Contacts of the helix formed by residues 263 - 274 (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 GLN 263 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259G MET* 3.4 28.9 - - + -
260G THR* 2.6 40.6 + - - +
262G ASP* 1.3 83.6 + - - +
264G ARG* 1.3 70.0 + - - +
266G GLN* 2.6 29.4 - - - +
267G ILE* 3.0 26.0 + - + +
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Residues in contact with ARG 264 (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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216G ILE* 3.7 33.0 - - - +
219G GLU* 3.0 14.8 - - - +
256G CYS* 3.4 21.0 + - - +
257G GLU 4.1 5.1 + - - -
259G MET* 2.6 46.1 + - + +
260G THR 2.5 29.7 + - - -
261G SER* 3.4 13.2 + - - +
262G ASP 3.3 6.3 + - - -
263G GLN* 1.3 72.5 - - - +
265G LYS* 1.3 53.3 + - - +
267G ILE* 2.7 13.2 + - - -
268G PHE* 2.2 62.8 + - + -
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Residues in contact with LYS 265 (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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215G GLU* 4.1 18.5 + - - -
219G GLU* 3.0 29.3 + - - +
222G LYS* 2.6 7.3 + - - +
262G ASP* 2.4 42.2 + - - +
263G GLN 2.8 0.2 - - - -
264G ARG* 1.3 74.2 - - - +
266G GLN* 1.3 64.6 + - + +
268G PHE 2.6 0.5 + - - -
269G SER* 2.6 35.1 + - - +
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Residues in contact with GLN 266 (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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262G ASP* 3.4 18.3 + - - +
263G GLN* 2.6 37.4 - - - +
265G LYS* 1.3 82.9 - - + +
267G ILE* 1.3 50.3 + - - +
268G PHE 2.3 18.6 + - - -
269G SER* 2.5 12.4 + - - +
270G ARG* 2.3 54.2 + - + +
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Residues in contact with ILE 267 (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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252G ILE* 3.5 28.7 - - + +
259G MET* 4.2 12.8 - - + -
263G GLN* 3.0 35.3 + - + +
264G ARG* 2.9 24.9 - - - +
266G GLN* 1.3 79.0 - - - +
268G PHE* 1.3 73.8 + - + +
270G ARG* 3.3 22.9 - - + +
271G LEU* 3.7 1.9 + - - +
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Residues in contact with PHE 268 (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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216G ILE* 3.8 12.8 - - + -
219G GLU* 3.4 24.5 - - - -
220G VAL* 3.3 33.9 - - + -
222G LYS* 2.6 23.3 - - - +
223G LEU* 3.8 5.9 - - + +
249G LEU* 4.6 3.1 - - + -
252G ILE* 3.3 37.0 - - + -
253G LEU* 4.2 3.4 - - + -
256G CYS* 4.2 12.3 - - - -
259G MET* 6.0 0.4 - - + -
264G ARG* 2.2 38.9 + - + -
265G LYS 2.6 2.9 + - - +
266G GLN 2.3 6.7 + - - -
267G ILE* 1.3 86.1 - - + -
269G SER* 1.3 47.3 + - - -
270G ARG 2.6 4.7 - - - -
271G LEU* 2.5 14.8 + - + +
272G ALA 2.5 32.4 + - - -
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Residues in contact with SER 269 (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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222G LYS* 2.4 33.4 + - - +
265G LYS* 2.6 12.1 + - - +
266G GLN* 2.5 11.0 + - - -
268G PHE* 1.3 66.7 - - - +
270G ARG* 1.3 78.9 + - - +
272G ALA* 3.3 13.4 - - - +
273G GLU* 3.2 27.4 + - - +
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Residues in contact with ARG 270 (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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266G GLN* 2.3 54.5 + - + +
267G ILE* 3.3 19.3 - - + +
268G PHE 2.6 0.6 - - - -
269G SER* 1.3 89.3 + - - +
271G LEU* 1.3 64.8 + - + +
273G GLU* 3.4 31.7 + - - +
274G SER* 3.8 6.2 + - - -
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Residues in contact with LEU 271 (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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223G LEU* 3.4 17.7 - - + +
245G GLN* 4.3 12.8 - - + +
248G ILE* 3.1 47.3 - - + -
249G LEU* 3.5 30.1 - - + -
252G ILE* 3.3 31.2 - - + -
268G PHE* 2.5 14.8 + - + +
270G ARG* 1.3 73.3 - - + +
272G ALA* 1.3 67.7 + - - +
273G GLU 2.8 1.4 + - - -
274G SER* 2.9 29.1 + - - +
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Residues in contact with ALA 272 (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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222G LYS* 3.6 17.5 - - + -
223G LEU* 3.4 29.2 - - + +
224G TYR 4.9 4.5 + - - +
268G PHE 2.5 10.3 + - - +
269G SER* 3.3 24.7 - - - +
271G LEU* 1.3 72.6 - - - +
273G GLU* 1.3 63.3 + - - +
274G SER 3.4 6.6 + - - +
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Residues in contact with GLU 273 (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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269G SER* 3.2 22.0 + - - +
270G ARG* 3.4 33.5 + - - +
271G LEU 2.8 0.8 + - - -
272G ALA* 1.3 81.3 - - - +
274G SER* 1.3 63.3 + - - +
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Residues in contact with SER 274 (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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224G TYR 5.1 6.8 - - - +
245G GLN* 5.6 13.8 - - - +
248G ILE* 6.0 0.9 - - - +
270G ARG 3.8 6.3 + - - -
271G LEU* 2.9 29.2 + - - +
272G ALA 3.6 5.9 - - - +
273G GLU* 1.3 81.9 - - - +
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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