Contacts of the helix formed by residues 263 - 276 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ASP 3.5 3.8 - - - +
252A TYR 2.8 25.4 + - - -
253A ASP* 4.8 1.2 - - - +
254A GLN 3.6 9.9 + - - -
255A VAL* 4.6 2.2 - - - +
262A THR* 1.3 78.7 - - - +
264A ARG* 1.3 67.9 + - - +
265A MET* 2.7 35.7 + - - +
266A HIS* 3.2 35.8 + - + +
267A GLU* 3.1 14.7 + - - +
307A ILE 3.7 12.7 + - - -
308A CYS* 3.6 10.6 - - - +
167D GLU* 5.5 1.3 - - - +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 4.3 11.1 + - - -
58A GLU* 3.5 42.0 + - - +
169A GLN* 4.2 11.6 + - - -
226A GLN* 6.0 1.4 - - - +
251A ASP* 3.5 29.8 + - - +
254A GLN* 3.1 45.0 + - + +
255A VAL 2.9 26.5 + - - +
256A LEU* 3.9 18.4 - - + +
257A MET* 4.2 18.0 - - - +
258A GLU* 5.4 1.2 + - - -
262A THR 3.4 0.8 + - - -
263A ASN* 1.3 75.1 + - - +
265A MET* 1.3 55.2 + - - +
267A GLU* 2.7 26.7 + - - +
268A SER* 3.0 11.6 + - - -
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 4.4 9.2 - - - -
248A ALA 4.2 8.7 - - - +
249A LEU* 4.0 15.9 - - + +
251A ASP* 3.1 16.0 + - - +
252A TYR* 3.7 15.0 - - + -
263A ASN* 2.7 17.1 + - - +
264A ARG* 1.3 74.3 - - - +
266A HIS* 1.3 58.3 + - - +
268A SER* 3.4 7.6 + - - -
269A MET* 3.2 25.1 + - - +
308A CYS* 3.6 15.9 - - - -
309A TYR* 3.4 22.7 - - + +
325A ILE* 3.7 35.2 - - + -
329A PHE* 4.0 24.2 - - - -
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Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 4.8 4.9 - - + -
263A ASN* 3.1 36.1 + - + +
264A ARG 3.0 0.8 - - - -
265A MET* 1.3 75.8 - - - +
267A GLU* 1.3 60.3 + - - +
269A MET* 3.6 12.0 + - - +
270A LYS* 3.0 35.5 + - + +
307A ILE 5.6 0.2 - - - -
308A CYS* 3.1 39.8 - - - -
309A TYR* 5.4 2.9 - + - -
310A PRO* 5.9 0.6 - - - +
106D LEU* 5.5 3.4 - - + -
164D ARG* 3.2 30.5 + - - -
167D GLU* 3.2 16.5 + - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 5.0 8.1 - - + -
227A ARG* 3.2 23.8 + - - +
230A ARG* 2.9 36.7 + - - +
256A LEU* 3.5 38.2 - - + +
262A THR* 4.1 2.2 - - + -
263A ASN 3.1 4.6 + - - +
264A ARG 2.7 16.1 + - - +
266A HIS* 1.3 70.5 - - - +
268A SER* 1.3 53.9 + - - +
270A LYS* 3.1 33.7 + - - +
271A LEU* 2.7 37.9 + - - +
163C MET* 3.8 12.6 - - - +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 4.5 16.4 + - - +
59A SER* 5.8 0.3 - - - -
245A PHE* 3.6 10.6 - - - -
246A CYS 4.4 1.4 + - - -
247A VAL* 3.2 41.5 - - - +
248A ALA 4.9 0.3 + - - -
251A ASP* 6.0 0.4 - - - -
264A ARG 3.0 9.7 + - - -
265A MET* 3.5 13.2 - - - -
267A GLU* 1.3 77.6 - - - +
269A MET* 1.3 56.6 + - - +
271A LEU* 3.4 5.0 + - - -
272A PHE* 3.0 29.6 + - - +
329A PHE* 3.8 4.0 - - - -
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Residues in contact with MET 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 MET* 3.2 16.2 + - + +
266A HIS* 3.8 13.0 - - - +
267A GLU 3.2 0.2 - - - -
268A SER* 1.3 78.5 - - - +
270A LYS* 1.3 56.9 + - + +
272A PHE 3.4 0.3 + - - -
273A ASP* 3.0 23.9 + - - +
309A TYR* 3.9 28.0 - - + +
328A GLN* 3.6 38.4 - - + +
329A PHE* 3.4 30.5 - - + -
332A LEU* 3.1 26.1 - - + +
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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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227A ARG* 3.8 14.5 - - - +
262A THR* 4.1 12.3 - - - +
266A HIS* 3.0 23.3 + - + +
267A GLU* 3.1 31.8 + - - +
