Contacts of the helix formed by residues 260 - 269 (chain G) in PDB entry 2Q5E
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 ASP 260 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211G ARG* 2.9 35.1 + - + +
258G ALA* 4.2 4.0 - - - +
259G GLU* 1.3 79.6 - - - +
261G VAL* 1.3 62.6 + - - +
262G TYR* 3.3 15.4 + - - +
263G THR* 2.8 53.2 + - - +
264G SER* 3.6 8.3 + - - -
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Residues in contact with VAL 261 (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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102G ILE* 3.8 28.9 - - + -
210G LEU 4.1 4.3 - - - +
211G ARG 2.7 24.9 + - - +
212G LYS* 4.1 7.4 - - + -
213G THR 3.4 21.8 - - - +
214G LEU* 3.9 28.9 - - + -
229G ASN* 4.1 10.5 - - - +
255G LEU* 5.5 2.7 - - + +
258G ALA* 4.8 2.9 - - + -
260G ASP* 1.3 68.0 - - - +
262G TYR* 1.3 72.0 + - + +
264G SER* 4.0 9.5 - - - -
265G LEU* 3.3 28.9 + - + +
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Residues in contact with TYR 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G LEU* 3.2 28.7 + - - +
211G ARG* 3.8 22.4 - - + -
228G GLU* 3.6 41.1 + - + -
229G ASN* 2.9 36.3 + - - -
260G ASP* 3.3 19.1 + - - +
261G VAL* 1.3 78.7 - - + +
263G THR* 1.3 61.1 + - - +
265G LEU* 4.0 3.1 - - - +
266G GLY* 2.9 26.9 + - - -
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Residues in contact with THR 263 (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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260G ASP* 2.8 34.4 + - - +
262G TYR* 1.3 72.7 - - - +
264G SER* 1.3 68.8 + - - +
266G GLY* 3.2 3.7 + - - -
267G GLN* 2.9 35.5 + - - +
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Residues in contact with SER 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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254G GLU 5.1 2.1 + - - -
255G LEU* 3.3 27.1 - - - +
258G ALA* 3.2 28.9 - - - +
260G ASP 3.6 2.9 + - - -
261G VAL* 4.0 5.6 - - - -
263G THR* 1.3 72.8 - - - +
265G LEU* 1.3 57.0 + - - -
266G GLY 2.8 3.6 - - - -
267G GLN* 2.5 48.4 + - - +
268G LEU* 3.0 13.9 + - - +
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Residues in contact with LEU 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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214G LEU* 3.8 21.3 - - + -
228G GLU 3.3 26.2 - - - +
229G ASN* 4.6 0.2 - - - -
230G ALA 4.4 12.6 - - - +
231G VAL* 4.3 21.8 - - + -
251G ILE* 6.2 0.4 - - + -
255G LEU* 4.4 18.4 - - + +
261G VAL* 3.3 20.3 + - + +
262G TYR* 4.3 2.5 - - - +
264G SER* 1.3 78.2 - - - +
266G GLY* 1.3 63.4 + - - +
268G LEU* 3.5 22.5 + - + +
269G ARG* 2.9 43.5 + - - +
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Residues in contact with GLY 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 TYR 2.9 15.0 + - - -
263G THR* 3.3 6.7 - - - -
264G SER 2.7 5.9 + - - -
265G LEU* 1.3 76.1 - - - +
267G GLN* 1.3 59.6 + - - -
269G ARG* 3.6 16.2 + - - +
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Residues in contact with GLN 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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263G THR* 2.9 31.5 + - - +
264G SER* 2.5 43.8 + - - +
266G GLY* 1.3 70.1 - - - -
268G LEU* 1.3 68.9 + - + +
269G ARG 3.1 8.1 + - - +
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Residues in contact with LEU 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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126D ILE* 6.0 0.2 - - - +
251G ILE* 4.2 29.8 - - + +
254G GLU* 4.1 32.3 - - + +
255G LEU* 4.5 20.2 - - + -
264G SER* 3.0 14.7 + - - +
265G LEU* 3.7 24.7 - - + +
266G GLY 3.3 0.4 - - - -
267G GLN* 1.3 83.8 - - + +
269G ARG* 1.3 63.4 + - + +
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Residues in contact with ARG 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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125D PHE* 6.1 1.1 - - - -
126D ILE* 3.6 52.0 - - + +
128D PRO* 6.3 0.4 - - - +
137D GLN* 2.8 32.9 + - - +
230G ALA 4.3 15.6 + - - -
232G PRO* 4.8 4.6 - - - +
265G LEU* 2.9 49.3 + - - +
266G GLY* 3.6 15.1 + - - +
267G GLN 3.2 7.7 - - - +
268G LEU* 1.3 84.5 - - + +
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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