Contacts of the helix formed by residues 267 - 281 (chain C) in PDB entry 3OP5
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 ASP 267 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C ASN* 3.3 37.0 + - - +
265C LEU 3.3 0.6 - - - -
266C LYS* 1.4 75.6 - - - +
268C PRO* 1.4 65.1 - - - +
269C LYS* 3.5 12.1 + - - +
270C TYR* 3.3 26.3 + - + +
271C VAL* 3.3 18.2 + - - +
221D HIS 5.5 1.0 - - - +
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Residues in contact with PRO 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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221C HIS* 3.5 35.4 + - + +
225C ILE* 4.1 15.9 - - + -
233C HIS* 4.1 0.7 + - - -
265C LEU 4.6 1.3 - - - +
266C LYS 3.4 12.1 - - - +
267C ASP* 1.4 86.0 - - - +
269C LYS* 1.3 55.9 + - - +
271C VAL* 3.3 6.7 + - + +
272C ARG* 3.0 27.2 + - - +
221D HIS* 3.9 28.3 - - + +
225D ILE* 4.5 5.6 - - + -
265D LEU 6.0 0.4 - - - +
268D PRO* 3.6 23.6 - - + -
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Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C HIS* 4.6 3.4 - - - +
267C ASP* 3.3 9.1 - - - +
268C PRO* 1.3 71.1 - - + +
270C TYR* 1.4 59.2 + - - +
272C ARG* 3.2 37.9 + - - +
273C ASP* 2.9 40.9 + - - +
218D LYS 3.1 26.9 + - - -
220D CYS 3.8 17.5 - - - +
221D HIS 4.5 5.8 - - - +
222D ASP* 3.1 35.4 + - - +
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Residues in contact with TYR 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PRO 3.8 16.1 + - - -
261C TRP* 3.8 24.8 - - + -
263C ASP* 5.5 0.9 - - - +
264C ASN* 3.6 39.9 - - + -
267C ASP* 3.3 29.3 + - - +
269C LYS* 1.4 76.3 - - - +
271C VAL* 1.3 61.5 + - + +
273C ASP* 3.8 5.1 - - - +
274C SER* 2.9 43.5 + - - -
277C ARG* 5.5 7.0 + - - -
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ILE* 3.5 33.4 - - + +
233C HIS* 3.7 13.5 - - + +
261C TRP* 3.8 20.8 - - + +
264C ASN 3.4 24.2 - - - +
265C LEU* 3.9 22.7 - - + -
267C ASP 3.3 6.8 + - - +
268C PRO 3.3 7.6 + - - +
270C TYR* 1.3 78.1 - - + +
272C ARG* 1.4 55.5 - - - +
274C SER* 3.6 1.9 - - - -
275C LYS* 3.1 39.0 + - - +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C HIS* 4.4 6.0 + - + -
230C ILE* 4.7 1.9 - - + +
233C HIS* 3.6 43.5 + - + +
234C ASN* 3.6 22.8 + - - +
268C PRO 3.0 14.2 + - - +
269C LYS* 3.2 44.8 - - - +
270C TYR 3.3 0.2 - - - -
271C VAL* 1.4 74.6 - - - +
273C ASP* 1.4 86.7 + - - +
275C LYS* 3.2 6.1 + - - +
276C ILE* 3.0 44.6 + - + +
217D PRO 4.5 4.2 + - - -
218D LYS* 3.6 29.9 + - - +
220D CYS 5.7 0.8 + - - -
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 2.9 27.5 + - - +
270C TYR* 4.0 5.0 - - - +
272C ARG* 1.4 104.8 + - - +
274C SER* 1.3 55.7 + - - +
276C ILE* 3.6 13.0 + - - +
277C ARG* 3.1 28.8 + - - +
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PRO* 4.8 0.3 - - - +
261C TRP* 3.4 32.6 + - - +
270C TYR* 2.9 32.3 + - - -
271C VAL 3.6 5.4 - - - -
273C ASP* 1.3 75.9 - - - +
275C LYS* 1.3 54.7 + - - +
277C ARG* 3.5 16.3 + - - +
278C TYR* 3.1 47.0 + - - -
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Residues in contact with LYS 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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225C ILE 2.9 24.7 + - - -
