Contacts of the helix formed by residues 174 - 194 (chain B) in PDB entry 3CUQ
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 ILE 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.4 28.3 - - - +
64A PHE* 6.4 0.2 - - + -
172B LYS* 3.6 19.5 - - + +
173B ASN* 1.3 81.1 - - - +
175B SER* 1.3 75.5 - - - +
176B GLU 3.3 0.7 - - - -
177B ALA* 3.0 9.3 + - - +
178B PHE* 2.9 50.1 + - + -
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Residues in contact with SER 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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172B LYS 4.8 5.0 + - - -
173B ASN* 3.3 0.6 - - - +
174B ILE* 1.3 90.7 - - - +
176B GLU* 1.3 63.1 + - - +
177B ALA 3.1 1.5 + - - -
178B PHE* 4.2 7.4 - - - +
179B GLU* 3.8 21.8 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 4.0 24.2 + - + +
54A HIS* 3.4 16.9 - - + +
173B ASN* 3.3 29.6 + - - +
175B SER* 1.3 79.3 - - - +
177B ALA* 1.3 56.0 + - - +
180B ASP* 3.1 45.4 + - - +
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Residues in contact with ALA 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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50A PHE* 5.0 1.8 - - + -
54A HIS* 3.2 34.4 + - + +
57A GLU* 5.9 1.6 - - + +
64A PHE* 3.8 26.5 - - + -
174B ILE* 3.0 14.4 + - - +
176B GLU* 1.3 74.0 - - - +
178B PHE* 1.3 54.1 + - - +
179B GLU 2.6 17.6 + - - -
180B ASP 2.9 1.6 + - - -
181B LEU* 2.7 33.2 + - + +
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Residues in contact with PHE 178 (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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61A ASN* 6.1 0.2 - - - -
63A GLU 5.9 0.2 - - - -
64A PHE* 3.7 34.8 - + + -
67A GLN* 3.3 37.9 - - + -
174B ILE* 2.9 44.8 + - + +
175B SER* 4.2 6.0 + - - -
177B ALA* 1.3 74.7 - - - +
179B GLU* 1.3 63.6 + - - +
181B LEU* 4.2 9.1 - - + +
182B SER* 3.7 15.6 + - - -
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER 3.8 15.2 + - - +
177B ALA 2.6 5.5 + - - -
178B PHE* 1.3 77.9 - - - +
180B ASP* 1.3 58.2 + - - +
181B LEU 2.9 4.0 - - - -
182B SER* 2.7 36.0 + - - -
183B LYS* 3.1 27.1 + - - +
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 4.2 10.3 - - + -
54A HIS* 5.1 2.0 - - + -
176B GLU* 3.1 40.2 + - - +
177B ALA* 2.9 4.4 + - - -
179B GLU* 1.3 77.5 - - - +
181B LEU* 1.3 55.3 + - - +
183B LYS* 3.8 29.5 + - - +
184B LEU* 3.1 31.0 + - - +
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Residues in contact with LEU 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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50A PHE* 3.7 29.3 - - + -
58A ILE* 6.1 0.2 - - + -
64A PHE* 3.6 35.7 - - + -
67A GLN* 5.3 3.4 - - + -
68A PHE* 4.2 31.9 - - + +
71A MET* 3.9 24.5 - - + -
177B ALA 2.7 17.4 + - - +
178B PHE* 4.2 7.4 - - + +
180B ASP* 1.3 74.6 - - - +
182B SER* 1.3 65.9 + - - +
183B LYS 3.1 1.6 - - - -
184B LEU* 3.3 16.3 + - - +
185B MET* 3.4 19.8 + - + +
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Residues in contact with SER 182 (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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71A MET* 3.9 25.1 - - - +
178B PHE 3.7 11.1 + - - -
179B GLU* 2.7 29.1 + - - -
181B LEU* 1.3 80.5 - - - +
183B LYS* 1.3 57.8 + - - +
185B MET* 3.8 12.6 - - - +
186B ILE* 3.9 11.0 - - - +
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Residues in contact with LYS 183 (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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179B GLU* 3.1 21.9 + - - +
180B ASP* 3.8 29.7 + - - +
181B LEU 3.1 0.4 - - - -
182B SER* 1.3 75.1 - - - +
184B LEU* 1.3 65.7 + - - +
185B MET 3.1 2.2 - - - -
186B ILE* 2.9 36.1 + - + +
187B LYS* 3.4 10.9 + - + +
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Residues in contact with LEU 184 (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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43A PHE* 3.6 29.2 - - + -
46A ASN* 4.2 16.4 - - + +
47A LEU* 4.8 15.3 - - + +
50A PHE* 3.7 44.4 - - + -
87A TRP* 4.9 3.6 - - + -
180B ASP 3.1 14.7 + - - +
181B LEU* 3.3 13.7 - - - +
183B LYS* 1.3 73.8 - - - +
185B MET* 1.3 74.3 + - + +
187B LYS* 3.2 21.9 + - + +
188B ALA* 3.2 10.0 + - - +
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Residues in contact with MET 185 (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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50A PHE* 6.0 1.3 - - + -
