Contacts of the helix formed by residues 236 - 244 (chain A) in PDB entry 1NVT
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 THR 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ILE 5.2 0.9 - - - -
204A GLY* 4.4 14.1 - - - +
228A ASP* 2.6 31.7 + - - +
230A ILE* 3.9 23.6 - - + -
233A PRO* 3.5 23.6 - - + +
234A LEU 3.4 4.8 + - - +
235A GLU* 1.3 77.4 - - - +
237A VAL* 1.3 66.6 + - - +
238A LEU* 3.0 12.3 + - - +
239A LEU* 3.3 13.0 + - - +
240A LYS* 3.2 20.8 + - - +
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Residues in contact with VAL 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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203A ILE* 5.1 2.7 - - + +
204A GLY* 4.3 17.9 + - - +
209A ILE 3.0 26.0 - - - +
210A ASP* 4.9 2.0 - - - -
211A VAL* 3.5 24.5 - - + +
212A GLU 4.4 0.2 - - - -
213A PRO* 3.8 26.8 - - + +
236A THR* 1.3 77.0 - - - +
238A LEU* 1.3 63.3 + - + +
240A LYS* 3.8 23.2 - - - +
241A GLU* 3.3 25.6 + - - +
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Residues in contact with LEU 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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134A TYR* 6.3 0.2 - - + -
197A ILE* 4.8 2.0 - - + -
199A ASN* 3.5 36.1 - - + +
203A ILE 5.8 1.6 - - - +
213A PRO* 4.0 9.6 - - + -
214A ILE* 3.7 15.3 - - + +
215A VAL* 3.7 33.7 - - + +
220A LEU* 5.3 2.7 - - + -
226A VAL* 3.8 28.3 - - + -
227A MET 4.8 0.4 - - - +
228A ASP* 4.0 15.7 - - + +
236A THR* 3.0 9.8 + - - +
237A VAL* 1.3 84.8 - - + +
239A LEU* 1.3 62.9 + - + +
241A GLU* 3.6 3.7 + - + +
242A ALA* 3.2 19.4 + - - +
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Residues in contact with LEU 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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226A VAL* 3.4 31.2 - - + +
228A ASP* 4.3 11.7 - - + -
234A LEU 3.5 24.9 - - - +
235A GLU* 3.9 16.2 - - + -
236A THR* 3.3 18.4 + - - +
238A LEU* 1.3 76.0 - - - +
240A LYS* 1.3 62.1 + - - +
242A ALA* 3.3 4.4 + - - +
243A LYS* 2.9 29.3 + - - +
249A THR* 3.5 28.4 - - + +
250A ILE 4.1 10.1 - - - +
251A ASN* 4.1 16.4 - - + -
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Residues in contact with LYS 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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213A PRO* 6.4 0.2 - - - -
235A GLU* 4.4 13.6 + - + +
236A THR 3.2 13.0 + - - +
237A VAL* 3.8 27.4 - - - +
238A LEU 3.3 0.2 - - - -
239A LEU* 1.3 76.5 - - - +
241A GLU* 1.3 68.3 + - - +
243A LYS* 2.7 29.4 + - + +
244A LYS* 3.2 26.3 + - - +
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Residues in contact with GLU 241 (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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213A PRO* 3.6 20.1 - - + +
215A VAL 3.8 7.9 - - - +
216A LYS* 3.7 10.1 + - - +
217A ALA* 3.0 43.0 + - - +
220A LEU* 3.1 25.6 - - + +
237A VAL 3.3 13.7 + - - +
238A LEU* 3.7 5.4 - - - +
239A LEU 3.4 0.2 - - - -
240A LYS* 1.3 87.1 - - - +
242A ALA* 1.3 57.3 + - - +
244A LYS* 3.0 43.6 + - - +
245A VAL* 3.6 4.3 - - - +
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Residues in contact with ALA 242 (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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220A LEU* 3.9 6.5 - - + -
226A VAL* 4.0 29.2 - - + -
238A LEU 3.2 17.1 + - - +
239A LEU* 3.6 6.5 - - - +
240A LYS 3.0 1.0 - - - -
241A GLU* 1.3 75.2 - - - +
243A LYS* 1.3 59.6 - - - +
244A LYS 3.4 0.9 - - - -
245A VAL* 3.1 22.6 - - - +
247A ALA* 3.1 21.9 + - + +
249A THR* 4.0 13.5 - - + -
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Residues in contact with LYS 243 (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 GLU* 3.2 36.5 + - - +
239A LEU* 2.9 11.6 + - - +
240A LYS* 2.7 16.1 + - + +
242A ALA* 1.3 69.6 - - - +
244A LYS* 1.3 58.1 + - - +
245A VAL 2.9 11.5 + - - -
246A ASN* 3.3 15.2 + - - +
247A ALA 4.9 2.2 - - - +
249A THR* 4.8 16.9 + - + -
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Residues in contact with LYS 244 (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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217A ALA* 4.0 9.9 - - + -
240A LYS* 3.2 22.1 + - - +
241A GLU* 3.0 63.6 + - - +
243A LYS* 1.3 73.4 - - - +
245A VAL* 1.3 68.1 + - + +
246A ASN* 5.3 0.9 - - - -
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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