Contacts of the helix formed by residues 258 - 281 (chain Z) in PDB entry 5WTI
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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Z ILE 3.9 1.7 + - - +
257Z GLU* 1.3 76.7 - - + +
259Z ILE* 1.3 61.2 + - - +
260Z GLN* 2.8 23.4 + - - +
261Z ALA* 2.2 49.4 + - + +
262Z PHE* 3.0 21.0 + - - +
354Z TYR* 3.6 17.6 + - + -
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Residues in contact with ILE 259 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256Z LYS* 3.2 40.4 - - + +
257Z GLU* 4.1 7.4 - - - +
258Z ASP* 1.3 75.2 - - - +
260Z GLN* 1.3 60.3 + - - +
262Z PHE* 3.9 11.0 - - + -
263Z LYS* 2.6 40.6 + - + +
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Residues in contact with GLN 260 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257Z GLU 4.3 3.5 + - - +
258Z ASP* 2.8 27.8 + - - +
259Z ILE* 1.3 90.6 + - - +
261Z ALA* 1.3 57.3 + - + +
263Z LYS* 3.9 3.9 - - - +
264Z SER* 3.0 28.8 + - - -
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Residues in contact with ALA 261 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258Z ASP* 2.2 42.5 + - - +
260Z GLN* 1.3 66.2 - - - +
262Z PHE* 1.3 64.3 + - - +
264Z SER* 3.9 5.8 - - - -
265Z LEU* 3.0 31.8 + - + +
354Z TYR* 3.9 20.4 - - + -
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Residues in contact with PHE 262 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252Z GLU* 5.1 3.4 - - - -
255Z ILE* 4.0 20.6 - - + +
256Z LYS* 3.2 47.1 - - + -
258Z ASP 3.0 20.7 + - - +
259Z ILE* 3.5 13.9 - - + +
261Z ALA* 1.3 78.0 - - - +
263Z LYS* 1.3 63.3 + - + +
265Z LEU* 3.3 3.8 + - - +
266Z GLU* 2.9 48.4 + - - +
287Z ARG* 4.8 4.0 - - - -
354Z TYR* 3.2 18.0 + - - +
358Z TYR* 3.7 26.0 - + - -
361Z PHE* 4.8 13.0 - + - -
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Residues in contact with LYS 263 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259Z ILE* 2.6 30.2 + - + +
260Z GLN* 4.0 4.3 - - - +
262Z PHE* 1.3 75.7 - - + +
264Z SER* 1.3 57.5 + - - +
266Z GLU* 3.3 12.4 + - - +
267Z GLN* 2.9 28.8 + - - +
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Residues in contact with SER 264 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260Z GLN 3.0 20.3 + - - -
261Z ALA* 3.3 6.5 + - - -
262Z PHE 3.3 0.2 - - - -
263Z LYS* 1.3 76.7 - - - +
265Z LEU* 1.3 57.6 + - - +
267Z GLN* 3.5 7.1 + - - +
268Z TYR* 2.9 27.4 + - - +
338Z PHE* 3.5 23.3 - - - -
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Residues in contact with LEU 265 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261Z ALA* 3.0 23.2 + - + +
262Z PHE 3.8 0.9 - - - +
264Z SER* 1.3 72.4 - - - +
266Z GLU* 1.3 61.5 + - - +
268Z TYR* 3.3 8.9 + - + +
269Z GLU* 2.8 32.4 + - - +
288Z LEU* 3.9 24.0 - - + -
338Z PHE* 4.1 21.8 - - + -
339Z LEU* 4.7 15.3 - - + -
354Z TYR* 3.7 28.0 - - + -
355Z PRO* 5.3 5.6 - - + -
358Z TYR* 3.8 36.6 - - + -
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Residues in contact with GLU 266 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262Z PHE* 2.9 56.6 + - + +
263Z LYS* 3.3 10.1 + - - +
265Z LEU* 1.3 76.1 - - - +
267Z GLN* 1.3 57.7 + - - +
269Z GLU* 3.0 15.6 + - - +
270Z LYS* 2.8 29.1 + - - +
287Z ARG* 4.9 6.4 + - - +
358Z TYR* 3.8 9.4 + - - +
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Residues in contact with GLN 267 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263Z LYS 2.9 17.1 + - - +
264Z SER* 3.8 7.2 - - - +
266Z GLU* 1.3 75.4 - - - +
268Z TYR* 1.3 63.6 + - - +
270Z LYS* 3.2 11.4 + - - +
271Z GLU* 2.9 61.0 + - - +
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Residues in contact with TYR 268 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264Z SER 2.9 18.4 + - - +
265Z LEU* 3.6 9.9 - - + +
266Z GLU 3.3 0.2 - - - -
267Z GLN* 1.3 75.6 - - - +
269Z GLU* 1.3 60.1 + - - +
271Z GLU* 3.4 8.2 + - + +
272Z ARG* 2.9 62.3 + - + +
286Z TYR* 3.8 7.6 - + - -
288Z LEU* 3.6 31.9 - - + -
334Z SER* 3.1 32.8 + - - -
335Z VAL* 3.3 11.5 + - + +
338Z PHE* 3.8 41.9 - + + -
339Z LEU* 6.3 0.2 - - + -
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Residues in contact with GLU 269 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265Z LEU 2.8 14.2 + - - +
266Z GLU* 3.0 13.0 + - - +
268Z TYR* 1.3 74.9 - - - +
270Z LYS* 1.3 58.4 + - - +
272Z ARG* 2.8 5.2 + - - +
273Z GLN* 2.8 37.4 + - - +
286Z TYR* 3.8 29.8 - - + +
287Z ARG* 3.2 32.3 + - - +
288Z LEU* 3.8 16.3 + - + +
358Z TYR* 2.6 43.5 + - - -
