Contacts of the helix formed by residues 267 - 281 (chain C) in PDB entry 4OMD
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 ALA 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ASP* 3.1 33.5 + - + +
236C GLU* 4.9 0.6 + - - -
265C GLY 3.7 2.1 + - - +
266C PRO* 1.3 75.7 - - - +
268C ARG* 1.3 69.2 + - - +
269C LEU 3.5 0.9 - - - -
270C ALA* 3.1 3.0 + - - +
271C GLU* 2.9 23.3 + - - +
308C TYR* 4.6 0.8 + - - -
268D ARG* 6.3 0.2 - - - +
530D ASP* 5.5 3.1 - - - +
2J ARG* 5.6 0.4 - - - +
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Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ASP* 4.4 0.2 - - - +
267C ALA* 1.3 75.4 - - - +
269C LEU* 1.3 63.2 + - - +
271C GLU* 3.2 14.3 + - - +
272C GLU* 2.9 35.9 + - - +
266D PRO 5.1 4.9 + - - -
267D ALA* 6.3 0.2 - - - +
268D ARG* 3.2 35.3 - - - +
271D GLU* 4.1 27.7 + - - +
490D ARG* 3.3 34.4 - - - +
530D ASP* 3.8 11.3 + - - +
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Residues in contact with LEU 269 (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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233C ASP* 2.9 27.1 + - + +
234C ALA* 4.0 15.0 - - + +
237C ALA* 3.6 15.4 - - + +
268C ARG* 1.3 73.9 - - - +
270C ALA* 1.3 55.1 + - - +
272C GLU* 3.2 21.0 + - - +
273C ALA* 2.8 28.4 + - - +
449D LYS* 4.2 6.3 + - - +
451D ILE* 3.9 37.6 - - + +
488D GLN* 5.6 0.4 - - - +
490D ARG* 4.0 28.3 - - - +
565D LYS* 6.1 2.5 - - - -
567D THR* 4.1 15.3 - - + +
569D VAL* 4.2 10.3 - - + -
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ASP* 3.0 19.1 + - - +
236C GLU* 3.8 24.0 - - + +
237C ALA* 3.9 5.6 - - - +
240C LEU* 4.1 9.2 - - + +
266C PRO* 3.5 23.1 - - + -
267C ALA 3.1 1.1 + - - +
269C LEU* 1.3 75.2 - - - +
271C GLU* 1.3 58.7 + - - +
273C ALA* 3.0 9.8 + - - +
274C PHE* 2.9 33.3 + - - -
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Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C PRO* 3.8 29.8 - - + +
267C ALA* 2.9 21.3 + - - +
268C ARG* 3.5 14.7 + - - +
270C ALA* 1.3 75.4 - - - +
272C GLU* 1.3 59.4 + - + +
274C PHE* 3.0 12.5 + - + +
275C PHE* 2.9 29.9 + - - +
313C TYR* 5.0 4.0 - - + -
268D ARG* 4.0 30.6 + - - +
272D GLU* 5.6 1.6 - - - +
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Residues in contact with GLU 272 (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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268C ARG* 2.9 27.0 + - + +
269C LEU* 3.5 15.3 - - - +
271C GLU* 1.3 78.4 - - + +
273C ALA* 1.3 57.8 + - - +
275C PHE* 3.8 5.6 - - - +
276C ARG* 2.9 37.3 + - - +
271D GLU* 5.6 1.6 - - - +
275D PHE* 4.7 9.0 - - + -
313D TYR* 4.5 5.0 + - - +
449D LYS* 2.7 37.8 + - - +
488D GLN* 5.4 2.6 + - - +
490D ARG* 4.6 12.3 + - - -
571D TYR* 4.1 4.8 + - - -
602D FMT 3.9 19.2 - - - +
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Residues in contact with ALA 273 (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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237C ALA* 3.8 26.5 - - + +
240C LEU* 4.0 16.3 - - + +
241C GLY* 4.4 8.4 - - - +
269C LEU 2.8 13.7 + - - +
270C ALA 3.0 10.1 + - - +
272C GLU* 1.3 75.5 - - - +
274C PHE* 1.3 60.5 + - - +
276C ARG* 3.9 7.3 - - - +
277C GLY* 2.9 26.9 + - - -
289C PHE* 4.4 5.3 - - - -
449D LYS* 5.2 0.6 - - - +
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Residues in contact with PHE 274 (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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240C LEU* 3.7 26.2 - - + -
266C PRO* 4.1 15.9 - - + -
270C ALA 2.9 22.7 + - - -
271C GLU* 3.0 11.2 + - + +
273C ALA* 1.3 75.9 - - - +
275C PHE* 1.3 62.2 + - - +
277C GLY* 3.2 2.1 + - - -
278C VAL* 3.1 27.9 + - - +
