Contacts of the helix formed by residues 202 - 211 (chain G) in PDB entry 2NN6
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 202 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104G GLN* 2.8 41.1 - - - +
201G VAL* 1.3 69.9 - - - +
203G LEU* 1.3 57.1 + - - +
204G GLY 3.1 4.9 - - - +
205G LEU* 2.6 54.5 + - + +
206G ILE 2.8 10.7 + - - -
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Residues in contact with LEU 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G SER 5.0 3.6 - - - +
104G GLN* 3.4 9.4 + - - +
105G GLN* 3.9 29.2 - - - +
106G LYS 4.6 11.0 - - - +
107G ARG 4.9 2.0 - - - +
108G TYR* 5.4 13.5 - - + -
109G VAL* 6.0 3.1 - - + -
201G VAL 3.7 7.0 - - - +
202G THR* 1.3 71.8 - - - +
204G GLY* 1.3 67.9 + - - +
206G ILE* 2.5 40.0 + - + -
207G ARG* 2.7 42.3 + - + +
232G MET 4.8 3.8 - - - +
233G ASN 5.3 3.4 - - - +
234G GLY* 5.3 2.0 - - - +
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Residues in contact with GLY 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G GLN* 3.0 32.8 + - - -
202G THR* 3.1 0.4 - - - -
203G LEU* 1.3 77.6 - - - +
205G LEU* 1.3 60.1 + - - +
207G ARG* 3.6 15.4 + - - +
208G LYS* 3.0 39.6 + - - +
257G GLU* 4.9 0.4 - - - -
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Residues in contact with LEU 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G VAL* 5.1 5.6 - - + -
202G THR* 2.6 47.3 + - + +
203G LEU 2.6 2.4 + - - -
204G GLY* 1.3 69.1 - - - +
206G ILE* 1.3 54.4 + - - +
207G ARG 2.8 2.3 + - - -
208G LYS* 2.8 5.0 + - - -
209G LEU* 2.4 57.1 + - + +
253G LEU 4.5 7.0 - - - +
254G GLU 4.4 15.9 - - - +
256G CYS* 5.2 0.2 - - + -
257G GLU* 2.8 59.5 - - + +
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Residues in contact with ILE 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G VAL* 3.4 22.9 - - + +
202G THR 2.8 15.3 + - - +
203G LEU* 2.5 35.1 + - + +
205G LEU* 1.3 70.4 - - - +
207G ARG* 1.3 67.2 + - + +
209G LEU* 3.4 10.7 - - - +
210G LEU* 2.8 29.9 + - + +
230G PHE* 5.5 3.4 - - + -
231G GLY 3.3 21.5 - - - +
232G MET* 3.0 41.5 - - + +
234G GLY* 3.1 20.0 - - - +
236G ILE* 5.5 4.9 - - + -
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Residues in contact with ARG 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ARG* 5.3 3.4 - - - +
100G TRP* 4.3 16.8 - - - -
102G ASP* 2.6 41.5 + - - +
103G SER 3.9 22.2 + - - +
104G GLN* 4.8 5.6 - - - +
203G LEU* 2.7 45.8 + - + +
204G GLY* 3.6 13.6 - - - +
205G LEU 2.8 0.4 + - - -
206G ILE* 1.3 70.3 - - + +
208G LYS* 1.3 56.0 + - + +
210G LEU* 2.6 28.9 + - - +
211G ALA* 2.9 12.2 + - - -
232G MET* 5.9 10.3 - - + -
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Residues in contact with LYS 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LYS 5.5 4.6 + - - -
204G GLY* 3.0 17.6 + - - +
205G LEU* 2.8 7.4 + - - +
207G ARG* 1.3 78.6 - - + +
209G LEU* 1.3 61.5 - - + +
211G ALA* 3.5 10.8 + - + +
214G CYS* 3.3 23.7 - - - +
216G ILE* 4.7 2.1 - - - +
257G GLU* 2.8 37.7 + - + +
258G HIS* 5.8 2.4 - - - -
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Residues in contact with LEU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G VAL* 4.7 14.4 - - + -
205G LEU* 2.4 68.1 + - + +
206G ILE* 3.4 10.5 - - + +
208G LYS* 1.3 69.3 - - + +
210G LEU* 1.3 61.8 + - - +
211G ALA 3.5 0.2 - - - -
214G CYS* 3.3 15.5 - - - -
216G ILE* 4.3 25.9 - - + +
217G ILE* 3.8 12.6 + - - +
230G PHE* 5.6 3.0 - - + -
236G ILE* 6.0 3.8 - - + -
253G LEU* 4.9 5.8 - - + +
256G CYS* 3.8 30.7 - - + -
257G GLU* 5.3 1.8 - - - +
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Residues in contact with LEU 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G HIS* 3.0 41.5 - - + +
206G ILE* 2.8 19.6 + - + +
207G ARG* 2.6 13.3 + - - +
209G LEU* 1.3 77.3 - - - +
211G ALA* 1.3 63.8 + - - -
212G PRO* 3.2 7.1 - - - +
214G CYS* 4.3 0.7 - - - -
217G ILE* 4.4 16.7 - - + +
230G PHE* 4.3 31.0 - - + +
232G MET* 4.2 8.5 - - - -
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Residues in contact with ALA 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G ARG 2.9 8.7 + - - +
208G LYS* 3.6 19.3 - - + +
209G LEU 3.5 0.8 - - - -
210G LEU* 1.3 77.2 - - - +
212G PRO* 1.3 62.7 - - + +
213G ASP* 3.0 20.4 - - - +
214G CYS* 2.6 41.3 + - + +
217G ILE* 3.6 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