Contacts of the helix formed by residues 236 - 249 (chain B) in PDB entry 3H44
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 ASP 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B GLU* 5.0 6.0 - - - +
234B GLY 3.8 2.7 + - - +
235B ILE* 1.3 74.8 - - - +
237B VAL* 1.3 62.5 + - - +
238B ARG* 3.0 9.7 + - - +
239B GLN* 3.0 43.0 + - - +
240B GLU* 3.1 25.6 + - - +
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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
----------------------------------------------------------
103B ILE* 5.1 7.2 - - + -
106B LEU* 4.6 15.7 - - + -
109B PHE* 4.4 17.9 - - + -
179B LYS* 4.1 17.9 - - + +
226B LEU* 3.8 21.5 - - - +
227B GLU* 5.0 2.5 - - - -
230B PRO* 3.6 32.1 - - + -
231B ASN* 5.0 5.2 - - - +
235B ILE* 4.1 7.6 - - + +
236B ASP* 1.3 75.9 + - - +
238B ARG* 1.3 66.0 + - - +
240B GLU* 3.1 8.2 + - + +
241B LEU* 2.9 23.3 + - + +
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Residues in contact with ARG 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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173B LEU 2.9 23.0 + - - -
174B PHE* 2.7 26.6 + - + +
175B ASP* 4.7 1.0 - - - +
176B GLU* 3.0 41.1 + - - +
179B LYS* 3.8 16.5 - - + +
236B ASP* 3.0 6.6 + - - +
237B VAL* 1.3 74.9 - - - +
239B GLN* 1.3 58.1 + - - +
241B LEU* 3.2 11.8 + - - +
242B LEU* 3.0 50.5 + - + +
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Residues in contact with GLN 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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236B ASP* 3.0 33.7 + - - +
238B ARG* 1.3 75.4 - - - +
240B GLU* 1.3 67.1 + - - +
242B LEU* 3.1 12.1 + - - +
243B LYS* 2.6 58.6 + - - +
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Residues in contact with GLU 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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100B PRO* 5.4 4.7 - - - +
103B ILE* 4.9 10.6 - - + +
106B LEU* 3.8 20.6 - - + +
235B ILE* 3.5 34.5 - - + +
236B ASP 3.1 15.9 + - - +
237B VAL* 3.1 10.0 + - + +
239B GLN* 1.3 87.8 + - - +
241B LEU* 1.3 57.6 + - - +
243B LYS* 3.3 32.1 - - - +
244B PHE* 2.9 32.4 + - - +
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Residues in contact with LEU 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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106B LEU* 3.7 23.3 - - + +
109B PHE* 4.4 16.4 - - + -
110B LEU* 3.8 38.8 - - + +
113B MET* 4.1 13.2 - - + -
174B PHE* 3.6 34.5 - - + -
179B LYS* 4.7 9.0 - - + -
237B VAL* 2.9 20.4 + - + +
238B ARG* 3.3 15.7 - - - +
239B GLN 3.2 0.2 - - - -
240B GLU* 1.3 76.7 - - - +
242B LEU* 1.3 52.4 + - - +
244B PHE* 3.7 4.1 - - - +
245B HIS* 2.7 36.2 + - - +
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Residues in contact with LEU 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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172B PRO* 4.6 8.7 - - + +
174B PHE* 3.3 26.9 - - + -
238B ARG* 3.0 57.1 + - + +
239B GLN* 3.5 9.2 - - + +
241B LEU* 1.3 72.6 - - - +
243B LYS* 1.3 67.3 + - - +
245B HIS* 3.1 4.6 + - + +
246B SER* 2.8 28.6 + - - -
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Residues in contact with LYS 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 GLN* 2.6 49.9 + - - +
240B GLU* 3.3 29.0 + - - +
241B LEU 3.4 0.2 - - - -
242B LEU* 1.3 70.2 - - - +
244B PHE* 1.3 53.1 + - - +
246B SER* 3.8 3.9 - - - -
247B ALA* 2.8 41.8 + - + +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.7 29.8 - - + -
98B SER* 3.5 27.6 - - - -
99B ASP* 4.6 2.5 - - - -
100B PRO* 4.3 19.3 - - + -
106B LEU* 4.1 11.2 - - + -
107B SER* 3.8 30.5 - - - -
110B LEU* 3.3 23.1 - - + -
240B GLU 2.9 18.3 + - - +
241B LEU 3.8 2.5 - - - +
243B LYS* 1.3 75.5 - - - +
245B HIS* 1.3 64.6 + - - +
247B ALA* 4.3 4.5 - - - -
248B TYR* 3.0 52.4 + + + +
249B TYR* 4.5 6.7 - + - -
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Residues in contact with HIS 245 (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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110B LEU* 4.1 9.9 - - + -
114B LEU* 3.9 15.5 - - + -
168B PHE 3.2 20.9 + - - -
169B PHE* 4.2 14.1 - - - -
170B LEU 4.7 4.0 - - - -
172B PRO* 3.5 29.1 - - + +
174B PHE* 4.1 13.9 - + + -
241B LEU 2.7 21.8 + - - +
242B LEU* 3.7 5.3 - - + +
244B PHE* 1.3 73.8 - - - +
246B SER* 1.3 59.8 + - - +
249B TYR* 2.9 65.4 + + + +
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Residues in contact with SER 246 (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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242B LEU 2.8 20.4 + - - -
243B LYS* 3.9 3.4 - - - -
245B HIS* 1.3 78.1 + - - +
247B ALA* 1.3 59.7 + - - +
248B TYR 3.2 0.9 + - - -
249B TYR 4.4 3.5 + - - -
281B LYS* 2.7 50.5 + - - +
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Residues in contact with ALA 247 (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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243B LYS* 2.8 24.5 + - + +
244B PHE* 3.3 4.2 + - - +
246B SER* 1.3 77.3 - - - +
248B TYR* 1.3 75.2 + - + +
281B LYS* 4.8 4.8 - - - +
283B VAL* 3.6 26.0 - - - +
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Residues in contact with TYR 248 (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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92B VAL* 4.1 8.8 - - - +
94B ILE* 3.6 39.9 - - + +
98B SER* 4.5 15.7 + - - -
244B PHE* 3.0 54.3 + + + +
246B SER 3.2 0.6 - - - -
247B ALA* 1.3 95.1 - - + +
249B TYR* 1.3 62.2 + - + +
250B SER* 2.9 13.2 + - - -
253B LEU* 3.8 17.2 - - - +
283B VAL* 4.1 20.0 - - + -
284B PRO 5.7 1.1 - - - -
286B PRO* 5.4 4.7 - - + -
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.7 36.3 - - + -
94B ILE* 5.0 4.9 - - + -
107B SER* 5.1 2.6 + - - -
110B LEU* 3.4 19.7 - - + +
111B GLN 5.0 0.2 + - - -
114B LEU* 3.9 12.8 - - + -
147B THR* 3.3 18.8 + - - +
149B TYR* 2.7 31.4 + + - -
169B PHE* 4.0 17.1 - + + +
244B PHE* 4.5 14.8 - + - -
245B HIS* 2.9 52.3 + + + +
246B SER 5.0 3.4 - - - +
248B TYR* 1.3 83.5 - - + +
250B SER* 1.3 54.4 + - - +
251B SER 4.1 0.3 + - - -
254B MET* 3.1 19.6 - - + +
278B VAL* 4.7 2.8 - - - +
279B GLU* 4.5 3.1 - - - +
281B LYS* 5.7 1.0 - - - +
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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