Contacts of the helix formed by residues 266 - 279 (chain C) in PDB entry 2OJW
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 GLY 266 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C ALA 3.3 25.1 - - - -
261C MET* 3.5 16.9 - - - -
263C GLU 3.1 8.2 + - - -
264C GLU 3.2 1.0 - - - -
265C ASN* 1.3 72.9 - - - +
267C LEU* 1.3 59.0 + - - +
268C LYS 3.1 2.2 - - - -
269C TYR* 3.0 13.4 + - - +
270C ILE* 2.9 27.8 + - - +
333C LYS 3.1 3.0 + - - -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASN 3.1 0.9 - - - +
266C GLY* 1.3 78.5 - - - +
268C LYS* 1.3 54.3 + - - +
270C ILE* 3.9 19.3 - - + -
271C GLU* 2.8 67.8 + - + +
325C ILE* 4.3 27.1 - - + -
329C VAL* 4.4 4.7 - - + +
330C GLY* 4.1 13.2 - - - +
333C LYS* 3.0 51.0 + - + +
334C LYS* 4.2 0.6 - - - +
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASN* 3.2 16.6 + - + +
267C LEU* 1.3 78.8 - - - +
269C TYR* 1.3 89.7 + - + +
271C GLU* 3.5 11.1 + - - +
272C GLU* 2.8 55.9 + - + +
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Residues in contact with TYR 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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258C THR* 5.3 0.4 - - - +
260C ALA* 3.8 37.0 - - + -
261C MET* 3.8 20.6 - - + +
263C GLU* 6.1 0.4 - - - -
265C ASN 5.1 1.8 - - - -
266C GLY* 3.0 13.4 + - - +
268C LYS* 1.3 111.5 - - + +
270C ILE* 1.3 64.0 + - - +
272C GLU* 3.5 25.2 + - - +
273C ALA* 3.1 23.9 + - - +
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Residues in contact with ILE 270 (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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261C MET* 3.6 24.4 - - + +
266C GLY 2.9 15.4 + - - +
267C LEU* 3.4 24.2 - - + +
269C TYR* 1.3 77.0 - - - +
271C GLU* 1.3 58.3 + - - +
273C ALA* 3.3 3.3 + - - +
274C ILE* 3.0 35.8 + - + +
325C ILE* 4.4 4.7 - - + -
329C VAL* 3.5 31.4 - - + -
335C GLY 3.8 8.3 - - - +
336C TYR 3.7 19.1 - - - +
337C PHE* 3.5 29.4 - - + -
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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
----------------------------------------------------------
267C LEU* 2.8 52.5 + - + +
268C LYS* 3.9 9.1 - - - +
270C ILE* 1.3 73.1 - - - +
272C GLU* 1.3 61.1 + - - +
274C ILE* 3.5 8.5 + - + +
275C GLU* 3.1 23.0 + - - +
325C ILE* 4.6 13.1 - - + +
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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
----------------------------------------------------------
268C LYS* 2.8 43.8 + - + +
269C TYR* 3.7 30.1 - - - +
270C ILE 3.4 0.2 - - - -
271C GLU* 1.3 75.7 - - - +
273C ALA* 1.3 61.5 - - - +
275C GLU* 3.4 9.2 + - - +
276C LYS* 3.2 40.4 + - - +
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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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261C MET* 3.7 20.4 - - + -
269C TYR 3.1 15.3 + - - +
270C ILE 3.6 4.9 - - - +
272C GLU* 1.3 75.4 - - - +
274C ILE* 1.3 65.7 + - - +
276C LYS* 3.3 12.8 + - - +
277C LEU* 3.1 26.8 + - - +
337C PHE* 3.8 11.4 - - + -
359C CYS* 3.8 23.3 - - + +
360C LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 3.0 28.8 + - + +
271C GLU* 3.8 7.2 - - + +
272C GLU 3.4 0.2 - - - -
273C ALA* 1.3 74.0 - - - +
275C GLU* 1.3 64.1 + - - +
277C LEU* 3.2 10.7 + - - +
278C SER* 3.0 21.7 + - - -
312C PHE* 4.0 11.5 - - + -
314C ALA* 4.0 23.1 - - + -
323C ILE* 3.8 23.8 - - + -
325C ILE* 3.5 39.3 - - + -
337C PHE* 4.2 12.6 - - + -
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Residues in contact with GLU 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 3.1 14.2 + - - +
272C GLU* 3.4 13.5 - - - +
274C ILE* 1.3 77.6 - - - +
276C LYS* 1.3 62.9 + - + +
278C SER* 2.6 28.6 + - - -
279C LYS* 3.6 29.7 + - + +
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Residues in contact with LYS 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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272C GLU* 3.2 29.6 + - - +
273C ALA* 3.3 9.6 + - - +
275C GLU* 1.3 75.3 - - + +
277C LEU* 1.3 62.8 + - - +
279C LYS* 3.2 22.4 + - - +
280C ARG* 3.7 6.1 + - - +
358C THR* 3.7 31.5 - - + +
359C CYS* 3.1 24.9 + - - +
360C LEU* 5.1 0.2 - - - +
362C ASN* 2.8 34.6 + - - +
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Residues in contact with LEU 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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273C ALA 3.1 19.2 + - - +
274C ILE* 3.2 11.9 + - - +
276C LYS* 1.3 77.2 - - - +
278C SER* 1.3 56.8 + - - +
280C ARG* 3.0 25.6 + - - -
281C HIS* 3.7 2.6 + - - -
284C HIS* 3.4 38.1 - - + +
312C PHE* 4.0 17.0 - - + -
323C ILE* 4.2 16.2 - - + -
337C PHE* 3.5 34.3 - - + -
341C ARG* 4.0 8.8 + - - +
355C LEU* 4.0 8.1 - - + -
358C THR* 3.9 10.5 - - + -
359C CYS* 3.8 11.2 - - - -
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.0 8.8 + - - -
275C GLU* 2.6 33.9 + - - -
277C LEU* 1.3 74.3 - - - +
279C LYS* 1.3 69.0 + - - +
280C ARG 3.3 0.7 + - - -
281C HIS* 4.5 5.2 + - - +
312C PHE* 3.5 41.5 - - - +
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Residues in contact with LYS 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 GLU* 3.7 33.2 - - + +
276C LYS* 3.6 10.8 - - - +
277C LEU 3.1 1.0 - - - -
278C SER* 1.3 85.4 - - - +
280C ARG* 1.3 64.4 + - + +
281C HIS 3.8 1.7 + - - -
365C GLY 5.4 5.4 + - - +
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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