Contacts of the helix formed by residues 256 - 270 (chain O) in PDB entry 2D2I
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 ILE 256 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255O THR* 1.3 88.1 + - - +
257O THR* 1.3 69.4 + - - +
258O GLU* 4.0 23.8 - - + +
259O GLN* 2.8 33.8 + - + +
260O VAL* 3.2 11.3 + - - +
304O VAL* 3.5 9.2 - - - -
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Residues in contact with THR 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256O ILE* 1.3 73.6 - - - +
258O GLU* 1.3 63.7 + - - +
259O GLN 3.2 0.2 + - - -
260O VAL* 3.5 4.7 + - - +
261O ASN* 3.3 25.9 + - - +
299O SER 5.7 0.2 - - - +
302O THR* 3.6 30.5 - - + +
303O LEU* 3.8 6.6 - - - +
304O VAL* 3.1 38.5 + - - +
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Residues in contact with GLU 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256O ILE* 3.1 20.7 + - + +
257O THR* 1.3 81.9 - - + +
259O GLN* 1.3 59.8 + - - +
261O ASN* 3.7 7.9 + - + +
262O GLU* 3.0 48.3 + - + +
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Residues in contact with GLN 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O PHE* 3.9 16.3 - - + -
253O LYS* 5.4 5.5 + - - -
254O PRO 4.6 1.7 + - - +
255O THR* 2.5 41.4 + - - +
256O ILE* 2.8 22.5 + - + +
258O GLU* 1.3 79.0 + - - +
260O VAL* 1.3 65.0 + - - +
262O GLU* 3.1 13.5 + - + +
263O VAL* 3.1 26.2 + - + +
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Residues in contact with VAL 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O LEU* 5.1 5.4 - - + -
171O PHE* 3.9 13.0 - - + -
255O THR* 3.9 17.0 - - + +
256O ILE 3.2 14.3 + - - +
257O THR 3.7 1.1 - - - +
259O GLN* 1.3 74.9 - - - +
261O ASN* 1.3 68.0 + - - +
263O VAL* 3.0 13.0 - - + +
264O LEU* 2.9 37.9 + - + +
302O THR* 3.2 31.0 - - + -
304O VAL* 3.7 18.8 - - + -
310O VAL* 4.1 9.9 - - + -
312O VAL* 4.6 6.7 - - + -
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Residues in contact with ASN 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257O THR* 3.3 17.4 + - - +
258O GLU* 3.8 8.5 - - + +
259O GLN 3.2 0.6 - - - -
260O VAL* 1.3 83.0 - - - +
262O GLU* 1.3 57.7 - - + +
264O LEU* 3.5 7.9 + - - +
265O GLN* 2.8 31.4 + - - +
278O TYR* 3.4 26.1 - - - +
297O VAL* 4.4 1.0 - - - +
299O SER* 3.2 28.0 + - - +
302O THR* 2.5 35.9 + - - +
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Residues in contact with GLU 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O GLU* 3.0 46.0 + - + +
259O GLN* 3.1 14.7 + - + +
261O ASN* 1.3 75.2 - - + +
263O VAL* 1.3 57.4 + - + +
265O GLN* 3.2 12.2 + - - +
266O LYS* 2.7 37.1 + - - +
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Residues in contact with VAL 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O VAL* 3.8 15.9 - - + +
167O LEU* 5.0 2.0 - - + -
170O ASN* 3.7 31.4 - - - +
171O PHE* 3.9 22.0 - - + -
259O GLN* 3.1 14.3 + - + +
260O VAL* 3.0 21.3 - - + +
262O GLU* 1.3 77.2 - - + +
264O LEU* 1.3 70.1 + - + +
266O LYS* 3.2 6.9 + - - +
267O ALA* 2.9 25.8 + - - +
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Residues in contact with LEU 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O VAL* 4.2 10.8 - - + -
166O VAL* 4.2 15.7 - - + -
167O LEU* 3.8 23.8 - - + -
260O VAL* 2.9 38.2 + - + +
261O ASN* 3.6 9.4 - - - +
263O VAL* 1.3 80.1 - - + +
265O GLN* 1.3 62.7 + - - +
267O ALA* 3.3 3.5 + - - +
268O SER* 3.0 21.0 + - - -
276O ILE* 4.6 13.6 - - + +
278O TYR* 4.4 7.2 - - + -
297O VAL* 4.1 37.0 - - + -
312O VAL* 4.1 18.8 - - + -
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Residues in contact with GLN 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261O ASN 2.8 17.3 + - - +
262O GLU* 3.7 12.8 - - - +
264O LEU* 1.3 74.5 - - - +
266O LYS* 1.3 66.8 + - - +
268O SER* 2.8 23.6 + - - +
269O GLN* 3.1 32.2 + - - +
278O TYR* 3.6 46.8 + - + -
280O ASP* 5.6 0.7 - - - +
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Residues in contact with LYS 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262O GLU 2.7 21.7 + - - +
263O VAL* 3.5 9.2 - - - +
265O GLN* 1.3 69.4 - - - +
267O ALA* 1.3 59.0 + - - +
269O GLN* 2.8 33.3 + - - +
270O THR* 2.9 42.1 + - + +
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Residues in contact with ALA 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O VAL* 3.9 18.4 - - + -
263O VAL 2.9 12.8 + - - +
264O LEU 3.4 9.4 - - - +
266O LYS* 1.3 76.5 - - - +
268O SER* 1.3 63.4 + - - +
269O GLN 2.9 1.6 + - - -
270O THR* 2.9 8.9 + - - -
271O THR* 3.9 14.1 - - - +
272O MET* 2.8 46.4 + - + -
276O ILE* 4.7 1.3 - - + -
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Residues in contact with SER 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264O LEU 3.0 13.2 + - - -
265O GLN* 2.8 15.8 + - - +
267O ALA* 1.3 75.1 - - - +
269O GLN* 1.3 63.1 + - - +
272O MET* 4.2 5.8 - - - +
273O LYS* 3.2 23.4 - - - +
274O GLY 4.5 0.3 + - - -
276O ILE* 3.2 34.8 - - - +
277O LYS* 4.4 0.2 - - - -
278O TYR* 3.6 26.7 - - - +
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Residues in contact with GLN 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265O GLN* 3.1 36.9 + - + +
266O LYS* 2.8 21.0 + - - +
268O SER* 1.3 86.5 - - - +
270O THR* 1.3 67.0 + - + +
273O LYS* 3.8 18.7 - - - +
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Residues in contact with THR 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266O LYS* 2.9 51.9 + - + +
267O ALA* 2.9 1.3 + - - -
269O GLN* 1.3 86.4 - - + +
271O THR* 1.3 85.6 + - - +
272O MET 3.2 1.1 - - - -
273O LYS* 3.1 18.9 + - - +
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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