Contacts of the helix formed by residues 232 - 242 (chain B) in PDB entry 4WLU
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 GLU 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ARG* 5.3 0.3 + - - -
110B ARG* 5.8 1.8 + - - +
202B GLY* 4.2 8.0 - - - -
203B LYS* 4.1 17.6 + - - -
228B GLY 3.0 15.1 + - - +
229B ARG* 3.8 2.0 - - - +
231B GLN* 1.3 84.1 - - + +
233B ALA* 1.3 57.9 + - - +
234B GLY 3.3 2.9 - - - -
235B THR* 3.0 34.7 + - + +
236B GLU* 2.9 28.4 + - - +
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Residues in contact with ALA 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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70A HIS* 3.7 10.8 - - + -
176B ARG* 3.5 32.3 - - - +
180B PHE* 4.1 9.2 - - + -
229B ARG 3.1 17.6 + - - +
230B ILE 3.5 6.7 + - - +
231B GLN 3.5 1.8 - - - -
232B GLU* 1.3 76.7 - - - +
234B GLY* 1.3 62.2 + - - +
236B GLU* 3.2 12.5 + - - +
237B VAL* 3.1 26.5 + - - +
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 3.6 6.7 - - - -
110B ARG* 3.9 6.5 - - - +
176B ARG* 3.5 9.5 - - - +
231B GLN 5.1 0.2 + - - -
232B GLU 3.3 0.8 - - - -
233B ALA* 1.3 78.2 - - - +
235B THR* 1.3 57.2 + - - +
237B VAL* 3.4 5.0 + - - +
238B VAL* 3.0 30.8 + - - +
246B SER* 5.4 0.2 - - - -
401B LMR 3.5 36.0 - - - +
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Residues in contact with THR 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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104B ARG* 3.3 27.6 + - - +
107B GLY* 5.9 5.2 - - - +
108B MET 5.5 2.2 - - - +
110B ARG* 4.7 2.3 + - - +
232B GLU* 3.0 40.9 + - + +
234B GLY* 1.3 73.2 - - - +
236B GLU* 1.3 60.7 + - - +
238B VAL* 3.3 8.2 + - + +
239B LYS* 2.9 48.6 + - + +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 5.5 5.9 - - + +
70A HIS* 3.4 23.1 + - + +
180B PHE* 5.4 0.2 - - - -
229B ARG* 2.7 50.2 + - - +
232B GLU* 2.9 13.3 + - - +
233B ALA* 3.3 12.4 - - - +
235B THR* 1.3 77.6 - - - +
237B VAL* 1.3 57.1 + - - +
239B LYS* 3.6 11.4 + - - +
240B ALA* 3.1 26.5 + - + +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 4.5 0.9 - - - +
66A ALA* 4.4 4.9 - - + +
67A ASP* 4.2 28.0 - - + +
70A HIS* 3.3 35.9 - - + +
176B ARG* 4.5 6.5 - - - +
233B ALA 3.1 6.6 + - - +
234B GLY 3.8 6.7 - - - +
235B THR 3.3 0.2 - - - -
236B GLU* 1.3 73.3 - - + +
238B VAL* 1.3 66.8 + - - +
240B ALA* 3.1 6.5 + - - +
241B LYS* 2.9 30.3 + - + +
246B SER 4.3 2.7 - - - -
247B ALA* 3.7 34.3 - - + +
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Residues in contact with VAL 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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104B ARG* 4.2 29.2 - - + +
105B LYS 3.7 8.3 - - - +
106B PRO* 3.5 40.5 - - + +
107B GLY 5.1 0.4 - - - +
108B MET 6.1 0.4 - - - +
234B GLY 3.0 20.0 + - - +
235B THR* 3.5 11.4 - - + +
237B VAL* 1.3 77.0 - - - +
239B LYS* 1.3 61.2 + - + +
241B LYS* 3.3 3.3 + - - +
242B ALA 3.1 16.5 + - - -
243B GLY 4.2 0.7 + - - -
245B GLY 4.0 9.2 - - - +
246B SER* 3.7 27.6 - - - +
401B LMR 4.4 0.7 - - - +
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Residues in contact with LYS 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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106B PRO* 4.9 13.0 - - + -
235B THR* 2.9 37.2 + - + +
236B GLU* 3.7 10.0 - - - +
238B VAL* 1.3 77.1 - - + +
240B ALA* 1.3 63.4 + - - +
242B ALA* 3.0 18.2 + - - +
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Residues in contact with ALA 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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62A PRO* 4.3 10.4 - - + +
63A GLY* 3.6 17.9 + - - +
66A ALA* 3.8 27.4 - - + -
236B GLU* 3.1 16.0 + - + +
237B VAL 3.1 5.8 + - - +
239B LYS* 1.3 79.3 - - - +
241B LYS* 1.3 60.2 + - - +
242B ALA* 3.6 3.6 + - - +
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Residues in contact with LYS 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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38A GLN* 5.0 4.6 + - - +
60A HIS* 4.9 4.0 + - - -
63A GLY* 3.7 33.9 - - - +
64A VAL* 4.5 7.0 - - - +
67A ASP* 3.3 14.3 + - - -
237B VAL* 2.9 16.6 + - - +
238B VAL 3.3 1.1 + - - +
240B ALA* 1.3 73.2 - - - +
242B ALA* 1.3 70.8 + - - +
243B GLY 3.3 0.7 - - - -
244B ALA* 3.1 37.2 + - + +
245B GLY* 3.4 27.6 - - - +
246B SER* 2.8 28.6 + - - +
248B THR* 3.1 23.4 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 4.0 9.4 - - - -
238B VAL 3.1 6.0 + - - -
239B LYS 3.0 17.5 + - - +
240B ALA 4.4 3.8 - - - +
241B LYS* 1.3 79.5 - - - +
243B GLY* 1.3 57.4 + - - +
244B ALA* 5.3 0.2 - - - +
58D ILE* 5.2 9.8 - - + +
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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