362Z CYS* 3.8 2.4 - - - -
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Residues in contact with LYS 270 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266Z GLU 2.8 18.1 + - - +
267Z GLN* 3.2 17.2 + - - +
269Z GLU* 1.3 72.6 - - - +
271Z GLU* 1.3 57.6 + - - +
273Z GLN* 3.7 14.5 + - - +
274Z GLU* 3.3 23.4 + - - +
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Residues in contact with GLU 271 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267Z GLN* 2.9 46.4 + - - +
268Z TYR* 3.9 7.6 - - + +
270Z LYS* 1.3 77.5 - - - +
272Z ARG* 1.3 58.4 + - - +
273Z GLN 3.2 0.4 - - - -
274Z GLU* 3.4 7.9 + - - +
275Z GLN* 2.9 28.8 + - - +
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Residues in contact with ARG 272 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B A 6.1 1.0 - - - -
3E T 4.6 4.4 + - - -
4E A 3.2 35.2 + - - -
268Z TYR* 2.9 46.4 + - + +
269Z GLU 2.8 6.3 + - - +
271Z GLU* 1.3 75.5 - - - +
273Z GLN* 1.3 57.2 + - - +
275Z GLN* 3.1 27.2 + - - +
276Z LEU* 2.9 41.5 + - + +
286Z TYR* 3.4 37.3 + - + -
332Z ASP* 2.9 28.3 + - - -
334Z SER* 3.6 20.2 + - - -
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Residues in contact with GLN 273 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Z GLU* 2.8 28.6 + - - +
270Z LYS* 3.9 10.3 + - - +
272Z ARG* 1.3 74.5 - - - +
274Z GLU* 1.3 60.2 + - - +
276Z LEU 3.3 0.5 + - - -
277Z LEU* 2.9 30.2 + - - +
284Z ASN* 3.3 38.5 + - - +
285Z GLU* 3.6 13.5 - - - +
286Z TYR* 3.0 41.5 + - + +
287Z ARG* 5.0 0.7 - - - +
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Residues in contact with GLU 274 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270Z LYS 3.3 16.5 + - - +
271Z GLU* 3.8 6.7 - - - +
273Z GLN* 1.3 77.8 - - - +
275Z GLN* 1.3 61.2 + - - +
277Z LEU* 3.5 7.6 + - - +
278Z ARG* 3.1 35.4 + - - +
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Residues in contact with GLN 275 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B A 4.0 12.9 + - - -
4E A 5.8 1.0 + - - -
271Z GLU 2.9 18.9 + - - +
272Z ARG* 3.1 36.5 + - - +
273Z GLN 3.2 0.2 - - - -
274Z GLU* 1.3 76.8 - - - +
276Z LEU* 1.3 70.7 + - - +
278Z ARG* 3.3 23.6 + - - +
279Z ASP* 2.3 63.3 + - - +
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Residues in contact with LEU 276 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E A 3.5 43.5 - - + +
5E A 3.6 24.7 - - - +
272Z ARG* 2.9 30.1 + - + +
273Z GLN 3.3 0.6 + - - +
275Z GLN* 1.3 91.4 - - - +
277Z LEU* 1.3 54.3 + - - +
280Z THR* 2.5 52.5 + - + +
284Z ASN* 3.6 15.5 - - - +
286Z TYR* 3.8 26.7 - - + -
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Residues in contact with LEU 277 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273Z GLN 2.9 16.7 + - - +
274Z GLU* 4.0 7.9 - - - +
275Z GLN 3.3 0.2 - - - -
276Z LEU* 1.3 77.7 - - - +
278Z ARG* 1.3 58.0 + - - +
281Z LEU* 3.1 45.0 + - - +
282Z ASN 3.9 11.9 - - - +
283Z THR* 4.1 29.2 - - + +
284Z ASN* 3.9 1.9 - - - +
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Residues in contact with ARG 278 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274Z GLU* 3.1 26.1 + - - +
275Z GLN* 3.8 26.1 - - - +
276Z LEU 3.3 0.2 - - - -
277Z LEU* 1.3 79.6 - - - +
279Z ASP* 1.3 67.9 + - - +
281Z LEU* 3.4 14.5 - - - +
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Residues in contact with ASP 279 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B U 2.6 27.9 + - - +
119B A 3.2 44.0 + - - +
275Z GLN* 2.3 49.9 + - - +
276Z LEU 4.3 0.2 - - - +
278Z ARG* 1.3 92.0 + - - +
280Z THR* 1.3 68.8 + - + +
281Z LEU* 3.3 7.5 + - - +
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Residues in contact with THR 280 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B U 4.9 4.8 - - - +
118B U 3.7 11.9 - - - +
4E A 3.6 25.6 - - + -
5E A 3.3 34.6 + - - +
276Z LEU* 2.5 42.5 + - + +
279Z ASP* 1.3 74.4 - - + +
281Z LEU* 1.3 67.2 + - - +
282Z ASN* 3.2 29.2 + - - +
767Z VAL* 5.9 2.4 - - - +
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Residues in contact with LEU 281 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B U 5.5 0.2 - - - +
277Z LEU* 3.1 27.9 + - - +
278Z ARG 3.4 22.4 - - - +
279Z ASP 3.7 7.6 - - - +
280Z THR* 1.3 81.1 + - - +
282Z ASN* 1.3 63.5 + - - +
283Z THR* 4.2 1.9 + - - +
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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
------------------------------------------------------------
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