Contacts of the helix formed by residues 187 - 199 (chain B) in PDB entry 5J3V
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 SER 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B TYR* 3.2 42.4 + - - -
185B HIS* 3.1 10.5 + - - -
186B SER* 1.3 81.2 + - - +
188B PRO* 1.3 74.8 - - - +
189B LYS* 3.5 7.3 + - - +
190B ILE* 3.3 12.9 + - - +
191B ARG* 3.3 15.2 + - - +
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Residues in contact with PRO 188 (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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186B SER 3.6 5.1 - - - +
187B SER* 1.3 87.8 - - - +
189B LYS* 1.3 61.4 + - + +
191B ARG* 3.5 24.2 + - - +
192B SER* 3.0 31.0 + - - -
228B GLU* 4.1 33.0 - - + +
231B VAL* 3.4 4.9 - - + +
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Residues in contact with LYS 189 (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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142B TYR* 3.3 26.0 - - + +
146B GLU* 4.9 9.4 - - + -
187B SER* 3.2 2.8 + - - +
188B PRO* 1.3 81.9 - - + +
190B ILE* 1.3 58.1 + - - +
192B SER* 3.3 3.9 + - - -
193B HIS* 2.9 52.1 + - + +
228B GLU* 5.2 6.9 + - - -
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Residues in contact with ILE 190 (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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142B TYR* 3.6 20.9 - - + -
145B CYS* 4.1 13.5 - - - +
146B GLU* 3.8 34.1 - - + +
149B PHE* 3.8 12.6 - - + -
182B PHE* 3.5 33.7 - - + +
185B HIS* 3.4 42.0 - - + +
187B SER* 3.3 2.7 + - - +
189B LYS* 1.3 76.0 - - - +
191B ARG* 1.3 62.7 + - - +
193B HIS* 3.3 7.6 + - + +
194B ALA* 3.1 20.8 + - - +
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Residues in contact with ARG 191 (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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182B PHE 4.1 7.2 - - - -
183B PHE* 3.3 28.0 - - - +
184B LYS* 4.4 1.3 - - - +
185B HIS* 3.2 32.2 + - + +
186B SER 3.1 26.5 + - - -
187B SER 3.3 7.2 + - - +
188B PRO* 3.9 24.6 - - - +
189B LYS 3.3 0.4 - - - -
190B ILE* 1.3 76.4 - - - +
192B SER* 1.3 59.1 + - - +
194B ALA* 3.0 16.5 + - - +
195B VAL* 3.1 22.3 + - + +
223B LEU* 4.5 9.6 - - + +
226B ASP* 2.8 38.5 + - - -
231B VAL* 4.3 13.0 - - + +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLN* 4.7 0.2 - - - +
188B PRO 3.0 19.7 + - - -
189B LYS* 3.8 5.8 - - - -
191B ARG* 1.3 77.1 - - - +
193B HIS* 1.3 64.3 + - - +
194B ALA 3.1 0.2 - - - -
195B VAL* 4.7 2.5 - - - -
196B ALA* 3.3 12.1 + - - +
230B GLU* 3.2 31.6 + - - +
231B VAL* 3.7 18.5 - - - +
234B ASN* 3.2 27.9 + - - +
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Residues in contact with HIS 193 (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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146B GLU* 4.8 11.6 + - + +
149B PHE* 3.3 47.7 + - + +
150B GLY* 3.5 23.1 + - - -
153B GLN* 3.2 24.0 + - - +
189B LYS* 2.9 45.3 + - + +
190B ILE* 3.7 7.6 - - + +
191B ARG 3.2 0.2 - - - -
192B SER* 1.3 80.1 - - - +
194B ALA* 1.3 58.0 + - - +
196B ALA* 4.1 2.8 - - - +
197B CYS* 3.3 18.9 + - - -
