Contacts of the helix formed by residues 258 - 272 (chain C) in PDB entry 2O1S
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 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C ASP* 3.4 29.7 + - + +
256C GLY 3.4 0.8 - - - -
257C HIS* 1.3 76.9 - - - +
259C VAL* 1.3 64.2 + - - +
260C LEU* 3.3 8.5 + - - +
261C GLY* 2.7 32.3 + - - -
262C LEU* 2.9 24.8 + - - +
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Residues in contact with VAL 259 (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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28C LEU* 4.3 3.1 - - + -
29C PRO* 4.0 31.0 - - + -
32C CYS* 3.8 22.4 - - - -
58C GLU* 3.7 29.0 - - + +
61C VAL* 3.9 17.0 - - + -
62C ALA* 4.1 5.2 - - + +
257C HIS 3.7 5.3 + - - -
258C ASP* 1.3 72.7 + - - +
260C LEU* 1.3 76.2 + - + +
262C LEU* 3.4 4.7 + - - +
263C ILE* 3.0 41.6 + - + +
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Residues in contact with LEU 260 (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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25C LYS* 3.7 45.3 - - + +
26C GLU* 5.3 4.9 - - - +
28C LEU* 4.7 0.4 - - + -
29C PRO* 4.1 16.8 - - + -
258C ASP* 3.3 6.5 + - - +
259C VAL* 1.3 91.8 - - + +
261C GLY* 1.3 66.8 + - - +
263C ILE* 3.7 14.5 - - + +
264C THR* 3.2 26.2 + - - -
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Residues in contact with GLY 261 (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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255C ASP 5.9 0.2 - - - -
258C ASP* 2.7 32.1 + - - -
260C LEU* 1.3 73.9 - - - +
262C LEU* 1.3 58.1 + - - +
264C THR* 3.6 4.9 + - - -
265C THR* 3.0 31.7 + - - -
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Residues in contact with LEU 262 (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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58C GLU 4.3 4.5 - - - +
59C LEU* 4.0 33.7 - - + +
62C ALA* 3.8 9.0 - - + -
254C VAL* 3.9 21.1 - - + -
255C ASP 3.9 14.8 - - - +
256C GLY* 3.6 27.1 - - - +
258C ASP 2.9 19.8 + - - +
259C VAL 3.7 4.5 - - - +
261C GLY* 1.3 76.3 - - - +
263C ILE* 1.3 55.6 + - - +
265C THR* 4.4 3.6 - - - -
266C LEU* 2.7 44.3 + - + +
278C LEU* 4.5 10.8 - - + -
280C ILE* 4.2 13.5 - - + -
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Residues in contact with ILE 263 (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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25C LYS* 4.1 26.9 - - + +
28C LEU* 3.3 34.8 - - + -
62C ALA* 3.7 19.7 - - + -
65C TYR* 3.8 15.3 - - + -
66C VAL* 3.7 21.7 - - + +
259C VAL* 3.0 32.0 + - + +
260C LEU* 3.3 12.3 + - + +
262C LEU* 1.3 76.5 - - - +
264C THR* 1.3 62.6 + - - +
267C LYS* 3.0 27.0 + - + +
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Residues in contact with THR 264 (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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25C LYS* 4.5 13.1 + - - +
260C LEU 3.2 10.8 + - - -
261C GLY* 3.8 9.2 - - - -
263C ILE* 1.3 82.0 - - - +
265C THR* 1.3 65.2 + - - +
267C LYS* 3.8 4.3 - - - +
268C ASN* 3.1 39.0 + - - +
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Residues in contact with THR 265 (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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251C ILE* 4.6 7.6 - - + -
254C VAL* 5.3 8.3 - - + +
261C GLY 3.0 17.4 + - - -
262C LEU* 3.7 7.8 - - - +
264C THR* 1.3 80.4 - - - +
