Contacts of the helix formed by residues 261 - 272 (chain A) in PDB entry 3DBD
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 ASN 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLU* 2.9 40.3 + - - +
140A ARG* 5.1 1.2 - - - +
259A HIS 3.8 1.8 + - - -
260A ILE* 1.3 73.6 - - + +
262A PRO* 1.3 64.7 - - - +
263A VAL* 2.9 37.9 + - - +
264A ALA* 3.0 17.8 + - + +
265A SER* 2.8 31.9 + - - -
290A PHE* 6.1 0.2 - - - -
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Residues in contact with PRO 262 (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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260A ILE 3.3 6.9 - - - +
261A ASN* 1.3 92.2 - - - +
263A VAL* 1.3 57.9 + - + +
265A SER* 2.9 21.3 + - - +
266A ALA* 3.0 18.5 + - - +
269A ARG* 4.5 1.7 + - - -
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Residues in contact with VAL 263 (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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261A ASN* 2.9 14.9 + - - +
262A PRO* 1.3 78.4 - - + +
264A ALA* 1.3 63.6 + - - +
266A ALA* 3.4 8.1 + - - +
267A LEU* 3.2 21.0 + - - +
288A ASP* 4.7 1.9 - - - +
289A GLU* 3.8 38.6 - - + +
290A PHE* 3.6 33.8 - - + +
293A SER* 4.6 6.5 - - - +
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Residues in contact with ALA 264 (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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136A GLU* 5.0 0.7 - - - +
227A LEU* 4.7 1.6 - - + +
231A LEU* 3.7 27.8 - - + -
260A ILE* 4.2 3.4 - - + -
261A ASN* 3.0 22.9 + - + +
263A VAL* 1.3 77.1 - - - +
265A SER* 1.3 59.8 + - - +
267A LEU* 3.3 5.7 + - - +
268A ILE* 3.1 34.1 + - - +
290A PHE* 3.8 24.6 - - + -
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Residues in contact with SER 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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256A VAL* 4.1 23.5 - - - +
260A ILE* 4.2 6.1 + - - +
261A ASN 2.8 14.7 + - - -
262A PRO* 2.9 28.5 + - - +
264A ALA* 1.3 69.2 - - - +
266A ALA* 1.3 59.9 + - - +
268A ILE* 3.8 11.0 - - - +
269A ARG* 3.1 52.7 + - - +
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Residues in contact with ALA 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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262A PRO 3.0 18.4 + - - +
263A VAL* 3.5 9.0 - - - +
264A ALA 3.2 0.2 - - - -
265A SER* 1.3 77.3 + - - +
267A LEU* 1.3 60.9 + - - +
269A ARG* 3.4 21.8 + - - +
270A ARG* 3.3 32.2 + - - +
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Residues in contact with LEU 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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147A ILE* 6.4 0.4 - - + -
227A LEU* 3.8 18.8 - - + -
263A VAL 3.2 7.2 + - - +
264A ALA* 3.7 8.1 - - - +
265A SER 3.3 0.2 - - - -
266A ALA* 1.3 76.4 - - - +
268A ILE* 1.3 63.2 + - - +
270A ARG* 3.3 18.4 + - - +
271A MET* 3.0 38.4 + - + +
280A PRO* 4.7 1.6 - - + -
285A LEU* 3.9 24.9 - - + -
288A ASP* 3.4 40.6 - - + +
290A PHE* 3.8 22.7 - - + -
291A PHE* 4.1 12.6 - - + -
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Residues in contact with ILE 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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224A GLY 4.1 6.5 - - - +
227A LEU* 3.8 26.7 - - + -
228A TYR* 3.8 41.5 - - + +
231A LEU* 4.2 12.3 - - + -
232A VAL* 5.7 1.1 - - + -
254A TYR* 4.9 1.1 - - + -
256A VAL* 4.4 11.9 - - + -
260A ILE* 4.9 6.7 - - + -
264A ALA 3.1 27.7 + - - +
265A SER* 3.8 9.2 - - - +
266A ALA 3.4 0.2 - - - -
267A LEU* 1.3 75.3 - - - +
269A ARG* 1.3 57.3 + - - +
271A MET* 3.3 8.4 + - - +
272A LEU* 2.9 49.4 + - + +
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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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254A TYR* 3.4 30.2 + - + +
256A VAL* 4.9 8.6 - - + +
262A PRO 4.5 1.2 + - - -
265A SER* 3.1 46.1 + - - +
266A ALA* 3.4 28.4 - - - +
267A LEU 3.3 0.2 - - - -
268A ILE* 1.3 76.4 - - - +
270A ARG* 1.3 58.9 + - + +
272A LEU 3.4 2.4 + - - -
273A HIS* 2.9 31.1 + - - +
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Residues in contact with ARG 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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266A ALA* 3.3 17.3 + - - +
267A LEU* 3.3 15.6 + - - +
268A ILE 3.3 0.4 - - - -
269A ARG* 1.3 76.0 - - + +
271A MET* 1.3 62.3 + - - +
273A HIS* 3.4 22.4 - - - +
278A LEU 4.9 8.7 + - - +
279A ARG* 3.4 6.8 - - - -
280A PRO* 3.2 47.7 - - + +
284A GLU* 5.2 4.9 + - - +
288A ASP* 2.8 31.7 + - - +
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Residues in contact with MET 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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143A MET* 4.3 9.6 - - + -
147A ILE* 5.2 1.6 - - + -
220A ILE* 3.9 8.7 - - + +
221A TRP* 3.4 22.7 + - - -
223A LEU* 3.6 22.7 - - + +
224A GLY* 3.5 31.4 - - - +
227A LEU* 3.9 15.0 - - - -
267A LEU* 3.0 41.5 + - + +
268A ILE* 3.3 4.7 + - - +
270A ARG* 1.3 76.3 - - - +
272A LEU* 1.3 58.1 + - - +
273A HIS 3.4 0.4 - - - -
279A ARG* 3.6 12.3 - - - -
280A PRO* 3.8 10.3 - - + -
285A LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 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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221A TRP* 3.4 53.2 - - + +
224A GLY 4.1 11.4 - - - +
225A CYS* 3.7 18.8 - - - +
228A TYR* 5.0 0.4 - - + -
236A PRO* 4.7 9.2 - - + -
237A PHE* 4.4 7.2 - - + -
252A ASN* 3.3 22.7 + - - +
254A TYR* 4.1 32.3 - - + +
268A ILE* 2.9 36.6 + - + +
269A ARG 3.4 3.1 - - - -
270A ARG 3.2 0.2 - - - -
271A MET* 1.3 75.9 - - - +
273A HIS* 1.3 64.8 + - - +
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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