Contacts of the helix formed by residues 259 - 281 (chain A) in PDB entry 1W3U
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 GLY 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A GLU 2.9 8.9 + - - -
257A GLU 3.1 2.5 + - - -
258A ARG* 1.3 79.3 - - - +
260A GLY* 1.3 66.8 + - - +
262A GLU* 4.0 4.2 + - - +
263A GLY* 3.0 17.6 + - - -
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Residues in contact with GLY 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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61A LEU* 3.7 17.3 - - - -
255A ILE* 2.9 19.8 + - - -
256A GLU* 3.4 7.7 + - - +
259A GLY* 1.3 81.9 - - - +
261A LEU* 1.3 59.2 + - - -
262A GLU 3.2 0.2 - - - -
264A VAL* 2.9 30.1 + - - +
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Residues in contact with LEU 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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61A LEU* 3.3 35.0 + - + +
62A LEU* 3.6 26.5 - - + -
179A LEU* 3.5 47.3 - - + +
180A SER 4.1 0.7 - - - +
181A ARG 3.7 15.3 - - - +
182A PRO* 3.6 23.4 - - + +
255A ILE* 4.0 13.9 - - + -
260A GLY* 1.3 71.7 - - - -
262A GLU* 1.3 58.5 + - - +
264A VAL* 3.6 4.8 - - - +
265A GLN* 2.9 30.7 + - - +
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Residues in contact with GLU 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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182A PRO* 4.0 15.2 - - + +
259A GLY 4.0 3.1 + - - +
260A GLY 3.2 0.8 - - - -
261A LEU* 1.3 79.3 - - - +
263A GLY* 1.3 63.7 + - - +
265A GLN* 3.0 24.2 - - - +
266A GLN* 3.2 25.9 + - - +
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Residues in contact with GLY 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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258A ARG 3.8 14.6 - - - -
259A GLY* 3.0 22.1 + - - -
260A GLY 3.6 0.4 - - - -
262A GLU* 1.3 76.4 - - - +
264A VAL* 1.3 64.8 + - - +
266A GLN* 3.1 11.0 + - - +
267A ALA* 3.0 22.7 + - - +
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Residues in contact with VAL 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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179A LEU 3.7 18.8 - - - +
180A SER 3.6 13.0 - - - +
254A TRP* 4.7 5.4 - - + -
255A ILE* 4.3 12.3 - - + -
258A ARG* 3.9 26.9 + - + -
260A GLY 2.9 18.5 + - - +
261A LEU* 3.6 14.8 - - + +
263A GLY* 1.3 76.4 - - - +
265A GLN* 1.3 61.1 + - - +
267A ALA* 4.3 5.8 - - + -
268A ASN* 2.7 38.4 + - - +
340A ASN* 4.0 23.6 - - + +
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Residues in contact with GLN 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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180A SER 3.4 13.9 - - - +
181A ARG* 3.4 23.6 - - + +
182A PRO* 3.4 18.1 + - + +
261A LEU 2.9 19.0 + - - +
262A GLU* 3.0 24.6 - - - +
263A GLY 3.2 0.2 - - - -
264A VAL* 1.3 79.6 - - - +
266A GLN* 1.3 58.3 + - - +
268A ASN* 3.7 3.7 - - - +
269A ARG* 2.8 32.0 + - + +
297A ASP* 5.2 1.9 - - - +
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Residues in contact with GLN 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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262A GLU* 3.2 19.9 + - - +
263A GLY* 3.1 12.3 + - - +
265A GLN* 1.3 81.0 - - - +
267A ALA* 1.3 63.3 + - - +
269A ARG* 3.3 7.5 + - + +
270A LYS* 3.1 22.0 + - - +
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Residues in contact with ALA 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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263A GLY 3.0 14.7 + - - +
264A VAL* 3.6 8.1 - - + +
266A GLN* 1.3 77.2 - - - +
268A ASN* 1.3 63.4 + - - +
270A LYS* 3.3 11.2 + - - +
271A LYS* 3.0 34.7 + - + +
344A TYR* 5.4 0.2 - - - -
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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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180A SER 3.8 11.7 + - - +
264A VAL* 2.7 21.3 + - - +
265A GLN* 3.8 4.5 - - - +
267A ALA* 1.3 78.0 - - - +
269A ARG* 1.3 58.8 + - - +
271A LYS* 2.9 31.4 + - - +
272A ALA* 2.8 32.8 + - - +
297A ASP* 4.5 8.8 - - + +
298A MET* 3.4 28.1 - - + +
340A ASN* 2.8 34.8 + - - +
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Residues in contact with ARG 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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265A GLN* 2.8 24.4 + - + +
266A GLN* 3.6 8.1 - - + +
268A ASN* 1.3 72.4 - - - +
270A LYS* 1.3 57.5 + - - +
272A ALA* 3.6 12.1 - - - +
273A SER* 2.8 57.2 + - - +
276A TYR* 4.0 13.7 - - - +
295A ARG* 6.1 0.4 - - - +
297A ASP* 2.8 44.4 + - - +
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Residues in contact with LYS 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 GLN* 3.1 13.4 + - + +
267A ALA* 3.4 12.5 - - - +
269A ARG* 1.3 74.9 - - - +
271A LYS* 1.3 64.7 + - - +
273A SER* 3.4 5.0 + - - -
274A LEU* 3.1 23.6 + - - +
344A TYR* 3.7 47.1 - - + +
