Contacts of the helix formed by residues 257 - 277 (chain A) in PDB entry 1S0O
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 ASN 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A SER* 2.9 12.9 + - - +
256A ARG* 1.3 75.3 - - - +
258A LEU* 1.3 63.3 + - - +
259A GLU* 3.1 11.8 + - - +
260A GLU* 2.6 48.2 + - + +
261A ILE* 3.1 14.4 + - - +
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Residues in contact with LEU 258 (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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256A ARG 3.7 5.3 + - - -
257A ASN* 1.3 70.0 + - - +
259A GLU* 1.3 63.9 + - + +
261A ILE* 3.0 5.1 + - - -
262A LYS* 2.9 59.9 + - + +
316A VAL* 4.4 9.4 - - + -
319A LEU* 3.5 34.3 - - + -
320A GLN* 3.4 40.8 - - + +
323A LEU* 4.4 12.4 - - + +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASN* 3.1 10.3 + - - +
258A LEU* 1.3 84.0 - - + +
260A GLU* 1.3 57.6 + - - +
262A LYS* 3.1 38.2 + - - +
263A PRO* 3.2 23.4 - - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 6.2 0.7 - - - -
253A ARG* 2.6 47.9 + - - +
255A SER* 2.6 35.3 + - - +
257A ASN* 2.6 29.8 + - - +
259A GLU* 1.3 71.9 - - - +
261A ILE* 1.3 59.9 - - - +
263A PRO* 3.7 8.2 - - - +
264A TYR* 3.7 21.3 - - + -
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 4.0 12.6 - - - -
255A SER* 3.5 29.4 - - - +
256A ARG* 3.9 11.2 - - - -
257A ASN 3.4 14.1 - - - +
258A LEU* 3.0 7.2 + - - +
260A GLU* 1.3 79.3 - - - +
262A LYS* 1.3 66.0 + - - +
263A PRO 3.4 0.4 - - - -
264A TYR* 3.0 20.8 + - - +
265A LEU* 3.1 6.5 + - + -
319A LEU* 3.7 27.1 - - + -
323A LEU* 4.6 2.7 - - + -
330A ILE* 4.1 18.6 - - + -
333A ILE* 3.8 30.3 - - + -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 2.9 44.3 + - + +
259A GLU* 3.1 34.0 + - - +
261A ILE* 1.3 75.3 - - - +
263A PRO* 1.3 73.7 - - + +
265A LEU* 2.8 12.0 + - + +
266A PHE* 2.7 51.9 + - + -
316A VAL* 4.2 22.5 - - + +
319A LEU* 4.9 1.7 - - + +
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Residues in contact with PRO 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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259A GLU 3.2 19.7 - - - +
260A GLU* 3.7 8.7 - - - +
261A ILE 3.5 3.8 - - - -
262A LYS* 1.3 90.4 - - + +
264A TYR* 1.3 59.7 + - + +
266A PHE* 3.4 9.6 + - + +
267A ARG* 2.9 41.1 + - - +
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Residues in contact with TYR 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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249A VAL* 4.2 15.5 - - + +
250A THR 4.3 3.8 - - - -
251A MET* 3.4 48.9 - - + +
252A LYS* 3.0 29.7 + - - +
253A ARG 4.8 0.6 + - - -
260A GLU* 3.7 25.8 - - + -
261A ILE 3.0 6.5 + - - +
263A PRO* 1.3 74.9 - - + +
265A LEU* 1.3 61.2 + - - +
267A ARG* 2.9 42.3 + - - +
268A ALA* 2.8 30.7 + - - +
333A ILE* 3.4 17.9 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ILE 3.1 7.9 + - - +
262A LYS* 2.8 15.8 + - - +
264A TYR* 1.3 74.8 - - - +
266A PHE* 1.3 63.1 + - + +
268A ALA* 3.3 7.7 + - - +
269A ILE* 3.0 31.6 + - + +
286A VAL* 4.4 8.1 - - + -
315A SER* 3.7 46.7 - - - +
316A VAL* 4.2 9.9 - - + +
319A LEU* 3.9 21.3 - - + -
333A ILE* 4.0 20.3 - - + +
334A GLY 4.1 23.8 - - - +
335A VAL* 4.6 5.4 - - + -
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 2.7 48.6 + - + +
263A PRO* 3.7 8.7 - - + +
265A LEU* 1.3 76.4 - - + +
267A ARG* 1.3 61.0 + - - +
269A ILE* 3.3 8.5 + - + +
270A GLU* 3.0 32.6 + - - +
312A TYR* 3.3 51.8 + + + +
315A SER* 4.3 3.6 - - - -
316A VAL* 3.8 31.6 - - + -
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Residues in contact with ARG 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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249A VAL* 5.1 15.4 - - + +
263A PRO* 2.9 20.0 + - - +
264A TYR* 2.9 54.1 + - - +
266A PHE* 1.3 76.0 - - - +
268A ALA* 1.3 64.3 + - - +
270A GLU* 3.2 8.7 + - + +
271A GLU* 3.0 42.9 + - + +
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Residues in contact with ALA 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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247A ARG* 3.6 36.9 - - + +
249A VAL* 5.1 5.6 - - + +