266C LEU* 1.3 62.4 + - - +
268C ASN* 3.3 8.7 + - - +
269C MSE 3.1 51.7 + - + +
278C LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 266 (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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59C LEU* 4.8 5.8 - - + -
62C ALA* 3.9 30.7 - - + +
63C LEU* 3.9 24.2 - - + +
66C VAL* 3.8 15.5 - - + -
67C TYR* 4.7 2.7 + - + -
175C LEU* 3.5 29.6 - - + -
177C ILE* 3.7 14.4 - - + -
262C LEU* 2.7 32.9 + - + +
263C ILE 4.1 1.1 - - - +
265C THR* 1.3 70.6 - - - +
267C LYS* 1.3 61.5 + - - +
269C MSE 3.7 3.0 - - + +
270C ARG* 2.8 34.1 + - - +
278C LEU* 3.9 17.3 - - + -
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Residues in contact with LYS 267 (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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25C LYS* 6.0 3.1 - - - +
66C VAL* 4.4 16.3 - - + +
263C ILE* 3.0 21.8 + - + +
264C THR* 3.8 5.8 - - - +
265C THR 3.3 0.2 - - - -
266C LEU* 1.3 78.3 - - - +
268C ASN* 1.3 67.4 + - - +
270C ARG* 3.4 13.6 + - - +
271C ASP* 3.5 31.7 + - - +
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Residues in contact with ASN 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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264C THR* 3.1 31.6 + - - +
265C THR* 3.3 8.5 + - - +
266C LEU 3.3 0.4 - - - -
267C LYS* 1.3 80.6 + - - +
269C MSE 1.3 63.8 + - + +
271C ASP* 3.3 16.0 + - - +
272C LEU* 3.4 19.7 + - + +
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Residues in contact with MSE 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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67C TYR* 5.1 0.9 - - - -
175C LEU* 4.3 21.8 - - + +
251C ILE* 3.7 37.5 - - + -
265C THR* 3.1 32.3 + - + +
266C LEU* 4.1 11.0 - - + +
268C ASN* 1.3 73.4 - - + +
270C ARG* 1.3 65.1 + - - +
271C ASP 3.1 1.8 - - - -
272C LEU* 3.3 34.2 + - + +
276C GLN* 4.0 15.5 - - - +
277C PHE 4.9 0.7 - - - +
278C LEU* 3.1 46.2 - - + -
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Residues in contact with ARG 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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66C VAL* 3.4 22.4 + - - +
67C TYR* 3.3 55.6 + - + +
68C ASN* 4.0 7.4 - - - +
72C ASP* 2.5 32.0 + - - -
145C ARG* 3.0 60.3 + - + +
266C LEU 2.8 19.4 + - - +
267C LYS* 3.7 9.4 + - - +
268C ASN 3.3 0.4 - - - -
269C MSE 1.3 78.0 - - - +
271C ASP* 1.3 65.8 + - - +
272C LEU 4.1 4.0 - - - +
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Residues in contact with ASP 271 (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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145C ARG* 2.6 31.7 + - - +
267C LYS* 3.5 30.5 + - - +
268C ASN* 3.3 9.0 + - - +
269C MSE 3.1 0.6 - - - -
270C ARG* 1.3 85.0 + - - +
272C LEU* 1.3 66.4 + - + +
273C LYS* 3.8 12.8 + - - +
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Residues in contact with LEU 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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173C ASP* 4.8 7.8 - - - +
174C MSE 5.7 0.5 + - - -
249C ASN* 3.8 11.0 - - - +
251C ILE* 5.4 0.9 - - + -
268C ASN* 3.4 16.1 + - + +
269C MSE 3.3 22.7 + - + +
270C ARG 4.1 4.3 - - - +
271C ASP* 1.3 82.6 - - + +
273C LYS* 1.3 64.0 + - - +
274C GLY 4.2 3.1 + - - +
276C GLN* 3.2 41.8 - - - +
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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