Contacts of the helix formed by residues 187 - 196 (chain B) in PDB entry 5Y7G
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 TRP 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 6.2 0.7 - - + -
26B PHE* 4.3 33.3 - + - -
29B VAL* 3.7 37.7 - - + -
67B VAL* 4.0 20.4 - - + +
68B MET* 3.7 42.2 - - + -
172B CYS* 4.4 7.0 - - + -
175B LEU* 4.8 4.0 - - + -
176B ARG* 3.8 50.3 - - + +
179B TYR* 4.9 1.3 - + - -
180B PHE* 4.4 11.4 - + - -
186B ASP* 1.3 72.5 - - + +
188B SER* 1.3 55.0 + - - +
189B GLU 3.0 6.7 - - - -
190B PHE* 3.0 47.4 + + + +
191B VAL* 4.0 2.7 + - - +
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Residues in contact with SER 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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68B MET* 5.6 1.9 - - - -
186B ASP* 3.1 25.8 + - - +
187B TRP* 1.3 75.2 - - - +
189B GLU* 1.3 57.1 + - - +
191B VAL* 3.1 16.9 + - - +
192B LEU* 2.7 52.9 + - - +
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Residues in contact with GLU 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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180B PHE* 4.2 10.1 - - + -
185B GLN* 3.1 38.8 + - - +
186B ASP* 3.4 20.0 + - - +
187B TRP 3.0 0.4 - - - -
188B SER* 1.3 79.2 + - - +
190B PHE* 1.3 55.0 + - - +
192B LEU* 3.6 5.9 - - - +
193B ALA* 2.7 36.6 + - - +
198B TYR* 3.6 18.2 - - + -
200B TYR* 2.1 45.9 + - + +
414B PHE* 3.9 11.9 - - + -
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Residues in contact with PHE 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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25B ASN* 3.2 44.0 - - + +
28B ALA* 5.4 4.7 - - + -
29B VAL* 3.3 29.8 - - + -
179B TYR* 3.3 36.6 - + - -
180B PHE* 4.4 5.8 - + - -
187B TRP* 3.0 34.8 + + + +
189B GLU* 1.3 81.2 - - - +
191B VAL* 1.3 65.9 + - - +
193B ALA* 3.0 9.4 + - - +
194B ASP* 3.0 17.5 + - - +
413B PRO* 5.8 0.7 - - + -
414B PHE* 3.9 22.6 - + - -
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Residues in contact with VAL 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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18B GLU* 5.9 1.6 - - - +
21B TYR* 3.9 36.8 - - + +
25B ASN* 4.2 5.1 - - - +
68B MET* 6.4 1.6 - - - -
187B TRP 4.4 2.5 - - - +
188B SER* 3.4 28.7 - - - +
190B PHE* 1.3 76.0 - - + +
192B LEU* 1.3 61.8 + - + +
194B ASP* 3.1 8.0 + - - +
195B LEU* 2.9 41.3 + - + +
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Residues in contact with LEU 192 (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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188B SER* 2.7 43.4 + - - +
189B GLU* 3.6 4.9 - - - +
191B VAL* 1.3 77.1 - - + +
193B ALA* 1.3 61.2 + - - +
195B LEU* 3.1 9.4 + - + +
196B GLY 3.0 18.2 + - - -
197B ILE* 3.1 37.3 + - + -
198B TYR* 3.8 40.4 - - + +
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Residues in contact with ALA 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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189B GLU 2.7 20.5 + - - +
190B PHE 3.5 4.0 - - - +
192B LEU* 1.3 72.2 - - - +
194B ASP* 1.3 64.8 + - - +
196B GLY* 3.2 12.6 + - - -
198B TYR* 3.2 21.6 + - - +
199B ARG* 5.2 3.1 - - - +
200B TYR* 4.8 3.1 - - + +
414B PHE* 3.6 25.1 - - + -
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Residues in contact with ASP 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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18B GLU* 5.6 6.1 - - - +
25B ASN* 4.8 10.9 + - - +
190B PHE* 3.0 16.5 + - - +
191B VAL* 3.7 8.9 - - - +
193B ALA* 1.3 81.9 - - - +
195B LEU* 1.3 60.6 + - - +
196B GLY* 3.2 1.3 + - - -
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Residues in contact with LEU 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 VAL* 2.9 28.1 + - + +
192B LEU* 3.1 11.2 + - + +
194B ASP* 1.3 75.9 - - - +
196B GLY* 1.3 59.8 - - - +
197B ILE* 3.7 20.1 + - + +
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Residues in contact with GLY 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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192B LEU 3.0 2.8 + - - -
193B ALA 3.2 9.1 + - - -
194B ASP 3.2 4.6 - - - -
195B LEU* 1.3 79.5 - - - +
197B ILE* 1.3 68.3 + - - +
198B TYR 3.6 1.6 - - - -
199B ARG* 3.7 36.0 + - - +
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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