Contacts of the helix formed by residues 264 - 276 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.6 17.5 - - + -
50A ALA* 3.3 19.1 + - + -
51A LEU* 3.5 13.1 - - + +
56A THR* 2.8 47.7 + - - -
60A CYS* 5.1 0.4 - - - -
263A GLN* 1.3 85.6 + - - +
265A ALA* 1.3 61.5 + - - +
266A GLY* 3.2 29.2 - - - -
267A VAL* 2.6 44.7 + - + +
268A LEU* 3.3 4.0 + - - +
47B LEU* 5.4 1.6 - - + -
236B GLY* 3.3 26.5 + - - +
237B PHE* 3.5 41.6 - + + +
263B GLN* 5.6 0.2 - - - +
267B VAL* 6.2 2.5 - - + -
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 4.0 33.4 + - + +
58A GLY 5.5 1.0 + - - +
60A CYS* 3.8 19.9 - - + +
64A CYS* 3.8 21.8 - - - -
263A GLN 3.4 3.4 + - - -
264A TYR* 1.3 72.7 - - - +
266A GLY* 1.3 64.3 + - - +
268A LEU* 2.9 15.5 + - - +
269A ARG* 3.2 20.1 + - - +
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.3 18.2 - - - +
50A ALA* 3.4 23.1 - - - +
264A TYR* 3.0 27.2 + - - -
265A ALA* 1.3 79.7 - - - +
267A VAL* 1.3 55.5 + - - +
269A ARG* 3.5 5.8 + - - +
270A MET* 3.2 20.3 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.1 20.4 - - + -
237A PHE* 3.5 24.5 - - + +
239A LEU* 3.4 20.9 - - + +
263A GLN* 3.4 29.6 - - + +
264A TYR* 2.6 25.6 + - + +
266A GLY* 1.3 71.2 - - - -
268A LEU* 1.3 59.4 + - - +
270A MET* 3.0 21.3 - - - +
271A GLY 2.8 22.9 + - - -
264B TYR* 6.3 2.2 - - + -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS* 4.1 16.6 - - - -
64A CYS* 4.7 8.1 - - - +
65A THR* 4.3 10.5 - - + -
68A PHE* 3.6 40.0 - - + -
92A ALA* 4.3 13.2 - - + -
239A LEU* 3.8 15.3 - - + -
262A ASN* 5.4 0.4 - - + -
263A GLN* 3.6 32.3 - - + +
264A TYR 3.4 16.6 - - - +
265A ALA* 2.9 9.3 + - - +
267A VAL* 1.3 76.3 - - - +
269A ARG* 1.3 57.3 + - + +
271A GLY* 2.9 3.1 + - - -
272A VAL* 2.9 31.4 + - - +
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 4.0 16.1 - - + +
49A GLU 5.3 0.4 + - - -
50A ALA* 3.8 29.8 - - - +
53A ASP* 3.2 29.1 + - - +
55A THR* 4.6 3.0 + - - -
56A THR* 3.4 19.1 - - - +
265A ALA* 3.2 16.0 + - - +
266A GLY 3.7 6.7 - - - +
268A LEU* 1.3 74.4 - - + +
270A MET* 1.3 65.8 + - - +
272A VAL* 3.3 9.9 + - - +
273A GLU* 3.1 23.6 + - - +
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Residues in contact with MET 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.8 34.4 - - + +
44A LEU* 3.8 19.7 - - + -
46A ALA* 4.2 4.5 - - - +
47A LEU* 3.7 14.4 - - + -
228A LEU* 4.9 3.4 - - + -
234A LEU* 4.1 16.2 - - + -
237A PHE* 3.5 59.0 - - + -
266A GLY 3.2 14.2 + - - +
267A VAL* 3.0 18.4 + - + +
269A ARG* 1.3 78.2 - - - +
271A GLY* 1.3 57.2 - - - +
273A GLU* 3.4 2.9 + - - +
274A ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.6 9.2 - - - -
228A LEU* 3.6 11.7 - - - -
239A LEU* 3.6 21.3 - - - -
267A VAL 2.8 9.7 + - - -
268A LEU 2.9 5.5 + - - -
270A MET* 1.3 75.3 - - - +
272A VAL* 1.3 66.7 + - - +
274A ALA* 3.0 11.6 + - - +
275A LEU* 3.0 18.0 + - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 3.8 14.6 - - + +
68A PHE* 3.5 36.9 - - - +
71A GLU* 3.9 16.3 - - + +
74A ARG* 5.9 0.7 - - - +
268A LEU 2.9 16.2 + - - +
269A ARG* 3.3 12.1 + - - +
271A GLY* 1.3 76.3 - - - +
273A GLU* 1.3 61.5 + - - +
275A LEU* 3.6 4.2 + - - +
276A LYS* 3.2 46.6 + - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.3 46.2 - - + +
43A PRO* 3.7 2.8 - - + +
46A ALA* 4.2 12.4 - - + +
269A ARG 3.1 14.1 + - - +
270A MET 3.7 4.0 - - - +
272A VAL* 1.3 79.6 - - - +
274A ALA* 1.3 65.1 + - - +
276A LYS* 3.0 38.8 + - - +
277A THR* 3.4 6.8 + - - -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.8 15.5 - - + +
228A LEU* 4.1 14.6 - - + -
232A TYR* 3.0 37.6 - - + -
234A LEU* 4.3 4.3 - - + -
270A MET 2.9 18.3 + - - +
271A GLY 3.0 5.3 + - - +
273A GLU* 1.3 77.5 - - - +
275A LEU* 1.3 61.3 + - - +
277A THR* 2.6 25.5 + - - -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.9 22.4 - - + -
71A GLU* 3.7 26.2 - - + +
72A ALA* 3.7 35.4 - - + +
75A TRP* 4.1 33.2 - - + +
228A LEU* 4.3 8.3 - - + -
232A TYR* 3.5 30.4 + - + +
241A PHE* 4.3 11.4 - - + -
271A GLY 3.0 14.3 + - - +
274A ALA* 1.3 76.1 - - - +
276A LYS* 1.3 59.0 + - - +
277A THR 3.2 5.0 + - - +
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.6 24.5 - - - +
74A ARG* 5.6 1.3 - - - +
272A VAL* 3.2 37.2 - - - +
273A GLU* 3.0 30.7 + - - +
275A LEU* 1.3 74.8 - - - +
277A THR* 1.3 65.8 + - - +
278A PRO* 3.3 6.8 - - - +
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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