264A TYR 2.8 12.5 + - - +
265A LEU* 3.4 11.2 - - - +
267A ARG* 1.3 78.1 - - - +
269A ILE* 1.3 57.9 + - - +
271A GLU* 5.7 0.2 - - - -
272A SER* 2.8 31.2 + - - -
333A ILE 4.6 3.1 - - - +
334A GLY* 4.1 12.6 - - - -
335A VAL* 3.7 8.3 - - + -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.0 20.7 + - + +
266A PHE* 3.6 18.6 - - + +
267A ARG 3.2 0.4 - - - -
268A ALA* 1.3 75.1 - - - +
270A GLU* 1.3 65.6 + - - +
272A SER* 3.3 1.4 + - - -
273A TYR* 3.0 41.1 + - + -
308A LYS* 4.3 2.2 - - + -
311A ALA* 3.6 20.9 - - + +
312A TYR* 3.8 30.7 - - + -
315A SER* 3.2 31.4 - - - +
335A VAL* 3.9 24.0 - - + -
337A PHE* 4.4 2.0 - - + -
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Residues in contact with GLU 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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266A PHE 3.0 10.5 + - - +
267A ARG* 3.2 10.7 + - + +
269A ILE* 1.3 78.5 - - - +
271A GLU* 1.3 65.0 + - + +
273A TYR* 3.4 3.9 + - - +
274A TYR* 3.3 19.8 + - - +
308A LYS* 3.2 40.9 + - - +
312A TYR* 2.8 29.4 + - - +
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Residues in contact with GLU 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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247A ARG* 2.4 53.1 + - + -
249A VAL* 5.4 0.6 - - - +
267A ARG* 3.0 35.8 + - + +
268A ALA 4.1 2.7 - - - +
270A GLU* 1.3 76.5 - - + +
272A SER* 1.3 64.0 + - - +
274A TYR* 3.2 11.6 + - + +
275A LYS* 3.1 29.8 + - + +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.8 3.0 - - - +
246A GLY* 3.4 5.7 - - - -
247A ARG* 3.3 24.0 + - - +
268A ALA 2.8 21.9 + - - -
269A ILE 3.7 1.1 - - - -
270A GLU 3.3 0.2 - - - -
271A GLU* 1.3 77.4 - - - +
273A TYR* 1.3 57.2 + - - +
275A LYS* 3.0 15.2 + - - +
276A LEU* 2.9 29.7 + - - +
335A VAL* 3.4 7.3 - - - +
337A PHE* 3.5 29.8 - - - -
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 3.0 21.2 + - + +
270A GLU 3.8 4.7 - - - +
272A SER* 1.3 73.3 - - - +
274A TYR* 1.3 67.0 + - - +
276A LEU* 3.1 34.6 + - + +
277A ASP 3.5 6.9 + - - +
279A ARG 5.6 1.3 - - - -
280A ILE* 6.1 3.8 - - + -
281A PRO* 4.3 5.4 - - + +
306A ILE* 2.5 36.4 + - - +
307A SER* 3.3 8.8 + - - -
308A LYS* 3.7 47.6 - - + -
311A ALA* 3.9 10.1 - - + -
337A PHE* 3.4 31.6 - + - -
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Residues in contact with TYR 274 (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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79A GLU* 6.0 2.0 - - - -
270A GLU 3.3 9.7 + - - +
271A GLU* 3.2 14.8 + - + +
272A SER 3.2 0.2 - - - -
273A TYR* 1.3 76.7 - - - +
275A LYS* 1.3 71.5 + - + +
277A ASP* 3.0 16.6 + - - +
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Residues in contact with LYS 275 (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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242A ARG* 4.6 17.5 + - - +
245A ILE* 3.4 24.4 - - + +
246A GLY 3.0 24.0 + - - +
247A ARG* 4.4 11.2 - - - +
271A GLU* 3.1 17.5 + - - +
272A SER* 3.0 9.7 + - - +
274A TYR* 1.3 83.9 - - + +
276A LEU* 1.3 62.2 + - - +
277A ASP* 3.0 8.8 + - - +
279A ARG* 3.3 16.6 + - - -
1906D T 3.6 24.7 + - - -
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Residues in contact with LEU 276 (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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245A ILE* 3.8 22.0 - - + -
272A SER 2.9 15.8 + - - +
273A TYR* 3.1 45.5 + - + +
275A LYS* 1.3 75.7 - - - +
277A ASP* 1.3 64.1 + - - +
279A ARG* 2.8 44.1 + - + +
281A PRO* 3.9 25.4 - - + -
337A PHE* 4.1 12.3 - - + -
340A PHE* 3.4 34.8 - - + -
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Residues in contact with ASP 277 (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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273A TYR 3.5 6.8 + - - +
274A TYR 3.0 12.3 + - - +
275A LYS 3.0 9.4 - - - +
276A LEU* 1.3 80.7 - - - +
278A LYS* 1.3 78.8 + - - +
279A ARG* 4.2 10.9 + - - +
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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
------------------------------------------------------------
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