Contacts of the helix formed by residues 168 - 181 (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 CYS 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.3 14.6 - - + -
63B LEU* 5.3 2.5 - - + -
99B TRP* 3.3 50.4 + - + +
166B LEU* 3.4 18.6 - - + +
167B ARG* 1.3 78.3 - - - +
169B MET* 1.3 63.2 + - - +
170B ALA* 3.1 4.8 + - - -
171B LEU* 3.7 6.2 + - - +
172B CYS* 3.5 25.2 + - - -
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Residues in contact with MET 169 (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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66B MET 5.2 0.9 - - - +
67B VAL* 3.8 46.2 - - + +
69B ARG 6.0 1.1 - - - +
70B LYS 6.2 0.2 - - - +
71B GLY 5.5 5.8 - - - +
72B THR* 4.3 17.7 - - - +
166B LEU* 4.2 18.8 - - + +
167B ARG 3.5 3.4 - - - -
168B CYS* 1.3 76.5 - - - +
170B ALA* 1.3 57.2 + - - +
171B LEU 3.5 0.2 - - - -
172B CYS* 3.7 5.6 - - - -
173B ASP* 2.9 65.0 + - - +
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Residues in contact with ALA 170 (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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167B ARG 5.1 2.6 + - - +
168B CYS 3.1 3.0 + - - -
169B MET* 1.3 78.2 - - - +
171B LEU* 1.3 66.1 + - + +
173B ASP* 3.3 4.7 + - - +
174B ARG* 3.0 25.8 + - - +
222B LEU* 5.3 4.4 - - + +
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Residues in contact with LEU 171 (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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44B GLN* 4.0 26.0 - - + +
45B GLU* 3.6 37.7 - - + +
48B PHE* 5.7 11.0 - - + -
168B CYS 3.7 4.9 + - - +
169B MET 3.5 0.2 - - - -
170B ALA* 1.3 81.0 - - + +
172B CYS* 1.3 56.5 + - - +
174B ARG* 3.5 35.6 - - - +
175B LEU* 2.8 40.3 + - + +
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Residues in contact with CYS 172 (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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26B PHE* 5.2 9.2 - - - -
48B PHE* 4.7 21.3 - - - -
63B LEU* 6.2 1.8 - - - -
67B VAL* 4.0 38.8 - - + -
166B LEU* 5.9 0.2 - - - -
168B CYS* 3.5 20.0 + - - +
169B MET* 3.3 13.9 + - - +
170B ALA 3.2 0.8 - - - -
171B LEU* 1.3 76.1 - - - +
173B ASP* 1.3 62.6 + - - +
175B LEU* 3.4 7.2 + - - +
176B ARG* 3.0 28.1 + - - +
187B TRP* 4.4 7.1 - - + -
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Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 2.9 48.6 + - - +
170B ALA* 3.8 4.4 - - - +
172B CYS* 1.3 76.3 - - - +
174B ARG* 1.3 58.0 + - - +
176B ARG* 3.4 32.3 + - - +
177B LEU* 2.8 30.8 + - - +
183B LEU* 3.6 9.1 - - + +
222B LEU* 4.8 6.7 - - + -
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Residues in contact with ARG 174 (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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45B GLU* 3.8 19.1 - - - -
170B ALA 3.0 14.1 + - - +
171B LEU* 3.5 30.5 - - - +
172B CYS 3.2 0.2 - - - -
173B ASP* 1.3 76.4 - - - +
175B LEU* 1.3 57.7 + - + +
177B LEU* 3.2 2.8 + - - +
178B MET* 2.9 50.8 + - + +
215B ARG* 3.7 15.6 - - - +
218B VAL* 3.5 15.6 - - + +
219B ASP* 2.2 43.4 + - - +
222B LEU* 3.5 41.5 - - + +
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Residues in contact with LEU 175 (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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26B PHE* 5.7 3.1 - - + -