68A PHE* 4.5 14.8 - - + +
71A MET* 4.2 39.5 - - + -
72A CYS* 4.5 8.1 - - - -
75A ILE* 4.0 34.1 - - + +
77A VAL* 5.7 0.7 - - - -
87A TRP* 4.0 31.6 - - + -
181B LEU* 3.6 21.1 - - + +
182B SER 3.8 8.5 - - - +
183B LYS 3.1 0.8 - - - -
184B LEU* 1.3 83.0 - - + +
186B ILE* 1.3 54.5 + - + +
188B ALA* 3.2 7.0 + - - +
189B LYS* 2.8 37.5 + - + +
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Residues in contact with ILE 186 (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 SER 3.9 8.5 - - - +
183B LYS* 2.9 29.1 + - + +
185B MET* 1.3 75.4 - - + +
187B LYS* 1.3 65.6 + - + +
189B LYS* 3.0 23.4 + - + +
190B GLU* 3.1 36.3 + - - +
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Residues in contact with LYS 187 (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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42A MET* 6.4 1.6 - - + -
43A PHE* 3.6 18.4 - - + -
46A ASN* 4.5 20.4 - - + +
183B LYS* 3.9 12.8 - - - +
184B LEU* 3.2 14.7 + - + +
186B ILE* 1.3 79.4 - - + +
188B ALA* 1.3 61.3 + - - +
190B GLU* 3.4 15.6 - - + +
191B MET* 3.2 21.6 - - + +
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Residues in contact with ALA 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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43A PHE* 3.2 30.6 - - + -
75A ILE* 4.6 9.6 - - + -
77A VAL* 5.4 2.0 - - + -
87A TRP* 4.5 14.6 - - + -
184B LEU 3.2 4.9 + - - +
185B MET* 3.2 10.7 + - - +
187B LYS* 1.3 73.5 - - - +
189B LYS* 1.3 59.9 + - - +
190B GLU 3.0 2.9 - - - -
191B MET* 2.8 28.9 + - - +
192B VAL* 3.0 15.4 + - + +
224B MET* 4.9 4.7 - - - +
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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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74A THR* 5.2 10.8 + - - +
75A ILE* 3.8 36.5 + - + +
185B MET 2.8 16.1 + - - +
186B ILE* 3.0 19.0 + - + +
188B ALA* 1.3 72.9 - - - +
190B GLU* 1.3 58.1 + - - +
192B VAL* 3.1 11.1 + - + +
193B GLU* 2.7 61.0 + - + +
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Residues in contact with GLU 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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39A GLN* 5.2 12.4 - - - +
186B ILE* 3.1 37.4 - - - +
187B LYS* 3.4 16.3 - - + +
188B ALA 2.9 0.2 + - - -
189B LYS* 1.3 75.4 - - - +
191B MET* 1.3 68.0 - - + +
192B VAL 3.0 1.3 - - - -
193B GLU* 3.2 18.5 - - - +
194B LEU* 3.1 33.9 + - + +
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Residues in contact with MET 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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39A GLN* 3.4 47.1 + - + +
40A LEU* 4.6 4.5 - - - -
42A MET* 4.9 7.4 - - + -
43A PHE* 3.7 31.6 - - + +
46A ASN* 6.0 0.2 - - - +
187B LYS* 3.2 27.3 + - + +
188B ALA 2.8 8.7 + - - +
190B GLU* 1.3 81.3 - - + +
192B VAL* 1.3 51.0 + - - +
194B LEU 3.9 1.6 - - - +
195B SER* 2.7 33.3 + - - -
220B TYR* 3.7 27.8 + - + +
224B MET* 3.9 25.6 - - + +
226B ILE* 4.2 5.1 - - - +
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Residues in contact with VAL 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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75A ILE* 3.4 42.2 - - + +
76A GLY* 5.1 1.6 - - - -
77A VAL* 4.1 10.5 - - + -
188B ALA* 3.0 14.5 + - + +
189B LYS* 3.3 9.2 - - + +
190B GLU 3.0 0.2 - - - -
191B MET* 1.3 75.2 - - + +
193B GLU* 1.3 71.7 + - + +
195B SER* 2.5 23.4 + - - -
196B LYS* 3.5 23.8 + - + +
224B MET* 5.5 1.1 - - - -
226B ILE* 3.9 30.7 - - + -
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Residues in contact with GLU 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 LYS* 2.7 43.8 + - + +
190B GLU* 3.2 24.4 - - - +
192B VAL* 1.3 73.9 - - + +
194B LEU* 1.3 72.5 + - + +
195B SER 3.1 6.4 + - - -
196B LYS* 3.5 27.5 + - - +
197B SER* 4.0 9.0 + - - -
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Residues in contact with LEU 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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36A MET* 3.1 31.6 - - + +
39A GLN* 5.6 4.7 - - - +
190B GLU* 3.1 18.3 + - + +
191B MET 3.9 3.5 - - - +
193B GLU* 1.3 90.7 - - + +
195B SER* 1.3 58.7 + - - +
197B SER* 4.9 9.9 - - - +
198B ILE* 3.9 8.3 - - + +
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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