
32C VAL* 3.6 27.8 - - + -
35C ARG* 6.1 0.2 - - + -
36C LEU* 4.6 4.3 - - + -
93C LEU* 4.0 14.1 - - + -
95C LEU* 4.0 17.9 - - + -
269C PHE* 3.6 30.7 - - + -
286C ALA* 2.9 33.0 + - + +
287C VAL* 3.6 16.8 - - + +
289C LEU* 1.3 74.1 - - - +
291C GLY* 1.3 62.2 - - - +
293C LEU* 3.1 7.6 + - - -
294C PHE* 2.9 37.7 + - + -
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Residues in contact with GLY 291 (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* 4.2 10.0 - - - +
36C LEU* 4.7 1.6 - - - -
39C LEU* 3.5 11.1 - - - +
287C VAL 2.8 15.3 + - - -
288C ALA 3.2 4.7 + - - -
289C LEU 3.2 0.2 - - - -
290C MET* 1.3 77.0 - - - +
292C SER* 1.3 58.9 + - - +
294C PHE 3.4 4.5 + - - -
295C GLY 3.4 1.0 + - - -
296C GLU* 2.9 44.8 + - - +
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Residues in contact with SER 292 (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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252C HIS* 2.9 37.1 + - - -
255C MET* 3.6 18.9 - - - +
256C GLU* 4.0 15.9 - - - +
259C ALA* 3.3 13.2 - - - +
288C ALA 3.0 8.7 + - - -
289C LEU* 3.2 7.6 + - - -
291C GLY* 1.3 70.6 - - - +
293C LEU* 1.3 67.7 + - - +
294C PHE 3.1 1.3 - - - -
295C GLY* 3.2 10.7 + - - -
296C GLU* 3.9 16.2 + - - +
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Residues in contact with LEU 293 (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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91C PHE* 5.2 0.4 - - + -
223C LEU* 3.8 28.0 - - + -
255C MET* 3.8 16.4 - - - +
258C LEU* 4.1 24.9 - - + -
259C ALA* 3.3 20.6 - - - +
264C ILE* 4.1 22.2 - - + -
267C ALA* 4.0 14.1 - - + -
269C PHE* 3.8 18.8 - - + -
289C LEU 2.9 12.6 + - - +
290C MET 3.4 8.5 - - - +
292C SER* 1.3 75.3 - - - +
294C PHE* 1.3 77.4 + - + +
295C GLY 3.4 0.2 + - - -
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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
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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