Contacts of the helix formed by residues 226 - 237 (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 GLN 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLY* 4.1 9.5 - - - +
58A GLU* 4.7 2.8 - - - +
200A ARG* 4.2 7.5 - - - +
203A THR 4.0 12.0 - - - +
224A GLY 3.6 0.8 - - - -
225A GLY* 1.3 81.5 + - - +
227A ARG* 1.3 67.7 + - - +
228A SER* 3.3 4.5 - - - +
229A GLU* 2.8 21.0 + - + +
230A ARG* 3.2 6.0 + - - +
257A MET* 5.0 12.9 - - + +
258A GLU* 3.8 20.9 - - - +
264A ARG* 6.0 1.6 - - - +
378A ALF 2.9 32.3 - - - -
31C PHE* 3.0 50.5 - - + -
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Residues in contact with ARG 227 (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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225A GLY 3.6 1.0 + - - -
226A GLN* 1.3 71.8 - - - +
228A SER* 1.3 63.7 + - - +
229A GLU 3.2 0.9 + - - -
230A ARG* 3.1 41.7 + - - +
231A LYS* 4.3 6.2 + - - -
256A LEU* 3.7 8.2 - - - +
258A GLU* 3.2 28.1 + - + +
259A ASP* 3.0 28.7 + - - +
262A THR* 4.5 4.4 + - - +
267A GLU* 3.2 37.4 + - - +
270A LYS* 3.8 11.5 - - - +
162C LEU* 4.2 20.3 + - - +
163C MET* 4.2 12.9 - - - +
164C GLY* 4.5 4.3 - - - -
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Residues in contact with SER 228 (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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226A GLN* 4.4 1.8 - - - +
227A ARG* 1.3 77.6 - - - +
229A GLU* 1.3 61.2 + - - +
230A ARG 3.4 0.2 - - - -
231A LYS* 3.2 35.8 - - - +
232A LYS* 4.8 5.0 - - - -
31C PHE* 4.0 13.2 - - - -
34C GLU* 3.2 52.5 + - - +
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Residues in contact with GLU 229 (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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203A THR 4.2 6.1 - - - +
204A LYS* 3.1 20.2 - - + +
205A GLY* 2.8 37.0 + - - +
223A VAL* 5.3 0.3 - - - +
224A GLY* 3.2 36.5 + - - +
226A GLN* 2.8 24.1 + - + +
228A SER* 1.3 82.1 + - - +
230A ARG* 1.3 61.6 + - - +
231A LYS 3.4 1.1 - - - -
232A LYS* 2.9 44.4 + - - +
233A TRP* 3.6 6.8 - - - -
31C PHE* 4.6 4.0 - - + -
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Residues in contact with ARG 230 (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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56A ALA* 4.1 20.6 - - - +
57A GLY 4.7 0.8 - - - +
225A GLY 2.8 22.2 + - - +
226A GLN* 3.2 6.6 + - - +
227A ARG* 3.1 30.0 + - - +
229A GLU* 1.3 74.0 - - - +
231A LYS* 1.3 65.8 + - - +
232A LYS 3.0 2.5 - - - -
233A TRP* 2.9 51.0 + - + +
234A PHE* 3.9 4.9 - - - -
256A LEU* 5.7 2.2 - - - +
258A GLU* 4.7 4.0 + - - -
267A GLU* 2.9 30.5 + - - +
271A LEU* 3.8 31.9 - - - +
163C MET* 3.1 26.7 + - - +
164C GLY 3.6 16.7 - - - +
165C MET* 4.2 4.0 - - - -
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Residues in contact with LYS 231 (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 4.3 3.8 + - - -
228A SER* 3.2 35.8 + - - +
230A ARG* 1.3 77.5 - - - +
232A LYS* 1.3 73.3 + - + +
233A TRP 3.1 4.3 + - - -
234A PHE* 3.5 16.7 + - - +
235A GLU* 3.2 11.2 - - - +
164C GLY* 3.9 9.9 + - - -
166C THR 5.1 1.6 - - - +
169C GLU* 3.7 42.5 + - + +
170C GLN* 5.1 24.0 - - + +