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Residues in contact with ALA 194 (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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149B PHE* 3.6 18.6 - - + -
179B PHE* 3.9 9.8 - - - +
182B PHE 4.0 10.5 - - - +
183B PHE* 3.9 22.9 - - + -
190B ILE 3.1 11.4 + - - +
191B ARG* 3.0 10.7 + - - +
193B HIS* 1.3 76.4 - - - +
195B VAL* 1.3 64.3 + - - +
196B ALA 3.1 1.8 - - - -
197B CYS* 3.3 9.7 + - - +
198B VAL* 3.3 21.1 + - - +
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Residues in contact with VAL 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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183B PHE* 3.5 36.8 - - + -
191B ARG* 3.1 18.5 + - - +
192B SER* 3.8 2.9 + - - -
194B ALA* 1.3 74.7 - - - +
196B ALA* 1.3 59.4 + - - +
197B CYS 3.2 0.9 + - - -
198B VAL* 3.6 0.8 + - - -
199B ASN* 2.9 40.5 + - - +
216B PHE* 5.4 0.2 - - + -
220B LEU* 4.0 12.6 - - + -
223B LEU* 4.4 11.0 - - + -
231B VAL* 5.2 8.1 - - + +
234B ASN* 3.7 39.3 - - + +
235B VAL* 4.5 1.3 - - + +
238B ALA* 4.9 1.3 - - + -
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Residues in contact with ALA 196 (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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153B GLN* 3.4 34.4 - - - +
157B GLU* 4.3 9.2 - - - +
192B SER 3.3 18.2 + - - +
193B HIS 4.4 2.0 - - - +
194B ALA 3.1 0.8 - - - -
195B VAL* 1.3 79.6 - - - +
197B CYS* 1.3 59.8 + - - +
199B ASN* 4.4 7.1 + - - +
200B GLN* 3.8 17.5 + - - +
234B ASN* 3.8 16.5 - - - +
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Residues in contact with CYS 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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149B PHE* 4.1 12.1 - - - -
152B LEU 4.4 0.2 - - - -
153B GLN* 3.6 34.3 - - - -
156B CYS* 4.3 10.9 - - - +
179B PHE* 3.6 29.4 - - + -
193B HIS 3.3 18.8 - - - +
194B ALA 3.3 7.5 + - - +
195B VAL 3.2 0.4 - - - -
196B ALA* 1.3 79.2 - - - +
198B VAL* 1.3 63.4 + - - +
199B ASN 3.3 1.8 - - - -
200B GLN* 3.4 21.3 + - - +
201B PHE* 3.7 15.1 - - - -
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Residues in contact with VAL 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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176B ILE* 5.0 5.2 - - + -
179B PHE* 4.2 14.1 - - + -
180B LEU* 3.9 12.3 - - + -
183B PHE* 3.7 20.9 - - + -
194B ALA 3.3 18.1 + - - +
195B VAL 3.6 3.5 + - - +
197B CYS* 1.3 72.9 - - - +
199B ASN* 1.3 61.2 + - - +
200B GLN 3.1 6.0 + - - -
201B PHE* 3.2 15.4 + - - -
202B ILE* 3.4 9.3 - - - +
209B LEU* 3.5 31.6 - - + +
216B PHE* 3.5 30.5 - - + -
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Residues in contact with ASN 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 VAL* 2.9 23.2 + - - +
196B ALA* 4.7 7.1 - - - +
197B CYS 3.3 1.0 - - - -
198B VAL* 1.3 78.7 - - - +
200B GLN* 1.3 62.8 + - + +
201B PHE 3.2 1.2 + - - -
202B ILE* 3.7 16.8 + - + +
203B ILE* 4.7 3.3 + - - +
216B PHE* 4.0 4.2 - - - -
234B ASN* 3.1 30.7 + - - +
237B ARG* 3.9 18.6 - - - +
238B ALA* 3.3 30.7 - - - +
241B MET* 3.7 25.9 - - + +
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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