289C PHE* 3.6 29.5 - + - -
291C TRP* 3.5 31.4 - + - -
308C TYR* 4.1 19.5 - + + -
311C SER* 5.0 4.9 - - - -
313C TYR* 3.6 24.9 - + + -
314C THR* 3.5 27.6 - - + -
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Residues in contact with PHE 275 (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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271C GLU 2.9 15.4 + - - +
272C GLU* 3.9 5.2 - - - +
274C PHE* 1.3 74.7 - - - +
276C ARG* 1.3 61.7 + - - +
278C VAL* 3.4 7.0 - - + +
279C SER* 2.7 44.7 + - - -
313C TYR* 3.2 29.8 - + + +
601C FMT 4.1 12.3 - - - -
602C FMT 3.5 18.6 - - - -
272D GLU* 4.6 11.0 - - + -
275D PHE* 3.2 53.4 - + + -
276D ARG* 3.9 22.9 - - + -
279D SER* 4.6 2.7 - - - -
280D GLN* 4.6 4.7 - - - -
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Residues in contact with ARG 276 (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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244C PRO* 6.3 0.9 - - - -
272C GLU 2.9 28.8 + - - +
273C ALA* 4.0 6.5 - - - +
275C PHE* 1.3 74.5 - - - +
277C GLY* 1.3 56.3 + - - +
280C GLN* 2.7 64.4 + - + +
281C GLY 3.5 0.7 + - - -
275D PHE* 3.9 11.0 - - + -
447D GLN* 2.8 49.3 + - - -
449D LYS* 3.9 34.1 - - - +
571D TYR* 4.4 0.6 - - - -
601D FMT 3.6 10.7 + - - -
602D FMT 3.0 30.0 + - - +
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Residues in contact with GLY 277 (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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240C LEU 5.9 0.7 - - - -
244C PRO* 5.5 5.6 - - - -
273C ALA 2.9 15.3 + - - -
274C PHE 3.6 4.3 - - - -
275C PHE 3.1 0.2 - - - -
276C ARG* 1.3 77.9 - - - +
278C VAL* 1.3 58.2 + - - +
281C GLY* 2.9 20.9 + - - -
287C SER* 2.8 38.1 + - - -
289C PHE* 4.3 4.7 - - - -
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Residues in contact with VAL 278 (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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274C PHE 3.1 12.9 + - - +
275C PHE* 3.4 15.0 - - + +
277C GLY* 1.3 74.7 - - - +
279C SER* 1.3 64.7 + - - +
284C GLY 4.3 2.8 - - - +
286C GLY* 3.3 20.9 + - - -
287C SER 4.0 13.7 - - - +
289C PHE* 4.3 4.7 - - + -
313C TYR* 3.9 40.6 - - + +
390C TRP* 3.4 47.8 + - + +
601C FMT 4.5 6.7 - - - -
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Residues in contact with SER 279 (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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275C PHE* 2.7 44.4 + - - -
276C ARG 3.7 1.8 - - - -
278C VAL* 1.3 80.7 - - - +
280C GLN* 1.3 77.9 + - - +
284C GLY* 3.5 22.6 - - - +
601C FMT 5.0 1.7 - - - -
275D PHE* 4.4 0.3 - - - -
279D SER* 4.7 9.8 + - - -
280D GLN* 4.5 7.4 + - - +
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Residues in contact with GLN 280 (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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244C PRO* 5.3 2.2 - - + -
245C ASN* 3.7 8.5 + - - +
276C ARG* 2.7 49.2 + - + +
279C SER* 1.3 91.4 - - - +
281C GLY* 1.3 67.9 + - - +
283C GLY* 3.5 5.0 + - - -
284C GLY* 3.1 12.8 + - - +
275D PHE* 4.6 2.2 - - - -
279D SER* 4.6 9.7 + - - +
447D GLN* 5.1 2.4 - - - +
601D FMT 3.6 22.4 + - - +
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Residues in contact with GLY 281 (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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244C PRO* 3.6 17.6 - - - +
276C ARG 3.5 2.8 + - - -
277C GLY* 2.9 20.1 + - - -
280C GLN* 1.3 78.6 - - - +
282C ARG* 1.3 68.0 + - - -
284C GLY 2.9 10.9 + - - -
286C GLY* 2.9 16.7 + - - -
287C SER* 3.6 11.7 - - - -
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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