Contacts of the helix formed by residues 232 - 245 (chain B) in PDB entry 6DU2
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 THR 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B PRO 5.3 0.2 - - - -
134B HIS* 3.8 25.6 - - - +
230B SER 3.5 10.6 + - - +
231B ASP* 1.3 82.8 + - - +
233B GLU* 1.3 57.2 + - - +
234B LEU 3.3 2.5 - - - -
235B HIS* 3.2 9.0 + - + +
236B ASP* 2.8 54.0 + - - -
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Residues in contact with GLU 233 (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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132B ARG* 3.2 14.1 - - - +
133B PRO 5.7 0.2 + - - -
221B PRO 5.0 2.4 - - - +
222B VAL* 3.7 26.6 - - + -
223B ALA* 4.0 23.7 + - - +
231B ASP* 2.4 30.8 + - - +
232B THR 1.3 67.3 - - - +
234B LEU* 1.3 62.7 + - - +
236B ASP* 3.3 8.1 + - - +
237B LEU* 3.1 35.3 + - + +
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Residues in contact with LEU 234 (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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100B THR 4.1 8.5 - - - +
101B LEU* 4.0 16.2 - - + -
132B ARG* 3.6 29.9 - - + +
133B PRO 4.0 10.5 + - - +
134B HIS 4.5 1.3 - - - +
135B VAL* 3.7 33.2 - - + +
138B PHE* 3.4 43.5 - - + -
205B LEU* 4.4 11.0 - - + -
222B VAL* 4.8 6.7 - - + -
231B ASP* 4.4 0.2 + - - -
232B THR 3.3 0.4 - - - -
233B GLU* 1.3 77.8 - - - +
235B HIS* 1.3 62.7 + - - +
237B LEU* 3.3 16.1 + - + +
238B LEU* 2.9 18.0 - - - +
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Residues in contact with HIS 235 (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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134B HIS* 3.7 36.2 + + + +
137B GLU* 3.2 31.4 + - - -
232B THR* 3.2 13.4 + - + +
234B LEU* 1.3 78.3 - - - +
236B ASP* 1.3 81.6 + - - +
237B LEU 3.1 1.6 + - - -
238B LEU* 3.1 22.6 + - - +
239B PRO* 3.6 7.3 - - - +
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 2.8 42.5 + - - +
233B GLU* 3.7 8.9 + - - +
235B HIS* 1.3 89.7 - - - +
237B LEU* 1.3 59.1 + - - +
238B LEU 3.5 0.2 - - - -
239B PRO* 3.7 13.7 - - - +
240B PHE* 4.9 2.6 + - - +
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Residues in contact with LEU 237 (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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138B PHE* 4.5 1.8 - - + -
205B LEU* 3.9 25.1 - - + -
220B VAL* 3.9 24.2 - - + -
221B PRO 4.7 4.5 - - - +
222B VAL* 3.9 20.9 - - + -
233B GLU* 3.1 27.0 + - + +
234B LEU* 3.6 14.4 - - + +
235B HIS 3.1 1.2 - - - -
236B ASP* 1.3 79.4 - - - +
238B LEU* 1.3 65.0 + - - +
239B PRO 3.4 0.7 - - - -
240B PHE* 3.0 25.7 + - + +
241B PHE* 3.1 28.1 + - + -
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Residues in contact with LEU 238 (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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134B HIS 5.8 0.2 - - - +
137B GLU* 4.2 10.8 - - + +
138B PHE* 3.8 35.9 - - + +
141B ARG* 3.4 40.8 - - + -
142B MET* 4.7 6.1 - - + +
145B LEU* 5.4 0.6 - - + +
234B LEU 2.9 26.7 - - - +
235B HIS* 3.1 24.0 + - - +
237B LEU* 1.3 77.4 - - - +
239B PRO* 1.3 58.5 - - + +
241B PHE* 3.0 7.9 + - - +
242B GLU* 2.7 42.5 + - + +
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Residues in contact with PRO 239 (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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235B HIS 3.6 11.0 - - - +
236B ASP* 3.7 11.2 - - - +
237B LEU 3.5 3.6 - - - -
238B LEU* 1.3 93.5 - - + +
240B PHE* 1.3 61.5 + - - +
242B GLU* 3.4 16.8 + - + +
243B GLN* 3.4 24.9 + - - +
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Residues in contact with PHE 240 (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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220B VAL* 4.0 31.0 - - + -
236B ASP 4.9 1.9 + - - +
237B LEU* 3.0 22.2 + - + +
239B PRO* 1.3 78.6 - - - +
241B PHE* 1.3 66.9 + + - +
243B GLN* 3.3 16.1 + - + +
244B LEU* 3.1 50.5 + - + +
253B VAL* 4.6 15.3 - - + -
254B LEU* 4.4 17.5 - - + -
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Residues in contact with PHE 241 (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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93B VAL* 4.8 6.1 - - + -
138B PHE* 4.1 9.4 - + - -
142B MET* 3.6 37.2 - - + -
145B LEU* 4.5 2.9 - - + -
146B PHE* 3.4 27.3 - + + -
203B LEU* 4.4 13.9 - - + -
204B ILE 6.5 0.2 - - - -
205B LEU* 3.9 16.8 - - + -
220B VAL* 3.8 34.1 - - + -
237B LEU* 3.1 56.2 + - + -
238B LEU* 3.0 9.0 + - + +
240B PHE* 1.3 76.0 - + - +
242B GLU* 1.3 66.5 + - - +
244B LEU* 4.3 5.8 - - + -
245B SER* 3.1 22.3 + - - -
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Residues in contact with GLU 242 (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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141B ARG* 2.5 53.1 + - - +
145B LEU* 3.5 11.2 - - + +
238B LEU* 2.7 28.0 + - + +
239B PRO* 3.4 13.7 - - + +
240B PHE 3.3 0.2 - - - -
241B PHE* 1.3 72.2 - - - +
243B GLN* 1.3 60.5 + - + +
245B SER* 2.6 23.7 + - - -
246B ARG* 3.7 16.3 + - - +
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Residues in contact with GLN 243 (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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239B PRO* 3.5 19.3 + - - +
240B PHE* 3.3 15.7 + - + +
241B PHE 3.2 0.4 - - - -
242B GLU* 1.3 75.1 - - + +
244B LEU* 1.3 66.6 + - + +
246B ARG* 3.1 39.3 + - - +
247B VAL* 3.5 13.1 - - - +
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Residues in contact with LEU 244 (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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91B ILE* 3.2 16.7 - - - +
146B PHE* 4.6 1.3 - - + -
203B LEU* 3.7 31.0 - - + -
220B VAL* 4.4 2.9 - - + -
240B PHE* 3.1 53.9 + - + +
241B PHE* 3.3 8.7 + - + +
243B GLN* 1.3 76.9 - - - +
245B SER* 1.3 61.3 + - - +
246B ARG 3.0 1.4 + - - -
247B VAL* 3.2 20.7 + - + +
250B VAL* 3.5 28.0 - - + -
253B VAL* 4.0 28.7 - - + -
254B LEU* 5.0 2.0 - - + -
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 4.1 8.3 + - - +
145B LEU* 3.8 33.0 - - - +
146B PHE* 3.7 24.4 - - - -
201B ARG* 4.8 6.1 + - - -
241B PHE 3.1 12.8 + - - -
242B GLU 2.6 24.4 + - - -
244B LEU* 1.3 76.0 - - - +
246B ARG* 1.3 62.1 + - - +
247B VAL 3.5 3.7 + - - +
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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