Contacts of the helix formed by residues 258 - 272 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D ASP* 3.1 27.1 + - + +
256D GLY 3.6 1.2 - - - -
257D HIS* 1.3 74.9 - - - +
259D VAL* 1.3 65.2 + - - +
260D LEU* 3.4 10.7 + - - +
261D GLY* 2.8 37.0 + - - -
262D LEU* 2.9 16.4 + - - +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.2 3.8 - - + -
29D PRO* 3.8 41.3 - - + -
32D CYS* 3.8 26.2 - - + -
58D GLU* 3.9 19.4 - - + +
61D VAL* 3.9 19.3 - - + -
62D ALA* 4.2 2.0 - - - +
257D HIS 3.5 6.1 + - - -
258D ASP* 1.3 72.9 + - - +
260D LEU* 1.3 73.6 + - + +
262D LEU* 3.3 6.1 + - - +
263D ILE* 3.1 42.3 + - + +
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 3.7 45.8 - - + +
26D GLU* 5.4 3.1 - - - -
28D LEU* 4.9 0.7 - - + -
29D PRO* 3.8 26.7 - - + -
258D ASP* 3.2 8.1 + - - +
259D VAL* 1.3 82.9 - - + +
261D GLY* 1.3 61.0 + - - +
263D ILE* 3.6 13.5 + - + +
264D THR* 3.1 25.6 + - - -
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Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D VAL* 5.6 4.9 - - - -
258D ASP* 2.8 28.8 + - - -
260D LEU* 1.3 77.0 - - - +
262D LEU* 1.3 62.3 + - - +
264D THR* 3.5 6.7 + - - -
265D THR* 3.2 25.1 + - - -
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 4.2 7.4 - - + +
59D LEU* 4.1 31.4 - - + +
62D ALA* 3.8 9.6 - - + -
254D VAL* 4.1 7.2 - - + -
255D ASP 3.7 11.9 - - - +
256D GLY* 3.6 27.1 - - - +
258D ASP 2.9 15.3 + - - +
259D VAL 3.6 6.3 - - - +
261D GLY* 1.3 76.2 - - - +
263D ILE* 1.3 54.8 + - - +
265D THR* 3.3 3.5 + - - -
266D LEU* 2.7 46.3 + - + +
278D LEU* 4.7 6.5 - - + -
280D ILE* 3.3 34.8 - - + -
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Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 5.4 11.4 - - + +
28D LEU* 3.3 34.5 - - + -
62D ALA* 3.8 22.0 - - - +
65D TYR* 3.8 20.4 - - + -
66D VAL* 3.4 22.1 - - + +
259D VAL* 3.1 26.6 + - + +
260D LEU* 3.9 12.1 - - + +
261D GLY 3.3 0.2 - - - -
262D LEU* 1.3 74.9 - - - +
264D THR* 1.3 67.7 + - - +
266D LEU* 4.5 0.7 - - - -
267D LYS* 2.9 30.5 + - + +
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Residues in contact with THR 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU 3.1 13.2 + - - -
261D GLY* 3.7 10.4 - - - -
262D LEU 3.3 0.2 - - - -
263D ILE* 1.3 79.9 - - - +
265D THR* 1.3 61.6 + - - +
267D LYS* 3.6 13.9 - - - +
268D ASN* 3.1 25.1 + - - +
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Residues in contact with THR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ILE* 4.6 8.7 - - + -
254D VAL* 5.1 11.6 - - + +
261D GLY 3.2 15.5 + - - -
262D LEU* 3.7 7.6 - - - -
263D ILE 3.1 0.6 - - - -
264D THR* 1.3 78.1 - - - +
266D LEU* 1.3 68.3 + - + +
267D LYS 3.1 2.2 + - - -
268D ASN* 3.3 8.5 + - - +
269D MSE 3.3 45.0 + - + +
278D LEU* 4.1 19.7 - - + -
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 4.7 3.6 - - + -
62D ALA* 3.7 30.7 - - + +
63D LEU* 3.8 34.5 - - + +
66D VAL* 3.7 16.5 - - + +
67D TYR* 4.6 4.6 + - + -
175D LEU* 5.0 5.6 - - + +
177D ILE* 4.9 6.1 - - + -
262D LEU* 2.7 36.0 + - + +
263D ILE 4.0 1.8 - - - +
265D THR* 1.3 75.6 - - + +
267D LYS* 1.3 62.9 + - - +
269D MSE 4.8 4.7 - - - +
270D ARG* 3.1 28.4 + - - +
278D LEU* 3.7 31.0 - - + -
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Residues in contact with LYS 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 6.3 1.6 - - - +
66D VAL* 4.6 26.8 + - + +
263D ILE* 2.9 22.2 + - + +
264D THR* 3.6 10.5 - - - +
265D THR 3.1 0.4 - - - -
266D LEU* 1.3 79.1 - - - +
268D ASN* 1.3 70.2 + - - +
270D ARG* 3.7 7.4 + - - +
271D ASP* 3.7 23.7 + - - +
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Residues in contact with ASN 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D THR* 3.1 27.1 + - - +
265D THR* 3.3 8.5 + - - +
267D LYS* 1.3 82.0 - - - +
269D MSE 1.3 66.6 + - + +
271D ASP* 3.0 17.7 + - - +
272D LEU* 3.1 23.0 + - + +
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Residues in contact with MSE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TYR* 5.0 0.2 - - - -
175D LEU* 4.0 23.9 - - + +
249D ASN 4.5 0.2 - - - +
251D ILE* 3.4 33.7 - - + -
265D THR* 3.3 28.5 + - + +
266D LEU* 4.4 1.8 - - - +
268D ASN* 1.3 73.5 - - + +
270D ARG* 1.3 67.0 + - - +
272D LEU* 3.0 35.9 + - + +
276D GLN* 4.0 23.9 - - + +
277D PHE 3.4 31.0 - - - +
278D LEU* 3.6 25.1 - - - -
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Residues in contact with ARG 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 3.8 23.9 + - - -
67D TYR* 3.3 42.6 + - + +
68D ASN* 4.3 10.7 - - - +
72D ASP* 2.9 31.5 + - - -
143D ASN* 5.1 5.9 + - - +
145D ARG* 3.4 46.2 + - + +
175D LEU* 5.9 0.7 - - - -
266D LEU 3.1 19.6 + - - +
267D LYS* 4.0 5.2 - - - +
268D ASN 3.2 0.2 + - - -
269D MSE 1.3 76.9 - - - +
271D ASP* 1.3 77.8 + - - +
272D LEU 3.9 0.7 - - - +
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Residues in contact with ASP 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ASN* 5.6 3.8 + - - -
145D ARG* 4.6 6.6 + - - +
267D LYS* 3.7 20.4 + - - +
268D ASN* 3.0 10.0 + - - +
270D ARG* 1.3 97.4 + - - +
272D LEU* 1.3 67.3 + - + +
273D LYS* 3.8 6.2 + - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ARG* 3.8 13.5 + - - -
173D ASP* 4.7 1.4 - - - +
174D MSE 5.9 0.3 + - - -
249D ASN* 4.3 9.2 - - - +
251D ILE* 6.0 0.9 - - + -
268D ASN* 3.1 20.3 + - + +
269D MSE 3.0 33.3 + - + +
270D ARG 3.9 0.3 - - - +
271D ASP* 1.3 83.5 - - + +
273D LYS* 1.3 61.6 + - - +
274D GLY 4.6 1.7 - - - +
276D GLN* 3.4 32.5 - - - +
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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