Contacts of the helix formed by residues 186 - 201 (chain B) in PDB entry 3C39
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 GLY 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.2 5.2 - - - -
45B SER* 3.6 4.5 - - - -
161B VAL* 3.8 12.8 - - - -
162B ASN 3.0 14.6 + - - -
163B ASP* 2.8 24.7 - - - +
184B ALA 3.5 2.8 + - - -
185B GLY* 1.3 77.3 - - - +
187B PHE* 1.3 58.4 + - - -
188B LEU 3.2 0.2 + - - -
189B MET* 3.3 0.7 + - - +
190B LYS* 2.9 25.0 + - - +
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER 5.2 0.7 - - - -
4A ASN* 3.2 39.3 - - + -
416A ILE 4.9 12.9 - - - +
8B LEU* 4.1 7.4 - - + +
9B ASP* 3.7 40.2 - - + -
44B PRO* 4.3 11.7 - - + -
45B SER* 2.9 32.5 + - - +
48B PHE* 3.5 37.7 - + + -
186B GLY* 1.3 69.2 - - - -
188B LEU* 1.3 61.2 + - - +
190B LYS* 3.7 18.9 - - + +
191B LYS* 2.9 29.8 + - - +
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 6.3 1.3 - - + +
38B ARG* 5.2 2.9 - - + +
41B ALA* 3.6 46.6 + - + +
42B ALA* 4.7 3.1 - - + +
163B ASP* 2.7 42.2 + - - +
165B PHE* 4.7 4.0 - - + +
187B PHE* 1.3 70.8 - - - +
189B MET* 1.3 64.9 + - - +
191B LYS* 3.2 18.7 + - + +
192B GLU* 2.9 53.3 + - + +
393B THR* 3.8 17.0 - - + +
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASN* 3.6 51.6 - - + +
163B ASP* 3.0 8.1 + - - +
164B ALA 3.9 17.9 - - - +
165B PHE* 3.7 31.6 - - - -
168B ALA* 4.3 9.9 - - + -
185B GLY* 4.5 2.0 - - - -
186B GLY 3.6 6.7 - - - +
188B LEU* 1.3 77.1 - - - +
190B LYS* 1.3 61.7 + - - +
192B GLU* 3.7 0.7 - - - +
193B LEU* 3.0 45.0 + - + +
409B GLY 4.8 4.9 - - - +
410B VAL* 4.1 18.4 - - + -
413B LEU* 4.6 12.6 - - + -
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 5.7 0.6 + - - -
415A ASN* 5.9 5.7 - - - +
416A ILE 5.4 10.2 - - - +
7B THR* 4.0 23.8 + - + -
9B ASP* 2.9 39.9 + - - +
10B LYS* 5.9 0.6 - - - +
185B GLY* 5.2 0.6 - - - -
186B GLY 2.9 17.4 + - - +
187B PHE* 3.7 21.0 - - + +
188B LEU 3.2 0.2 - - - -
189B MET* 1.3 76.6 - - - +
191B LYS* 1.3 56.5 + - - +
193B LEU* 3.9 3.3 - - - +
194B ASN* 3.0 55.8 + - - +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 4.9 21.3 + - + +
187B PHE 2.9 20.5 + - - +
188B LEU* 3.7 17.7 - - + +
190B LYS* 1.3 73.1 - - - +
192B GLU* 1.3 64.5 + - + +
194B ASN* 3.5 5.0 - - - +
195B TYR* 3.0 47.8 + - + -
389B SER 4.3 4.2 + - - -
390B HIS* 2.7 43.3 + - + +
391B VAL 4.5 5.8 + - - +
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 3.4 45.3 - - + -
188B LEU* 2.9 31.4 + - + +
189B MET 3.7 0.9 - - - +
191B LYS* 1.3 75.7 - - - +
193B LEU* 1.3 57.3 + - - +
195B TYR* 3.3 2.9 + - - +
196B PHE* 3.1 39.3 + - - -
390B HIS* 3.0 27.0 + - + -
391B VAL 4.4 0.7 - - - +
392B SER* 2.7 21.7 + - - -
393B THR* 2.7 35.7 + - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.5 38.3 - - + +
165B PHE* 4.2 6.3 - - + -
189B MET* 3.0 37.1 + - + +
190B LYS* 4.1 3.4 - - - +
192B GLU* 1.3 70.6 - - - +
194B ASN* 1.3 62.1 + - - +
196B PHE* 3.9 3.1 - - - +
197B ALA* 2.9 34.1 + - - +
401B LEU* 4.1 17.2 - - + +
407B LEU* 3.9 26.9 - - + -
410B VAL* 3.5 34.8 - - + -
413B LEU* 5.7 0.9 - - + -
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Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.4 16.0 - - - +
3B SER* 5.7 1.2 - - - +
190B LYS* 3.0 43.0 + - - +
191B LYS* 3.5 6.9 - - - +
193B LEU* 1.3 78.2 + - - +