226C GLU 3.4 17.9 + - - -
228C THR 2.6 34.7 + - - +
230C ILE* 3.6 11.3 - - + +
233C HIS* 2.9 23.8 + - + +
245C GLU* 4.8 1.1 - - - +
249C TYR* 3.5 24.4 + - + +
261C TRP* 3.5 36.3 - - + +
271C VAL* 3.1 18.1 + - - +
272C ARG 3.2 6.9 + - - +
274C SER* 1.3 75.3 - - - +
276C ILE* 1.4 57.7 + - - +
278C TYR* 3.5 2.5 + - - +
279C ARG* 3.0 30.0 + - - +
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Residues in contact with ILE 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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230C ILE* 3.8 30.5 - - + -
234C ASN* 4.7 7.0 - - - +
272C ARG* 3.0 43.7 + - + +
273C ASP* 3.8 13.5 - - - +
274C SER 3.4 0.2 - - - -
275C LYS* 1.4 73.8 - - - +
277C ARG* 1.3 57.6 + - - +
279C ARG* 3.3 5.3 + - - +
280C GLU* 3.0 29.8 + - + +
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Residues in contact with ARG 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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270C TYR* 5.5 6.9 + - - -
273C ASP 3.1 15.8 + - - +
274C SER* 3.7 16.7 + - - +
276C ILE* 1.3 76.7 - - - +
278C TYR* 1.3 102.8 + - + +
280C GLU* 3.4 8.2 + - - +
281C ASN* 3.0 27.9 + - + +
284C SER* 4.7 5.0 + - - +
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Residues in contact with TYR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TYR* 6.4 0.7 - - + -
260C PRO* 3.5 23.2 - - + +
261C TRP* 3.8 15.3 - + + -
274C SER* 3.1 38.1 + - - +
275C LYS 4.1 3.6 - - - +
276C ILE 3.4 0.2 - - - -
277C ARG* 1.3 106.8 + - - +
279C ARG* 1.3 59.9 + - - +
281C ASN 3.1 21.1 - - - +
282C ILE* 3.3 11.4 + - - +
284C SER* 3.6 28.0 - - - -
285C LEU* 3.5 44.2 - - + +
288C LYS* 3.5 25.6 + - + +
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Residues in contact with ARG 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ILE* 3.6 23.3 - - + -
241C ARG* 4.4 10.3 - - - +
245C GLU* 5.7 1.6 - - - -
249C TYR* 5.5 1.6 - - - +
275C LYS 3.0 18.2 + - - +
276C ILE* 3.5 6.3 - - - +
278C TYR* 1.3 73.7 - - - +
280C GLU* 1.3 67.6 + - - +
281C ASN 3.4 0.5 + - - -
282C ILE* 3.5 12.6 - - + +
306C VAL 5.1 0.8 + - - -
307C LYS* 2.8 83.1 + - + +
309C LEU 4.4 1.2 + - - -
366C EDO 3.2 29.3 + - - -
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Residues in contact with GLU 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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276C ILE* 3.0 19.3 + - + +
277C ARG* 3.6 9.4 - - - +
279C ARG* 1.3 82.9 + - - +
281C ASN* 1.3 58.6 + - + +
307C LYS* 3.4 22.2 + - - +
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Residues in contact with ASN 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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277C ARG* 3.0 12.5 + - + +
278C TYR 3.1 11.1 - - - +
280C GLU* 1.3 78.3 - - + +
282C ILE* 1.4 61.6 + - - +
283C ALA* 3.7 12.6 + - - +
284C SER* 2.7 53.9 + - - +
285C LEU 3.4 2.3 + - - -
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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