Contacts of the helix formed by residues 258 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A VAL* 6.2 0.2 - - + -
255A ASP* 3.4 29.3 + - + +
256A GLY 3.5 2.4 - - - -
257A HIS* 1.3 75.8 - - - +
259A VAL* 1.3 63.2 - - - +
260A LEU* 3.5 7.8 + - - +
261A GLY* 2.8 26.6 + - - -
262A LEU* 2.9 24.6 + - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.4 2.9 - - + -
29A PRO* 3.9 41.1 - - + -
32A CYS* 4.0 21.3 - - - -
58A GLU* 3.9 27.3 - - + +
61A VAL* 4.1 13.0 - - + -
62A ALA 4.2 3.1 - - - +
257A HIS 3.6 5.3 + - - -
258A ASP* 1.3 72.3 + - - +
260A LEU* 1.3 74.1 + - + +
262A LEU* 3.2 6.5 + - - +
263A ILE* 3.0 42.8 + - + +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.4 44.2 - - + +
26A GLU* 5.0 7.6 - - + -
28A LEU* 4.6 0.4 - - + -
29A PRO* 4.1 23.6 - - + -
258A ASP* 3.3 6.5 + - - +
259A VAL* 1.3 82.2 - - + +
261A GLY* 1.3 59.2 + - - +
263A ILE* 3.4 15.5 + - + +
264A THR* 2.9 30.0 + - - +
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 5.8 3.8 - - - -
258A ASP* 2.8 28.6 + - - -
260A LEU* 1.3 76.4 - - - +
262A LEU* 1.3 60.9 + - - +
264A THR* 3.5 9.1 - - - +
265A THR* 2.9 28.1 + - - -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU 4.4 4.9 - - - +
59A LEU* 4.1 30.5 - - + +
62A ALA* 3.9 9.6 - - + -
254A VAL* 3.9 16.4 - - + -
255A ASP 3.7 16.2 - - - +
256A GLY* 3.6 27.1 - - - +
258A ASP 2.9 21.9 + - - +
259A VAL 3.7 3.6 - - - +
261A GLY* 1.3 75.6 - - - +
263A ILE* 1.3 55.3 + - - +
265A THR* 3.2 4.1 + - - -
266A LEU* 2.6 44.6 + - + +
278A LEU* 4.6 10.5 - - + -
280A ILE* 4.1 19.1 - - + -
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 4.2 12.6 - - + +
28A LEU* 3.1 36.3 - - + -
62A ALA* 3.9 19.3 - - - -
65A TYR* 3.7 12.8 - - + -
66A VAL* 3.5 21.5 - - + +
259A VAL* 3.0 28.9 + - + +
260A LEU* 3.7 14.1 - - + +
261A GLY 3.4 0.2 - - - -
262A LEU* 1.3 76.9 - - - +
264A THR* 1.3 59.6 + - - +
266A LEU* 4.5 0.2 - - - -
267A LYS* 2.8 52.5 + - - +
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 5.2 10.1 - - - +
260A LEU 2.9 20.2 - - - +
261A GLY* 3.5 13.7 - - - +
263A ILE* 1.3 77.5 - - + +
265A THR* 1.3 60.9 + - - +
267A LYS* 3.8 6.9 - - - +
268A ASN* 3.1 35.1 + - - +
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 4.6 7.0 - - + -
254A VAL* 5.3 10.9 - - + +
261A GLY 2.9 22.2 + - - -
262A LEU* 3.2 8.2 + - - -
264A THR* 1.3 77.2 + - - +
266A LEU* 1.3 66.2 + - - +
268A ASN* 3.2 8.4 + - - +
269A MSE 3.1 43.3 + - + +
278A LEU* 4.0 22.2 - - + -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.6 6.5 - - + -
62A ALA* 3.8 36.3 - - + +
63A LEU* 4.1 18.8 - - + +
66A VAL* 4.0 13.2 - - + -
67A TYR* 4.6 4.2 + - + -
175A LEU* 3.6 29.2 - - + -
177A ILE* 3.7 15.7 - - + -
262A LEU* 2.6 28.2 + - + +
263A ILE 3.9 2.2 - - - +
265A THR* 1.3 73.4 - - - +
267A LYS* 1.3 58.1 + - - +
269A MSE 4.1 2.4 - - + +
270A ARG* 2.8 33.8 + - - +
278A LEU* 3.9 17.0 - - + -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.6 32.8 - - - +
65A TYR* 4.5 8.6 - - - -
66A VAL* 3.7 25.5 - - + +
263A ILE* 2.8 30.3 + - - +
264A THR* 3.8 7.9 - - - +
266A LEU* 1.3 79.2 - - - +
268A ASN* 1.3 66.6 + - - +
270A ARG* 3.7 5.2 + - - +
271A ASP* 3.7 24.9 + - - +
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A THR* 3.1 23.1 + - - +
265A THR* 3.2 9.7 + - - +
267A LYS* 1.3 84.3 - - - +
269A MSE 1.3 64.8 + - + +
271A ASP* 3.2 15.0 + - - +
272A LEU* 3.4 19.9 + - + +
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Residues in contact with MSE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A TYR* 4.9 0.7 - - - -
175A LEU* 3.9 18.0 - - + +
251A ILE* 3.9 26.5 - - + -
265A THR* 3.1 31.1 + - + +
266A LEU* 4.1 2.9 - - - +
268A ASN* 1.3 73.9 - - + +
270A ARG* 1.3 67.0 + - - +
271A ASP 3.0 2.9 + - - -
272A LEU* 3.1 31.8 + - + +
276A GLN* 3.6 33.0 - - + +
277A PHE 3.8 35.7 - - - +
278A LEU* 4.0 18.6 - - - -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 21.4 + - - +
67A TYR* 3.3 50.5 + - + +
68A ASN* 4.0 11.7 - - - +
72A ASP* 3.1 29.5 + - - -
143A ASN* 5.3 5.6 + - - +
145A ARG* 2.7 54.7 + - - +
175A LEU* 5.7 0.7 - - - -
266A LEU 2.8 18.8 + - - +
267A LYS* 3.9 8.8 + - - +
268A ASN 3.3 0.2 - - - -
269A MSE 1.3 78.0 - - - +
271A ASP* 1.3 65.9 + - - +
272A LEU 4.1 0.2 - - - +
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 4.3 7.4 + - - +
267A LYS* 3.7 15.6 + - - +
268A ASN* 3.2 10.6 + - - +
269A MSE 3.0 1.0 - - - -
270A ARG* 1.3 100.5 + - - +
272A LEU* 1.3 66.1 + - + +
273A LYS* 4.6 12.1 + - - -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 3.9 13.0 + - - -
173A ASP* 4.6 3.5 - - - +
174A MSE 5.8 0.3 + - - -
249A ASN* 4.4 8.3 - - - +
251A ILE* 5.9 0.7 - - + -
268A ASN* 3.4 14.4 - - + +
269A MSE 3.1 30.6 + - + +
271A ASP* 1.3 83.7 - - - +
273A LYS* 1.3 64.2 + - - +
274A GLY 4.6 1.9 - - - +
276A GLN* 3.7 31.6 - - - +
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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