30B LEU* 4.0 25.6 - - + -
33B ILE* 3.3 42.6 - - + +
41B LEU* 4.5 14.1 - - + -
45B GLU* 4.9 13.2 - - + +
48B PHE* 4.2 23.8 - - + -
49B ILE* 4.9 5.2 - - + -
171B LEU* 2.8 32.7 + - + +
172B CYS* 3.8 7.9 - - - +
173B ASP 3.3 0.4 - - - -
174B ARG* 1.3 71.7 - - + +
176B ARG* 1.3 69.9 + - - +
178B MET* 3.2 9.8 + - - +
179B TYR* 3.0 18.0 + - - +
187B TRP* 4.8 5.2 - - + -
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Residues in contact with ARG 176 (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 CYS 3.0 13.0 + - - +
173B ASP* 3.5 30.2 + - - +
175B LEU* 1.3 74.2 - - - +
177B LEU* 1.3 64.1 + - - +
179B TYR* 3.0 4.3 + - - +
180B PHE* 2.9 42.5 + - + +
182B ASN 4.7 1.5 + - - +
183B LEU* 2.7 54.9 + - - +
184B TRP 4.4 0.4 - - - -
185B GLN 3.1 25.4 + - - -
186B ASP* 4.9 6.4 + - - +
187B TRP* 3.8 42.6 - - + +
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Residues in contact with LEU 177 (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 ASP 2.8 17.9 + - - +
174B ARG 3.6 4.0 - - - +
175B LEU 3.1 0.2 - - - -
176B ARG* 1.3 76.9 - - - +
178B MET* 1.3 58.1 + - - +
181B GLY* 3.0 26.0 + - - -
182B ASN* 3.8 33.2 - - - +
183B LEU* 3.5 15.9 - - + +
212B PHE* 3.4 20.9 - - + -
218B VAL* 4.4 10.5 - - + +
221B TYR* 4.0 34.5 - - + -
222B LEU* 3.5 30.3 - - + +
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.7 8.1 - - + -
37B TYR* 2.7 60.1 + - + -
40B LEU* 4.5 13.0 - - + +
41B LEU* 5.0 5.2 - - - -
45B GLU* 5.0 1.1 - - - +
174B ARG* 2.9 35.4 + - - +
175B LEU* 3.2 20.6 + - - +
177B LEU* 1.3 78.6 - - - +
179B TYR* 1.3 60.6 + - - +
181B GLY 4.0 2.9 + - - -
212B PHE* 4.3 7.7 - - - -
215B ARG* 4.1 16.2 - - + +
218B VAL* 3.5 43.7 - - + -
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Residues in contact with TYR 179 (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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29B VAL* 4.0 30.1 - - + -
32B TRP* 3.6 45.5 + + + -
33B ILE* 4.3 5.8 - - + -
37B TYR* 4.8 4.8 + - - -
175B LEU 3.0 11.4 + - - +
176B ARG* 3.0 9.2 + - - +
178B MET* 1.3 80.3 - - - +
180B PHE* 1.3 90.4 + + - +
187B TRP* 4.9 0.9 - + + -
190B PHE* 3.3 39.0 - + - -
411B PHE* 4.2 7.3 - - - +
412B HIS* 3.5 24.4 - - + +
413B PRO* 3.8 10.6 - - - +
414B PHE* 3.6 14.4 - + - -
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Residues in contact with PHE 180 (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 ARG* 2.9 32.4 + - + +
179B TYR* 1.3 104.8 - + - +
181B GLY* 1.3 58.2 + - - +
182B ASN* 2.8 41.2 + - - +
185B GLN* 3.3 46.0 - - + -
186B ASP 3.4 28.3 - - - -
187B TRP* 4.4 9.2 - + - -
189B GLU* 4.2 6.7 - - + -
190B PHE* 4.4 8.5 - + - -
411B PHE* 3.6 6.1 - - - -
412B HIS* 3.3 23.4 + - - -
414B PHE* 4.0 13.0 - + - -
415B HIS* 5.0 0.5 - - - -
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Residues in contact with GLY 181 (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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177B LEU* 3.0 20.5 + - - -
178B MET 4.0 2.3 + - - -
179B TYR 3.5 2.4 - - - -
180B PHE* 1.3 76.2 - - - +
182B ASN* 1.3 58.8 + - - +
211B GLY* 5.0 0.9 - - - -
212B PHE* 3.9 13.7 - - - -
221B TYR* 4.1 2.1 - - - -
253B TRP* 3.8 26.6 - - - -
257B ARG* 5.6 0.2 + - - -
411B PHE* 4.0 17.4 - - - -
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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