Contacts of the helix formed by residues 263 - 277 (chain D) in PDB entry 1SHZ
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 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLU* 5.8 0.9 - - - +
251D ASP 4.1 0.3 - - - +
252D TYR 3.0 27.3 + - - +
253D ASP* 4.4 3.2 - - - +
254D GLN 3.8 11.1 + - - -
255D VAL* 4.5 2.2 - - - +
261D GLN 3.8 1.8 + - - -
262D THR* 1.3 78.9 - - - +
264D ARG* 1.3 63.9 + - - +
265D MET* 2.7 40.2 + - - +
266D HIS* 3.0 41.0 + - + +
267D GLU 3.1 9.4 + - - -
307D ILE* 4.2 11.5 + - - +
308D CYS* 3.5 9.1 - - - +
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Residues in contact with ARG 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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56D ALA* 5.5 1.7 - - - +
57D GLY 4.1 6.7 + - - -
58D GLU* 3.4 41.9 + - - +
169D GLN* 3.2 24.7 + - - -
251D ASP* 2.9 49.1 + - - +
254D GLN* 3.3 21.1 + - - +
255D VAL 2.8 29.8 + - - +
256D LEU* 3.8 20.2 - - + +
257D MET* 3.9 21.2 - - - +
262D THR 3.6 0.6 + - - -
263D ASN* 1.3 73.0 + - - +
265D MET* 1.3 60.6 + - - +
267D GLU* 3.5 3.8 + - - +
268D SER* 3.2 23.2 + - - -
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Residues in contact with MET 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D VAL* 4.9 6.5 - - - -
248D ALA 4.7 7.6 - - - +
249D LEU* 3.7 16.4 - - - +
251D ASP* 3.6 4.2 + - - +
252D TYR* 3.5 30.1 - - + -
263D ASN* 2.7 14.5 + - - +
264D ARG* 1.3 71.9 - - - +
266D HIS* 1.3 67.2 + - - +
268D SER* 3.3 7.7 + - - -
269D MET* 3.1 21.9 + - - +
308D CYS* 3.3 15.9 - - - -
309D TYR* 3.2 25.4 - - + +
325D ILE* 3.3 46.4 - - + -
329D PHE* 4.4 11.4 - - + -
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Residues in contact with HIS 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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106A LEU* 6.1 1.6 - - + -
164A ARG* 4.5 10.1 + - - -
167A GLU* 4.3 17.5 + - - -
262D THR* 4.8 5.4 - - + -
263D ASN* 3.0 32.3 + - + +
265D MET* 1.3 77.9 - - - +
267D GLU* 1.3 64.3 + - - +
269D MET* 3.3 11.9 + - - +
270D LYS* 3.3 31.4 + - + +
307D ILE 5.6 0.4 + - - -
308D CYS* 3.3 44.7 + - - -
309D TYR* 5.0 9.7 - + - -
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Residues in contact with GLU 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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56D ALA* 4.9 9.4 - - + -
227D ARG* 2.8 43.9 + - - -
230D ARG* 3.1 24.3 + - - +
256D LEU* 3.3 33.9 - - + +
262D THR* 3.9 8.4 - - + +
263D ASN 3.1 6.8 + - - +
264D ARG 3.7 8.3 - - - +
265D MET 3.2 0.4 - - - -
266D HIS* 1.3 77.6 - - - +
268D SER* 1.3 54.8 + - - +
269D MET 2.9 1.0 + - - -
270D LYS* 3.0 11.2 + - - +
271D LEU* 2.6 37.8 + - + +
163F MET* 3.6 17.6 - - - +
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Residues in contact with SER 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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56D ALA* 4.6 12.0 + - - +
245D PHE* 3.9 3.8 - - - -
247D VAL* 3.7 24.1 - - - +
248D ALA 5.1 1.2 + - - -
251D ASP* 6.1 0.5 - - - +
264D ARG 3.2 11.9 + - - -
265D MET* 3.3 12.5 + - - -
267D GLU* 1.3 77.1 - - - +
269D MET* 1.3 53.9 + - - +
271D LEU* 3.5 11.0 - - - +
272D PHE* 2.7 36.9 + - - +
329D PHE* 3.6 18.6 - - - -
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Residues in contact with MET 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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265D MET* 3.1 10.5 + - - +
266D HIS* 3.6 15.3 - - - +
267D GLU 2.9 2.0 + - - -
268D SER* 1.3 76.2 - - - +
270D LYS* 1.3 57.4 + - + +
272D PHE* 3.0 2.1 + - - +
273D ASP 2.7 32.7 + - - -
309D TYR* 3.6 30.1 - - + -
328D GLN* 3.8 42.0 - - + +
329D PHE* 3.8 26.9 - - + -
332D LEU* 3.3 29.5 - - + +
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Residues in contact with LYS 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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105A LYS 5.3 0.6 + - - -
107A HIS* 3.1 41.3 + - + +
227D ARG* 5.0 3.6 - - - +
262D THR* 5.5 5.7 + - - +