269A MET* 1.3 78.5 - - + +
271A LEU* 1.3 64.2 + - - +
273A ASP* 3.5 6.8 + - - +
274A SER 3.4 14.2 + - - -
160C LYS* 4.4 0.5 + - - -
163C MET* 3.5 28.9 - - - +
105D LYS 4.5 9.5 + - - +
106D LEU* 4.8 5.8 - - - +
107D HIS* 3.6 47.4 - - + +
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Residues in contact with LEU 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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55A GLY 3.5 9.4 - - - +
56A ALA* 3.5 33.9 - - + +
230A ARG* 3.8 27.8 - - - +
233A TRP* 3.6 16.8 - - + -
245A PHE* 3.8 12.8 - - + -
267A GLU* 2.7 18.3 + - - +
268A SER* 3.7 5.2 - - - +
270A LYS* 1.3 78.5 - - - +
272A PHE* 1.3 58.9 + - - +
274A SER* 3.3 4.1 + - - -
275A ILE* 3.3 23.6 + - - +
163C MET* 4.0 6.2 - - - -
165C MET* 3.7 34.8 - - + -
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.6 34.9 - + + -
268A SER 3.0 17.3 + - - +
269A MET 3.7 3.8 - - - +
271A LEU* 1.3 72.0 - - - +
273A ASP* 1.3 61.3 + - - +
274A SER 3.1 1.8 - - - -
275A ILE* 4.7 1.8 - - + -
276A CYS* 3.0 54.6 + - + +
286A ILE* 4.1 15.7 - - + -
288A LEU* 3.4 24.9 - - + -
329A PHE* 3.5 37.9 - + + -
330A GLU 4.7 0.2 - - - -
332A LEU* 4.0 11.7 - - + -
333A ASN 5.8 0.2 - - - -
341A ILE* 3.4 38.4 - - + -
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Residues in contact with ASP 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 MET 3.0 16.8 + - - +
270A LYS* 3.8 8.1 - - - +
271A LEU 3.3 0.2 - - - -
272A PHE* 1.3 76.7 - - - +
274A SER* 1.3 59.4 + - - +
276A CYS* 4.5 2.5 - - - -
277A ASN* 3.6 21.0 + - - +
332A LEU* 2.9 54.1 - - + +
334A LYS* 3.2 23.7 + - - -
160C LYS* 4.7 7.4 + - - +
107D HIS* 5.4 8.5 - - + -
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Residues in contact with SER 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 3.4 6.4 + - - -
271A LEU 3.3 9.1 + - - -
272A PHE 3.1 0.6 - - - -
273A ASP* 1.3 80.5 - - - +
275A ILE* 1.3 61.9 + - - +
277A ASN* 4.2 1.9 - - - +
278A ASN* 3.6 26.2 + - - +
160C LYS* 3.1 43.4 - - - +
163C MET* 4.2 4.9 - - - -
165C MET* 3.7 21.8 + - - +
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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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54A LEU* 3.5 21.1 - - + -
233A TRP* 3.8 15.7 - - + -
237A PHE* 5.6 1.3 - - + -
243A ILE* 4.1 20.0 - - + -
245A PHE* 3.4 36.6 - - + -
271A LEU 3.3 12.0 + - - +
272A PHE* 4.0 5.4 - - + +
274A SER* 1.3 75.8 - - - +
276A CYS* 1.3 63.7 + - - +
277A ASN 3.0 1.8 - - - -
278A ASN* 2.9 23.4 + - - +
281A PHE* 3.2 36.2 - - + +
286A ILE* 5.1 5.4 - - + -
165C MET* 4.1 15.7 - - + -
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Residues in contact with CYS 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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272A PHE* 3.0 35.2 + - + +
273A ASP* 5.0 1.6 - - - -
275A ILE* 1.3 80.5 - - - +
277A ASN* 1.3 68.9 + - - +
278A ASN 3.5 1.3 + - - +
281A PHE 5.0 1.7 - - - +
286A ILE* 3.7 26.5 - - + +
332A LEU 5.4 1.1 - - - +
333A ASN* 4.0 19.3 - - - -
339A LYS* 3.9 13.6 - - - +
341A ILE* 3.9 30.1 - - - -
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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
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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