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Residues in contact with LYS 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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267A ALA* 3.0 24.9 + - + +
268A ASN* 2.9 27.0 + - - +
270A LYS* 1.3 78.4 - - - +
272A ALA* 1.3 63.8 + - - +
274A LEU* 3.3 4.5 + - - +
275A ILE* 3.3 24.0 + - - +
338A ILE* 3.0 24.0 + - + -
339A TYR 2.8 29.5 + - - -
340A ASN 3.4 4.6 + - - +
342A VAL 2.9 23.6 + - - +
344A TYR* 3.8 31.9 - - + +
347A CYS* 3.8 22.8 - - - +
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Residues in contact with ALA 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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268A ASN 2.8 16.7 + - - +
269A ARG* 3.6 4.7 - - - +
271A LYS* 1.3 78.5 - - - +
273A SER* 1.3 58.8 + - - +
275A ILE* 3.1 2.4 + - - -
276A TYR* 2.8 35.0 + - + -
297A ASP* 3.2 33.2 - - - +
300A ILE* 3.8 7.7 - - + +
338A ILE* 3.7 21.8 - - + -
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Residues in contact with SER 273 (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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269A ARG* 2.8 42.5 + - - +
270A LYS* 3.8 5.8 - - - -
271A LYS 3.3 0.2 - - - -
272A ALA* 1.3 77.1 - - - +
274A LEU* 1.3 62.3 + - - +
276A TYR* 4.5 4.0 - - - +
277A ASP* 2.8 39.5 + - - +
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Residues in contact with LEU 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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270A LYS 3.1 13.4 + - - +
271A LYS 3.5 9.4 - - - +
273A SER* 1.3 78.3 - - - +
275A ILE* 1.3 60.8 + - - +
277A ASP* 3.5 6.2 + - + +
278A ALA* 3.1 20.3 + - - +
344A TYR* 3.7 32.1 - - + +
347A CYS* 3.9 10.1 - - + +
348A GLU* 3.8 36.8 - - + +
351A VAL* 3.7 17.4 - - + +
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Residues in contact with ILE 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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271A LYS 3.3 14.3 + - - +
272A ALA 3.1 6.9 + - - +
274A LEU* 1.3 74.0 - - - +
276A TYR* 1.3 67.9 + - - +
278A ALA* 3.1 3.8 + - - +
279A ILE* 3.0 27.5 + - + +
300A ILE* 3.9 32.1 - - + -
302A PHE* 5.1 2.2 - - + -
336A ALA* 4.4 5.2 - - + -
338A ILE* 3.9 28.3 - - + -
347A CYS* 3.9 15.5 - - + -
350A LEU* 4.0 25.8 - - + -
351A VAL* 3.9 19.5 - - + -
354A MET* 4.6 9.4 - - - -
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Residues in contact with TYR 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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156A GLY 4.4 2.3 + - - -
269A ARG* 4.0 11.0 - - - +
272A ALA 2.8 27.0 + - - +
273A SER* 4.1 4.0 - - - +
275A ILE* 1.3 76.7 - - - +
277A ASP* 1.3 60.1 + - - +
279A ILE* 3.2 11.3 + - + +
280A ASP* 2.7 36.0 + - - +
288A GLY* 5.8 1.8 - - - -
290A VAL* 5.4 0.4 - - + +
295A ARG* 3.3 63.2 - - + +
296A SER 2.6 40.3 + - - -
297A ASP* 4.2 8.5 - - - -
299A ASN 4.3 0.9 + - - -
300A ILE* 3.5 39.3 - - + +
301A THR 4.9 4.8 + - - -
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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 SER* 2.8 31.4 + - - +
274A LEU* 3.7 6.5 - - + +
276A TYR* 1.3 80.0 - - - +
278A ALA* 1.3 57.4 + - - +
280A ASP* 4.3 8.0 - - - +
281A GLN* 2.8 62.5 + - - +
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Residues in contact with ALA 278 (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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274A LEU 3.1 14.6 + - - +
275A ILE 3.1 8.9 + - - +
277A ASP* 1.3 76.9 - - - +
279A ILE* 1.3 61.0 + - - +
281A GLN* 4.1 3.7 - - - +
282A SER* 3.3 20.6 + - - -
286A TYR* 4.2 3.3 - - - -
351A VAL* 3.9 25.6 - - + +
354A MET* 4.1 17.5 - - + -
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Residues in contact with ILE 279 (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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275A ILE* 3.0 21.0 + - + +
276A TYR* 3.5 16.2 - - + +
278A ALA* 1.3 76.5 - - - +
280A ASP* 1.3 72.2 + - - +
282A SER* 2.7 23.9 + - - -
284A GLY 5.1 0.7 + - - -
286A TYR* 3.5 26.0 - - + +
287A ARG* 4.0 0.4 - - - -
288A GLY* 3.6 27.6 - - - +
295A ARG* 4.6 1.6 - - - +
300A ILE* 3.8 28.3 - - + -
301A THR 4.9 1.1 - - - +
302A PHE* 3.8 21.3 - - + -
354A MET* 4.0 15.9 - - + -
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Residues in contact with ASP 280 (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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276A TYR* 2.7 23.3 + - - +
277A ASP* 4.0 8.6 - - - +
279A ILE* 1.3 78.5 - - - +
281A GLN* 1.3 60.2 + - + +
282A SER 3.3 2.6 + - - -
283A GLY 4.6 3.1 + - - -
284A GLY 5.5 0.9 + - - -
292A VAL* 5.4 2.3 - - - +
295A ARG* 2.7 43.8 + - - -
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Residues in contact with GLN 281 (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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277A ASP* 2.8 50.8 + - - +
278A ALA* 4.1 4.2 - - - +
280A ASP* 1.3 79.4 - - + +
282A SER* 1.3 54.4 + - - +
283A GLY 3.2 9.9 + - - -
358A LYS* 5.4 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