Contacts of the helix formed by residues 226 - 236 (chain A) in PDB entry 1NV9
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLY 2.7 0.8 + - - -
224A ASP* 3.0 30.4 + - + +
225A GLY* 1.3 76.1 - - - +
227A ASP* 1.3 70.0 + - - +
228A PHE 2.6 5.7 + - - -
229A TYR* 3.0 30.7 + - + -
230A ARG* 3.2 19.6 + - + +
251A GLN* 3.6 38.6 - - + +
254A GLU* 4.0 26.9 - - + +
255A LEU* 4.1 9.2 - - + -
258A ILE* 3.7 24.2 - - + -
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Residues in contact with ASP 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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221A GLY* 2.9 18.5 + - - +
222A GLY* 3.0 24.8 + - - -
223A GLU 4.8 1.2 + - - -
224A ASP* 4.2 5.0 - - - +
225A GLY 3.7 0.2 - - - -
226A LEU* 1.3 77.8 - - - +
228A PHE* 1.3 64.6 + - - +
230A ARG* 3.3 27.8 + - - +
231A GLU* 3.0 28.6 + - - +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.7 33.2 - - + -
180A PHE* 3.4 35.8 - + - -
196A SER* 3.8 6.1 - - - -
198A PRO* 3.4 34.1 - - + -
199A PRO* 4.1 23.4 + - + +
221A GLY* 5.2 1.7 - - - -
226A LEU 2.6 6.3 + - - -
227A ASP* 1.3 77.2 - - - +
229A TYR* 1.3 61.9 + + + +
231A GLU* 3.3 0.7 + - - +
232A PHE* 3.1 28.4 + - + +
245A MET* 3.6 28.0 - - + -
300A SAH 4.0 23.6 - + - -
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Residues in contact with TYR 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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198A PRO* 3.6 14.2 - - + +
199A PRO 4.9 3.4 - - - -
200A TYR* 3.5 32.0 - - + +
225A GLY 4.3 3.1 - - - -
226A LEU* 3.0 27.3 + - + +
228A PHE* 1.3 79.8 - + + +
230A ARG* 1.3 58.5 - - - +
232A PHE* 4.3 2.2 - - - +
233A PHE* 3.0 44.1 + + + +
245A MET* 3.1 37.2 - - + -
246A GLU 2.8 24.4 + - - -
247A ILE* 3.5 8.9 - - + -
251A GLN* 4.4 3.4 - - - -
255A LEU* 3.7 24.0 - - + -
258A ILE* 4.0 6.3 - - + +
275A LEU* 4.0 18.4 - - + -
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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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224A ASP* 4.6 11.3 + - - -
226A LEU* 3.2 23.2 + - - +
227A ASP* 3.3 32.6 + - - +
229A TYR* 1.3 78.3 - - - +
231A GLU* 1.3 61.9 + - - +
234A GLY* 3.3 19.8 + - - -
258A ILE* 4.1 34.6 - - + +
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Residues in contact with GLU 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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179A GLU* 3.8 4.9 - - - +
180A PHE* 3.4 32.4 - - + -
227A ASP* 3.0 20.2 + - - +
230A ARG* 1.3 79.0 - - - +
232A PHE* 1.3 61.8 + - - +
234A GLY* 4.9 0.2 - - - -
235A ARG* 2.6 66.3 + - - +
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Residues in contact with PHE 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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128A ILE* 3.6 31.4 - - + -
180A PHE* 3.8 15.0 - + + -
181A LEU* 4.8 1.3 - - + -
194A ILE* 3.9 30.7 - - + -
228A PHE* 3.1 25.5 + + + +
229A TYR* 4.1 3.4 - - - +
230A ARG 3.2 0.4 - - - -
231A GLU* 1.3 76.4 - - - +
233A PHE* 1.3 96.9 + + - +
234A GLY 2.9 7.7 + - - -
235A ARG 3.1 1.4 + - - -
236A TYR* 3.1 58.9 + + + +
238A THR* 4.4 9.2 - - + -
243A VAL* 4.2 10.8 - - + -
245A MET* 4.6 6.5 - - - -
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Residues in contact with PHE 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 TYR* 3.0 41.9 + + + +
232A PHE* 1.3 97.6 - + - +
234A GLY* 1.3 57.1 + - - +
235A ARG 3.6 0.2 - - - -
236A TYR 4.2 11.2 - - - +
238A THR* 4.6 7.0 - - + -
243A VAL* 4.2 19.5 - - + -
245A MET* 4.5 2.7 - - - -
255A LEU* 5.2 0.4 - - + -
258A ILE* 4.3 11.5 - - + +
259A VAL* 3.0 41.3 - - + -
262A THR* 5.3 1.3 - - + -
275A LEU* 4.1 29.2 - - + -
277A LEU* 4.0 24.0 - - + -
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Residues in contact with GLY 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 3.3 20.0 + - - -
231A GLU* 3.8 1.3 - - - -
232A PHE 2.9 1.6 - - - -
233A PHE* 1.3 79.4 - - - +
235A ARG* 1.3 58.6 + - - +
258A ILE* 5.8 0.2 - - - +
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Residues in contact with ARG 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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179A GLU* 2.9 19.3 + - - -
180A PHE* 4.1 7.0 - - + -
182A GLU* 2.4 46.7 + - - +
231A GLU* 2.6 64.6 + - + +
234A GLY* 1.3 79.8 - - - +
236A TYR* 1.3 79.3 + - + +
237A ASP 4.0 1.4 + - - -
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Residues in contact with TYR 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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180A PHE* 3.2 23.6 - + + +
181A LEU* 3.0 40.3 + - + -
182A GLU* 3.5 22.7 + - - -
185A LYS* 6.1 4.3 - - + -
188A PHE* 3.6 32.3 - + + -
232A PHE* 3.1 49.9 + + + +
233A PHE* 4.2 11.3 - - - +
234A GLY 3.8 0.4 - - - -
235A ARG* 1.3 95.8 + - + +
237A ASP* 1.3 64.0 + - - +
238A THR* 3.4 11.2 + - + +
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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