Contacts of the helix formed by residues 267 - 274 (chain C) in PDB entry 2OB1
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 SER 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ILE* 4.0 11.3 - - - +
237C SER* 4.3 17.7 - - - -
265C TYR 3.3 0.7 - - - -
266C ASN* 1.3 86.7 + - - +
268C LYS* 1.3 63.2 + - - +
269C GLU* 3.4 16.0 + - - +
270C LYS* 3.1 32.1 + - - +
271C TYR* 3.0 23.6 + - - +
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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
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234C ILE* 4.0 5.3 - - + +
267C SER* 1.3 73.1 - - - +
269C GLU* 1.3 82.8 + - - +
271C TYR* 3.4 4.9 + - - +
272C ALA* 3.0 30.0 + - - +
283C VAL* 3.5 35.1 + - + +
284C ASN* 4.0 6.2 + - - -
285C ASP* 3.8 17.5 - - + +
288C GLU* 3.1 39.3 + - - +
322C ILE* 3.6 25.8 - - + -
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C SER* 3.4 16.3 + - - +
268C LYS* 1.3 106.8 + - + +
270C LYS* 1.3 58.7 + - + +
271C TYR 3.1 0.2 - - - -
272C ALA* 3.4 6.4 + - - +
273C SER* 2.7 31.2 + - - -
283C VAL* 4.7 5.4 - - + -
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Residues in contact with LYS 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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237C SER* 5.4 3.4 - - - -
263C MET 5.5 0.4 + - - -
264C THR 3.6 12.5 + - - +
265C TYR* 3.2 30.5 - - + -
266C ASN* 2.8 34.0 + - - +
267C SER* 3.1 21.1 + - - +
269C GLU* 1.3 76.7 - - + +
271C TYR* 1.3 63.1 + - - +
273C SER* 3.2 22.6 + - - -
274C ARG 4.1 0.2 + - - -
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Residues in contact with TYR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.3 0.9 - - - +
230C SER* 2.6 20.2 + - - -
231C TYR 4.3 0.2 - - - -
232C ASP* 2.4 47.9 + - + +
233C PRO 4.8 2.0 - - - -
234C ILE* 4.2 14.6 - - + -
265C TYR* 3.9 19.0 - - + +
267C SER 3.0 18.0 + - - +
268C LYS* 3.5 9.6 - - - +
269C GLU 3.1 0.2 - - - -
270C LYS* 1.3 76.7 - - - +
272C ALA* 1.3 62.9 + - - +
273C SER 3.1 1.6 + - - -
274C ARG* 3.1 49.4 + - - -
275C TRP* 3.2 27.8 - + - -
283C VAL* 4.9 0.9 - - + -
322C ILE* 3.2 26.7 - - + -
324C MET* 3.7 13.5 - - + -
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Residues in contact with ALA 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 LYS 3.0 17.7 + - - +
269C GLU* 3.9 5.2 - - - +
270C LYS 3.4 0.2 - - - -
271C TYR* 1.3 76.1 - - - +
273C SER* 1.3 61.5 + - - +
274C ARG 3.2 0.4 - - - -
275C TRP* 3.1 20.4 + - - +
276C SER* 3.8 2.4 + - - -
281C VAL* 3.7 26.7 - - + +
283C VAL* 3.9 20.4 - - + -
324C MET* 4.0 12.1 - - + -
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Residues in contact with SER 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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265C TYR* 5.5 1.6 - - - -
269C GLU 2.7 22.7 + - - -
270C LYS* 3.2 17.0 + - - -
271C TYR 3.1 0.4 - - - -
272C ALA* 1.3 72.0 - - - +
274C ARG* 1.3 55.1 + - - +
275C TRP 3.0 5.6 - - - -
276C SER* 2.8 39.7 + - - +
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Residues in contact with ARG 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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204C LEU* 4.0 23.3 + - - +
205C CYS* 6.1 0.4 - - - +
209C ASN* 4.8 0.6 - - - +
212C SER* 2.9 34.6 + - - -
213C GLN* 2.8 45.8 + - - +
216C ILE* 3.6 16.5 - - + +
217C ASN* 4.6 0.2 - - - +
220C MET* 4.5 1.7 - - - +
232C ASP* 4.6 0.2 + - - -
261C THR* 4.1 10.7 + - - +
265C TYR* 3.4 53.6 + - + +
271C TYR* 3.1 52.1 + - - +
272C ALA 3.2 0.8 - - - -
273C SER* 1.3 76.7 - - - +
275C TRP* 1.3 70.3 + - + +
276C SER* 3.4 2.2 + - - -
277C ALA* 5.1 1.0 + - - +
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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