Contacts of the helix formed by residues 264 - 276 (chain B) in PDB entry 2DOU
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 TYR 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 5.2 2.0 - - + -
236A GLY* 3.1 29.8 + - - +
237A PHE* 3.5 37.6 - + + -
263A GLN* 5.4 0.7 - - - +
267A VAL* 6.3 2.9 - - + -
47B LEU* 3.6 17.0 - - + -
50B ALA* 3.4 13.2 + - + -
51B LEU* 3.3 26.9 - - + +
56B THR* 3.0 42.4 + - - -
60B CYS* 5.0 0.2 - - - -
263B GLN* 1.3 86.1 + - - +
265B ALA* 1.3 61.4 + - - +
266B GLY* 3.2 30.3 - - - -
267B VAL* 2.8 38.7 + - + +
268B LEU* 3.2 8.0 + - - +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLY* 5.8 0.4 - - - -
56B THR* 4.0 32.7 + - + +
58B GLY 5.6 0.4 - - - +
60B CYS* 3.8 19.3 - - + +
64B CYS* 3.9 22.7 - - - -
263B GLN 3.5 3.0 + - - -
264B TYR* 1.3 74.7 - - - +
266B GLY* 1.3 64.0 + - - +
268B LEU* 2.9 14.8 + - - +
269B ARG* 3.1 21.4 + - - +
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.4 16.7 - - - +
50B ALA* 3.4 22.6 - - - +
56B THR* 4.8 0.4 - - - -
264B TYR* 3.1 28.8 + - - -
265B ALA* 1.3 77.7 - - - +
267B VAL* 1.3 60.2 + - - +
269B ARG* 3.4 6.7 + - - +
270B MET* 3.1 17.8 + - - +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 6.2 2.7 - - + -
47B LEU* 3.6 21.7 - - + +
237B PHE* 3.6 29.6 - - + +
239B LEU* 3.3 21.7 - - + +
263B GLN* 3.4 24.7 - - + +
264B TYR* 2.8 25.1 + - + +
266B GLY* 1.3 70.7 - - - +
268B LEU* 1.3 59.1 + - - +
270B MET* 3.1 18.6 + - - +
271B GLY 2.8 23.2 + - - -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 4.0 18.8 - - - -
64B CYS* 4.9 5.6 - - - +
65B THR* 4.0 20.9 - - + -
68B PHE* 3.5 41.6 - - + -
92B ALA* 4.3 3.8 - - + -
239B LEU* 3.9 14.6 - - + -
262B ASN* 5.4 0.2 - - + -
263B GLN* 3.7 31.0 - - + +
264B TYR 3.4 15.0 - - - +
265B ALA* 2.9 10.0 + - - +
267B VAL* 1.3 77.8 - - - +
269B ARG* 1.3 59.2 + - + +
271B GLY* 2.9 15.6 + - - -
272B VAL* 3.0 18.9 + - - +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 4.2 15.7 - - + +
49B GLU* 5.2 1.4 + - - +
50B ALA* 4.0 28.1 - - - +
53B ASP* 2.8 32.3 + - - +
55B THR* 4.4 1.6 + - - -
56B THR* 3.4 17.0 - - - +
265B ALA* 3.1 15.8 + - + +
266B GLY 3.6 7.0 - - - +
268B LEU* 1.3 74.0 - - + +
270B MET* 1.3 66.7 + - - +
272B VAL* 3.1 20.3 + - - +
273B GLU* 3.2 14.0 + - - +
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Residues in contact with MET 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PRO* 3.3 37.9 - - + +
44B LEU* 3.8 20.6 - - + -
46B ALA* 4.2 5.8 - - - +
47B LEU* 4.0 11.7 - - + -
228B LEU* 4.8 3.1 - - + -
234B LEU* 3.4 39.9 - - + -
237B PHE* 3.5 40.2 - - + -
266B GLY 3.1 13.7 + - - +
267B VAL* 3.1 16.9 + - + +
269B ARG* 1.3 76.5 - - - +
271B GLY* 1.3 61.3 + - - +
273B GLU 3.3 0.5 + - - -
274B ALA* 2.8 30.1 + - - +
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Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.6 27.2 - - - -
228B LEU* 3.7 17.0 - - - +
239B LEU* 3.7 1.3 - - - -
267B VAL 2.8 14.1 + - - -
268B LEU 2.9 6.2 + - - -
270B MET* 1.3 78.8 - - - +
272B VAL* 1.3 60.4 + - - +
274B ALA* 3.2 3.3 + - - +
275B LEU* 3.1 21.0 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO* 4.0 12.8 - - + +
68B PHE* 3.6 31.9 - - - +
71B GLU* 4.1 15.1 - - + +
268B LEU 3.0 17.7 + - - +
269B ARG* 3.1 13.2 + - - +
271B GLY* 1.3 76.4 - - - +
273B GLU* 1.3 65.1 + - + +
275B LEU* 3.3 12.8 + - - +
276B LYS* 3.5 39.3 + - - +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.6 23.1 - - - +
43B PRO* 3.9 19.4 - - + +
46B ALA* 3.9 23.3 - - + -
269B ARG 3.2 6.5 + - - +
270B MET 3.3 6.5 + - - +
272B VAL* 1.3 81.0 - - + +
274B ALA* 1.3 64.4 + - - +
276B LYS* 3.0 36.4 + - - +
277B THR* 3.4 10.0 + - - -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PRO* 3.8 6.2 - - + +
228B LEU* 4.2 5.8 - - + -
232B TYR* 3.0 36.1 - - + -
234B LEU* 4.2 18.2 - - + -
270B MET 2.8 17.7 + - - +
271B GLY* 3.3 10.5 - - - +
272B VAL 3.2 0.2 - - - -
273B GLU* 1.3 77.1 - - - +
275B LEU* 1.3 62.7 + - - +
277B THR* 2.8 24.0 + - - -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.8 25.4 - - + -
71B GLU* 3.7 25.3 - - + +
72B ALA* 3.6 34.3 - - + +
75B TRP* 3.7 43.9 - - + -
228B LEU* 4.8 2.9 - - + -
232B TYR* 3.7 21.5 + - + +
241B PHE* 4.2 15.0 - - + -
271B GLY 3.1 9.6 + - - +
272B VAL 3.8 1.8 - - - +
273B GLU 3.3 0.2 - - - -
274B ALA* 1.3 78.4 - - - +
276B LYS* 1.3 57.3 + - - +
277B THR 3.2 6.4 + - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.6 26.9 - - - +
272B VAL* 3.6 34.7 - - + +
273B GLU* 3.0 31.0 + - - +
275B LEU* 1.3 75.3 - - - +
277B THR* 1.3 64.6 + - - +
278B PRO* 3.3 7.3 - - - +
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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