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Residues in contact with LYS 232 (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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204A LYS* 4.7 5.7 - - - +
205A GLY* 4.0 15.6 - - - +
206A ILE* 3.2 32.8 - - + +
228A SER 4.8 7.6 - - - -
229A GLU* 2.9 44.4 + - - +
230A ARG 3.0 0.8 - - - -
231A LYS* 1.3 84.9 - - + +
233A TRP* 1.3 61.0 + - + +
235A GLU* 2.7 26.6 + - - +
34C GLU* 5.8 2.0 + - - -
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Residues in contact with TRP 233 (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* 4.0 16.4 - - + -
55A GLY 3.5 34.5 - - - -
223A VAL* 3.0 36.3 - - + +
224A GLY 2.9 26.7 + - - -
225A GLY* 4.1 1.3 - - - -
229A GLU* 3.6 13.6 + - - -
230A ARG* 2.9 27.9 + - + +
232A LYS* 1.3 77.7 - - + +
234A PHE* 1.3 58.8 + - + +
235A GLU 2.8 11.9 + - - -
236A CYS* 2.9 21.3 + - - +
237A PHE* 3.4 23.4 - + + -
271A LEU* 3.6 26.9 - - + -
275A ILE* 3.8 23.6 - - + -
165C MET* 4.1 20.0 - - + -
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Residues in contact with PHE 234 (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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230A ARG 3.9 7.0 - - - -
231A LYS 3.9 15.9 - - - +
232A LYS 3.4 0.6 - - - -
233A TRP* 1.3 79.1 - - + +
235A GLU* 1.3 59.5 + - - +
236A CYS 2.9 6.1 + - - -
237A PHE* 3.6 44.7 + + + +
278A ASN* 5.0 7.0 - - - -
280A TRP* 5.7 7.0 - - - -
164C GLY 3.9 4.5 - - - -
165C MET* 3.1 54.7 - - + -
166C THR 3.7 13.2 - - - -
167C PRO* 4.1 32.3 - - + -
168C TRP* 6.5 0.9 - - + -
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Residues in contact with GLU 235 (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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206A ILE* 4.3 10.1 - - + -
231A LYS 3.2 10.2 - - - +
232A LYS* 2.7 43.8 - - - +
233A TRP 2.8 3.0 + - - -
234A PHE* 1.3 73.7 - - - +
236A CYS* 1.3 64.1 + - - +
237A PHE 3.9 0.2 - - - -
238A GLU* 3.1 17.2 - - - +
168C TRP* 5.9 3.4 - - - -
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Residues in contact with CYS 236 (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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50A LYS* 3.5 13.6 + - - +
52A LEU* 3.7 25.5 - - + +
206A ILE* 3.6 42.6 - - - -
221A PHE* 4.5 11.2 - - + -
223A VAL* 5.3 3.1 - - + -
233A TRP* 2.9 12.4 + - - +
235A GLU* 1.3 88.3 - - - +
237A PHE* 1.3 61.0 + - - +
238A GLU* 3.0 20.0 + - - +
240A VAL* 3.5 13.2 - - - +
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Residues in contact with PHE 237 (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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52A LEU* 4.4 10.5 - - + -
54A LEU* 5.4 5.8 - - + -
233A TRP* 3.4 46.0 - + + -
234A PHE* 3.6 39.4 + + + +
235A GLU 3.9 0.2 - - - -
236A CYS* 1.3 76.7 - - - +
238A GLU* 1.3 58.9 + - - +
239A GLY 3.8 1.4 + - - -
240A VAL* 3.9 13.4 + - - +
275A ILE* 5.6 0.7 - - + -
278A ASN* 3.8 19.7 - - - -
280A TRP* 3.2 45.4 - + + +
281A PHE* 3.4 33.1 - + + -
165C MET* 4.5 16.4 - - + -
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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