Contacts of the helix formed by residues 256 - 270 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255Q THR* 1.3 86.8 + - - +
257Q THR* 1.3 67.7 + - - +
258Q GLU* 4.0 23.3 - - + +
259Q GLN* 2.9 34.1 + - + +
260Q VAL* 3.3 11.4 + - - +
304Q VAL* 3.4 10.1 - - - -
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Residues in contact with THR 257 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256Q ILE* 1.3 73.4 - - - +
258Q GLU* 1.3 65.3 + - - +
259Q GLN 3.2 1.0 + - - -
260Q VAL* 3.5 3.9 + - - +
261Q ASN* 3.3 28.3 + - - +
302Q THR* 3.5 27.6 - - + +
303Q LEU* 3.9 6.9 - - - +
304Q VAL* 3.1 37.1 + - - +
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Residues in contact with GLU 258 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256Q ILE* 3.2 19.9 + - + +
257Q THR* 1.3 81.9 - - - +
259Q GLN* 1.3 59.5 + - - +
261Q ASN* 3.7 8.1 + - + +
262Q GLU* 3.0 49.2 + - + +
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Residues in contact with GLN 259 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q PHE* 3.7 18.6 - - + -
253Q LYS* 5.3 5.5 + - - -
254Q PRO 4.7 1.4 + - - -
255Q THR* 2.6 38.8 + - - +
256Q ILE* 2.9 22.5 + - + +
258Q GLU* 1.3 75.3 - - - +
260Q VAL* 1.3 65.9 + - - +
261Q ASN 3.1 1.3 - - - -
262Q GLU* 2.9 24.7 + - - +
263Q VAL* 3.0 20.7 + - + +
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Residues in contact with VAL 260 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167Q LEU* 5.1 3.6 - - + -
171Q PHE* 3.9 20.2 - - + -
255Q THR* 3.9 17.0 - - + +
256Q ILE 3.3 16.1 + - - +
257Q THR 3.8 0.7 - - - +
259Q GLN* 1.3 73.9 - - - +
261Q ASN* 1.3 60.9 + - - +
263Q VAL* 3.1 3.4 - - + +
264Q LEU* 3.0 48.5 + - + +
302Q THR* 3.3 29.6 - - + -
304Q VAL* 3.7 18.8 - - + -
310Q VAL* 4.1 8.7 - - + -
312Q VAL* 4.5 7.9 - - + -
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Residues in contact with ASN 261 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257Q THR* 3.3 18.4 + - - +
258Q GLU* 3.8 8.1 - - + +
259Q GLN 3.1 0.6 - - - -
260Q VAL* 1.3 82.3 - - - +
262Q GLU* 1.3 58.4 + - + +
264Q LEU* 4.2 9.3 - - - +
265Q GLN* 2.8 32.3 + - - +
278Q TYR* 3.5 32.4 - - - +
297Q VAL* 4.4 1.2 - - - +
299Q SER* 3.4 23.4 + - - +
302Q THR* 2.6 34.1 + - - +
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Residues in contact with GLU 262 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258Q GLU* 3.0 44.6 + - + +
259Q GLN* 2.9 15.8 + - + +
261Q ASN* 1.3 76.4 - - + +
263Q VAL* 1.3 62.1 + - + +
265Q GLN* 3.3 11.4 + - - +
266Q LYS* 2.7 31.8 + - - +
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Residues in contact with VAL 263 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166Q VAL* 3.8 18.5 - - + +
167Q LEU* 4.9 1.6 - - + -
170Q ASN* 3.8 30.1 - - + +
171Q PHE* 4.0 23.1 - - + -
259Q GLN* 3.0 17.1 + - + +
260Q VAL* 3.1 19.5 - - - +
262Q GLU* 1.3 75.8 - - + +
264Q LEU* 1.3 65.7 + - + +
266Q LYS* 3.1 7.6 + - - +
267Q ALA* 2.8 32.2 + - - +
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Residues in contact with LEU 264 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q VAL* 4.4 12.1 - - + -
166Q VAL* 4.1 14.8 - - + -
167Q LEU* 3.8 23.3 - - + -
260Q VAL* 3.0 35.6 + - + +
261Q ASN* 3.8 8.5 - - - +
263Q VAL* 1.3 82.0 - - + +
265Q GLN* 1.3 57.3 + - - +
267Q ALA* 3.5 5.7 + - - +
268Q SER* 3.1 27.0 + - - -
276Q ILE* 4.5 11.3 - - + +
278Q TYR* 4.4 4.2 - - + -
297Q VAL* 4.0 42.0 - - + -
312Q VAL* 4.1 17.3 - - + -
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Residues in contact with GLN 265 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261Q ASN 2.8 18.6 + - - +
262Q GLU* 3.7 12.2 - - - +
264Q LEU* 1.3 75.4 - - - +
266Q LYS* 1.3 66.1 + - - +
268Q SER* 2.9 19.5 + - - -
269Q GLN* 2.9 36.9 + - + +
278Q TYR* 3.6 47.3 + - + -
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Residues in contact with LYS 266 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262Q GLU 2.7 21.9 + - - +
263Q VAL* 3.4 8.5 - - - +
265Q GLN* 1.3 71.9 - - - +
267Q ALA* 1.3 57.4 + - - +
269Q GLN* 3.0 17.2 + - - +
270Q THR* 2.9 57.0 + - + +
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Residues in contact with ALA 267 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166Q VAL* 3.8 30.7 - - + -
263Q VAL 2.8 15.8 + - - +
264Q LEU* 3.5 6.3 - - - +
266Q LYS* 1.3 77.4 - - - +
268Q SER* 1.3 61.7 + - - +
269Q GLN 3.1 1.0 + - - -
270Q THR* 3.1 6.7 + - - -
271Q THR* 3.7 14.1 - - - +
272Q MET* 2.6 36.5 + - + -
273Q LYS 3.2 0.2 + - - -
276Q ILE* 4.7 2.2 - - + -
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Residues in contact with SER 268 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264Q LEU 3.1 15.8 + - - -
265Q GLN* 2.9 14.0 + - - +
267Q ALA* 1.3 75.4 - - - +
269Q GLN* 1.3 63.6 + - - +
272Q MET* 4.2 2.9 - - - +
273Q LYS* 3.1 22.6 - - - +
274Q GLY 4.4 0.5 + - - -
276Q ILE* 3.1 34.7 - - - +
277Q LYS* 4.4 0.4 - - - -
278Q TYR* 3.5 27.5 + - - +
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Residues in contact with GLN 269 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265Q GLN* 2.9 40.4 + - + +
266Q LYS* 3.0 17.3 + - - +
268Q SER* 1.3 87.0 - - - +
270Q THR* 1.3 65.6 + - + +
273Q LYS* 3.8 19.3 + - - +
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Residues in contact with THR 270 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266Q LYS* 2.9 51.0 + - + +
267Q ALA* 3.1 0.6 + - - -
269Q GLN* 1.3 85.7 - - + +
271Q THR* 1.3 84.6 + - - +
272Q MET 3.3 1.3 - - - -
273Q LYS* 3.2 17.5 + - - +
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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