266D HIS* 3.3 19.5 + - + +
267D GLU* 3.0 19.5 + - - +
269D MET* 1.3 80.3 - - + +
271D LEU* 1.3 61.9 + - - +
273D ASP* 4.1 6.5 - - - -
274D SER* 3.2 7.4 + - - -
159F SER* 5.2 0.9 + - - -
160F LYS* 2.8 26.6 + - - +
163F MET* 3.4 36.9 - - + +
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Residues in contact with LEU 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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55D GLY 3.7 4.7 - - - -
56D ALA* 3.4 40.4 - - + +
230D ARG* 4.3 11.0 - - - +
233D TRP* 3.9 20.2 - - + -
245D PHE* 3.5 19.9 - - + -
267D GLU* 2.6 24.0 + - + +
268D SER* 3.5 5.2 - - - +
270D LYS* 1.3 71.5 - - - +
272D PHE* 1.3 64.4 + - - +
274D SER* 3.5 4.1 + - - -
275D ILE* 3.4 21.3 + - + +
163F MET* 4.4 6.9 - - - -
165F MET* 3.4 35.0 - - + -
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Residues in contact with PHE 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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245D PHE* 3.5 40.6 - + + -
268D SER 2.7 21.6 + - - +
269D MET 3.5 2.7 - - - +
271D LEU* 1.3 70.3 - - - +
273D ASP* 1.3 69.1 + - - +
275D ILE* 3.4 4.1 + - + -
276D CYS* 2.8 51.8 + - + +
286D ILE* 4.5 12.1 - - + -
288D LEU* 4.2 26.9 - - + -
329D PHE* 3.2 50.3 - + + -
332D LEU* 4.2 7.2 - - + -
341D ILE* 4.2 21.3 - - + -
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Residues in contact with ASP 273 (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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269D MET 2.7 19.8 + - - +
270D LYS* 3.5 9.0 - - - +
272D PHE* 1.3 76.1 - - - +
274D SER* 1.3 65.5 + - - +
276D CYS* 3.7 2.6 - - - +
277D ASN* 3.2 41.4 + - - +
332D LEU* 3.7 32.0 - - + +
334D LYS* 4.4 11.3 + - - -
69F GLN* 5.2 1.9 - - - +
156F ASP* 4.7 4.3 - - - +
160F LYS* 3.1 22.7 + - - -
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Residues in contact with SER 274 (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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270D LYS 3.2 4.3 + - - -
271D LEU* 3.8 8.5 - - - -
272D PHE 3.3 0.2 - - - -
273D ASP* 1.3 84.5 + - - +
275D ILE* 1.3 66.9 + - - +
277D ASN 3.6 3.3 + - - -
278D ASN* 5.4 0.9 + - - -
65F HIS* 5.8 0.7 - - - -
69F GLN* 2.8 41.9 + - - +
160F LYS* 3.4 31.2 - - - +
165F MET* 3.6 25.9 + - - +
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Residues in contact with ILE 275 (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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54D LEU* 4.1 22.7 - - + -
233D TRP* 4.3 24.5 - - + -
234D PHE* 5.9 0.2 - - + -
237D PHE* 4.3 14.8 - - + -
243D ILE* 4.6 14.8 - - + -
245D PHE* 4.7 13.5 - - + -
271D LEU 3.4 13.6 + - - +
272D PHE* 3.4 8.4 + - + +
273D ASP 3.3 0.4 - - - -
274D SER* 1.3 84.3 + - - +
276D CYS* 1.3 72.1 + - - +
278D ASN* 3.1 24.3 + - - +
281D PHE* 3.4 25.4 - - + -
286D ILE* 5.5 4.7 - - + -
165F MET* 4.3 11.7 - - + -
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Residues in contact with CYS 276 (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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272D PHE* 2.8 49.9 + - + +
273D ASP* 3.7 5.4 - - - +
275D ILE* 1.3 79.5 - - - +
277D ASN* 1.3 59.2 + - - +
278D ASN 3.4 5.2 + - - +
281D PHE* 5.3 0.2 - - - +
286D ILE* 3.7 26.6 - - - +
332D LEU 4.1 11.0 - - - +
333D ASN* 3.5 35.7 - - - -
339D LYS* 4.2 7.8 - - - +
341D ILE* 4.3 3.4 - - - -
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Residues in contact with ASN 277 (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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273D ASP* 3.2 32.0 + - - +
274D SER 3.8 4.3 - - - -
275D ILE 3.2 0.2 - - - -
276D CYS* 1.3 76.7 - - - +
278D ASN* 1.3 58.4 + - - +
279D LYS* 3.9 4.7 + - - -
332D LEU 3.0 22.8 + - - -
333D ASN* 3.8 8.7 - - - +
334D LYS* 3.0 52.5 + - + +
335D ARG* 4.2 2.6 + - - +
68F LEU 3.5 10.4 - - - +
69F GLN* 3.6 20.4 - - - +
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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