Contacts of the helix formed by residues 225 - 240 (chain A) in PDB entry 2NTZ
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 LEU 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLU* 1.3 86.5 + - + +
227A PHE* 3.4 4.1 - - - +
228A ASP* 4.0 18.5 + - + -
229A GLN* 3.1 36.2 + - + +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A MSE 3.4 52.3 - - + +
221A GLY* 5.2 3.3 - - - -
222A ASN* 5.2 6.3 - - - +
225A LEU* 1.3 97.7 - - + +
227A PHE* 1.3 62.4 + - + +
229A GLN* 3.9 5.5 + - - +
230A LEU* 3.4 21.3 + - - +
267A LEU* 4.3 15.5 - - - +
268A THR* 5.5 1.0 + - - -
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Residues in contact with PHE 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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192A PRO* 3.6 26.2 - - + -
194A GLU* 3.0 47.6 - - + +
195A LEU* 4.2 24.2 - - + +
216A VAL 4.6 0.2 - - - -
217A GLY* 3.8 16.2 - - - -
220A MSE 3.5 22.7 - - + -
222A ASN* 3.0 38.4 - - - -
225A LEU 4.4 1.8 - - - +
226A GLU* 1.3 77.6 - - + +
228A ASP* 1.3 66.0 + - - +
230A LEU* 3.3 6.3 + - + +
231A ILE* 2.8 30.4 + - + +
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Residues in contact with ASP 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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194A GLU* 5.0 6.8 - - - +
225A LEU* 3.7 20.9 + - + +
226A GLU 3.4 0.8 - - - -
227A PHE* 1.3 79.0 - - - +
229A GLN* 1.3 64.1 + - - +
231A ILE* 3.0 29.4 + - - +
232A GLN* 3.2 21.2 + - + +
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Residues in contact with GLN 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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225A LEU* 3.1 29.8 + - + +
226A GLU* 3.9 3.5 + - - +
228A ASP* 1.3 77.5 - - - +
230A LEU* 1.3 73.9 + - - +
232A GLN* 2.8 28.2 + - - +
233A ASN* 2.6 40.7 + - - +
267A LEU* 2.9 48.2 - - - +
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Residues in contact with LEU 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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195A LEU* 4.5 23.6 - - + -
216A VAL* 5.2 0.2 - - + -
220A MSE 4.2 15.3 - - + -
226A GLU 3.4 14.5 + - - +
227A PHE* 3.3 5.1 + - + +
228A ASP 3.1 0.4 - - - -
229A GLN* 1.3 87.1 + - - +
231A ILE* 1.3 56.1 + - - +
232A GLN 2.6 15.5 + - - -
233A ASN* 3.4 6.6 + - - +
234A ILE* 2.9 29.9 + - + +
260A ILE* 3.8 10.1 - - + +
263A GLU* 2.6 43.7 - - + +
264A ALA* 3.1 25.8 - - + -
267A LEU* 4.4 2.0 - - + -
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Residues in contact with ILE 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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194A GLU* 4.4 24.0 - - + -
195A LEU* 5.0 6.3 - - + -
198A LEU* 3.6 31.8 - - + +
227A PHE* 2.8 31.7 + - + +
228A ASP* 3.0 25.3 + - - +
230A LEU* 1.3 75.9 - - - +
232A GLN* 1.3 65.6 + - - +
234A ILE* 3.5 11.6 - - - +
235A SER* 3.0 28.0 + - - -
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Residues in contact with GLN 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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228A ASP* 3.2 22.3 + - - +
229A GLN* 2.8 14.8 + - + +
230A LEU 2.6 1.0 + - - -
231A ILE* 1.3 88.8 + - - +
233A ASN* 1.3 56.4 + - - +
234A ILE 2.4 19.8 + - - -
235A SER* 2.5 22.2 + - - -
236A PRO* 3.1 11.1 - - - +
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Residues in contact with ASN 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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229A GLN* 2.6 58.5 + - - +
230A LEU* 3.5 4.7 - - - +
232A GLN* 1.3 76.6 - - - +
234A ILE* 1.3 51.7 + - - +
236A PRO* 3.9 2.1 - - - +
237A GLU* 2.6 28.1 - - - +
263A GLU* 2.8 32.2 + - + +
267A LEU* 5.1 0.8 - - - +
2W T 5.3 9.0 - - - -
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Residues in contact with ILE 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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198A LEU* 3.7 31.4 - - + -
230A LEU* 2.9 25.4 - - + +
231A ILE* 3.5 6.5 - - - +
232A GLN 2.4 12.5 + - - -
233A ASN* 1.3 69.2 - - - +
235A SER* 1.3 56.4 + - - +
236A PRO* 2.5 20.5 - - - -
237A GLU* 2.8 15.9 + - - +
238A ILE* 2.8 32.0 + - + +
256A ILE* 5.8 0.9 - - + +
259A LEU* 4.3 21.1 - - + +
260A ILE* 4.3 16.6 - - + +
263A GLU* 3.3 35.7 - - + -
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Residues in contact with SER 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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198A LEU* 6.1 0.7 - - - -
231A ILE* 3.0 25.0 + - - -
232A GLN* 2.5 22.6 + - - -
234A ILE* 1.3 69.7 - - - +
236A PRO* 1.3 64.6 - - - +
238A ILE* 2.6 31.5 - - - +
239A ASN* 2.9 10.7 + - - +
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Residues in contact with PRO 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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232A GLN 3.1 10.8 - - - +
233A ASN* 3.9 2.0 - - - +
234A ILE 2.5 6.7 - - - -
235A SER* 1.3 86.4 - - - +
237A GLU* 1.3 63.1 + - + +
238A ILE 2.7 6.5 + - - -
239A ASN* 2.8 7.7 + - + +
240A ASP* 2.4 39.4 + - - +
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Residues in contact with GLU 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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233A ASN 2.6 22.9 - - - +
234A ILE* 2.8 31.4 + - - +
236A PRO* 1.3 82.7 - - + +
238A ILE* 1.3 51.0 + - - +
240A ASP* 3.4 14.4 - - - +
241A ILE* 2.7 40.6 + - + +
259A LEU* 4.0 22.2 - - + +
263A GLU* 4.9 2.8 - - - +
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Residues in contact with ILE 238 (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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198A LEU* 3.8 32.3 - - + +
200A PRO* 6.0 2.2 - - + -
234A ILE* 2.8 28.0 + - + +
235A SER* 2.6 28.9 - - - +
236A PRO 2.7 1.6 + - - -
237A GLU* 1.3 76.3 - - - +
239A ASN* 1.3 80.2 + - + +
241A ILE* 3.2 19.9 + - - +
242A LEU* 3.7 2.9 + - - +
256A ILE* 3.2 39.2 - - + +
259A LEU* 4.7 5.4 - - + +
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Residues in contact with ASN 239 (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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235A SER* 3.2 15.0 - - - +
236A PRO* 2.8 4.1 + - - +
238A ILE* 1.3 80.4 - - + +
240A ASP* 1.3 53.4 - - - +
241A ILE 2.5 17.5 + - - -
242A LEU* 2.6 34.1 + - - +
243A SER* 3.5 10.0 + - - -
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Residues in contact with ASP 240 (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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236A PRO 2.4 32.7 + - - +
237A GLU* 3.4 17.6 - - - +
238A ILE 3.2 0.2 - - - -
239A ASN* 1.3 66.0 - - - +
241A ILE* 1.3 60.8 + - - +
243A SER* 4.5 10.9 - - - -
244A ILE* 3.9 17.2 - - - +
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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