195B TYR* 1.3 65.7 + - + +
197B ALA* 4.5 2.7 - - - +
198B LYS* 3.1 49.8 + - + +
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Residues in contact with TYR 195 (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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191B LYS* 3.0 42.3 + - + +
192B GLU 3.3 4.5 + - - +
194B ASN* 1.3 78.0 - - + +
196B PHE* 1.3 58.4 + - + +
198B LYS* 3.8 3.4 - - + +
199B ALA* 3.0 29.6 + - - +
367B ILE* 4.9 9.4 - - + -
369B ILE* 3.7 20.9 - - + +
389B SER* 3.4 31.5 + - - -
390B HIS* 3.4 50.5 - + + -
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 4.1 3.6 - + - -
192B GLU* 3.1 47.4 + - - +
193B LEU 4.5 1.1 - - - +
195B TYR* 1.3 77.8 - - + +
197B ALA* 1.3 58.6 + - - +
199B ALA* 3.6 4.4 + - + -
200B LEU* 3.1 33.6 + - + +
334B VAL* 4.4 15.5 - - + -
336B ASN* 5.9 0.9 - - - -
369B ILE* 3.6 29.6 - - + -
370B ILE 5.4 0.7 - - - -
371B GLY* 6.3 0.2 - - - -
390B HIS* 4.3 4.7 - - - -
392B SER* 3.8 12.3 - - - -
398B SER* 3.4 30.1 - - - -
401B LEU* 3.5 31.6 - - + -
402B LEU* 4.1 23.3 - - + -
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Residues in contact with ALA 197 (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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2B LEU* 3.5 22.4 - - + -
193B LEU 2.9 20.9 + - - +
194B ASN* 4.2 3.4 - - - +
196B PHE* 1.3 74.0 - - - +
198B LYS* 1.3 58.6 + - + +
200B LEU* 3.2 3.4 + - - -
201B GLU* 2.7 60.4 + - - +
401B LEU* 6.5 0.2 - - - -
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Residues in contact with LYS 198 (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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194B ASN* 3.1 38.5 + - + +
195B TYR* 3.9 3.6 - - + +
197B ALA* 1.3 79.9 - - + +
199B ALA* 1.3 62.0 + - - +
200B LEU 3.3 0.2 - - - -
201B GLU* 5.2 1.8 - - - -
202B SER* 3.3 35.0 + - - +
203B PRO* 3.9 1.0 - - - +
332B GLN* 4.4 2.5 - - - +
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Residues in contact with ALA 199 (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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195B TYR 3.0 19.5 + - - +
196B PHE* 3.8 9.0 - - + +
197B ALA 3.1 0.2 - - - -
198B LYS* 1.3 77.4 - - - +
200B LEU* 1.3 63.4 + - + +
203B PRO* 3.2 16.4 - - - +
207B PHE* 3.3 5.5 - - - -
332B GLN* 2.9 35.1 + - - +
334B VAL* 4.0 12.3 - - + -
369B ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 200 (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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196B PHE* 3.1 20.9 - - + +
197B ALA* 3.2 3.2 + - - +
199B ALA* 1.3 88.1 - - + +
201B GLU* 1.3 61.2 + - + +
203B PRO* 4.2 7.7 - - - +
207B PHE* 3.9 22.7 - - + -
225B ASN* 5.5 0.7 - - - +
226B MET* 3.9 21.8 - - + -
229B LYS* 3.7 29.7 + - + +
334B VAL* 4.9 0.7 - - + -
401B LEU* 4.5 10.8 - - + +
402B LEU* 3.7 40.4 - - + +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 5.2 4.7 - - - +
197B ALA* 2.7 45.8 + - - +
198B LYS* 5.2 1.5 + - - -
200B LEU* 1.3 76.4 - - + +
202B SER* 1.3 64.4 + - - +
203B PRO* 3.4 6.3 - - - +
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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
------------------------------------------------------------
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