Contacts of the helix formed by residues 176 - 188 (chain B) in PDB entry 3KHE
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 PHE 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.1 22.7 - - + -
43A THR* 3.7 28.9 - - + -
47A ARG* 5.3 2.9 - - - +
106A TYR* 5.0 3.4 - + - -
122B ARG* 4.7 4.7 - - - -
125B LEU* 4.0 8.5 - - + -
126B LEU* 3.7 40.2 - - + -
129B PHE* 3.5 43.4 - + + -
138B GLY 4.2 1.2 + - - -
175B ASP* 1.3 76.5 - - - +
177B GLU* 1.3 74.5 + - + +
179B PHE* 3.1 3.6 + + - +
180B VAL* 2.8 57.0 + - + +
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Residues in contact with GLU 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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36A LEU* 4.1 28.3 - - + +
37A GLU* 4.2 16.8 - - + +
40A LYS* 3.5 33.6 - - + +
43A THR* 4.5 5.2 - - - +
168B LYS* 4.3 15.5 - - - +
175B ASP* 3.0 18.1 + - - +
176B PHE* 1.3 97.5 + - + +
178B GLU* 1.3 61.3 + - - +
180B VAL* 3.4 6.0 + - - +
181B GLU* 3.2 22.0 + - - +
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Residues in contact with GLU 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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166B CYS* 3.1 28.1 - - - +
167B ASP* 4.0 1.2 - - - -
168B LYS* 3.1 33.5 + - + +
169B ASN* 3.0 14.9 + - - +
173B GLU 3.0 5.2 - - - +
174B VAL* 3.3 7.4 - - + -
175B ASP* 2.8 42.3 + - - +
177B GLU* 1.3 73.9 - - - +
179B PHE* 1.3 59.2 + - - +
181B GLU* 3.3 5.6 + - - +
182B MET* 2.9 29.5 + - - +
195B CA 2.5 30.2 - - - -
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Residues in contact with PHE 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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21B LEU* 4.2 14.8 - - + -
25B ALA* 3.7 31.0 - - + -
125B LEU* 3.6 42.2 - - + -
128B ALA* 4.1 12.1 - - + -
129B PHE* 3.9 25.6 - + + -
132B PHE* 4.3 5.8 - + - -
140B ILE* 4.1 21.1 - - + -
174B VAL* 3.7 8.7 - - + +
175B ASP 2.8 17.1 + - - +
176B PHE* 3.4 13.5 - + - +
178B GLU* 1.3 70.7 - - - +
180B VAL* 1.3 65.6 + - - +
182B MET* 3.3 24.5 + - + +
183B MET* 3.0 27.6 + - + +
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Residues in contact with VAL 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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36A LEU* 3.1 38.1 - - + -
125B LEU* 4.6 15.7 - - + -
176B PHE* 2.8 44.8 + - + +
177B GLU 3.8 4.3 - - - +
179B PHE* 1.3 76.7 - - + +
181B GLU* 1.3 57.9 + - - +
183B MET* 3.2 6.4 + - - +
184B GLN* 2.8 41.7 + - + +
191B VAL* 4.1 16.3 - - + +
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Residues in contact with GLU 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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165B GLU 5.3 2.2 - - - +
166B CYS* 5.6 3.1 - - + +
177B GLU 3.2 16.7 + - - +
178B GLU* 3.3 6.9 + - - +
180B VAL* 1.3 71.6 - - - +
182B MET* 1.3 67.4 + - - +
184B GLN* 3.0 31.0 + - - +
185B LYS* 3.0 51.2 + - - +
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Residues in contact with MET 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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19B GLN* 3.1 31.0 - - - +
21B LEU* 3.7 24.7 - - + -
22B ALA* 3.7 15.7 - - - +
162B VAL* 4.5 0.9 - - - -
165B GLU* 4.2 6.7 - - + +
166B CYS* 3.5 27.0 - - + +
178B GLU 2.9 13.8 + - - +
179B PHE* 3.4 28.5 - - + +
181B GLU* 1.3 78.6 - - - +
183B MET* 1.3 91.0 + - + +
185B LYS* 3.4 9.5 + - - +
186B ILE* 2.9 34.7 + - + +
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Residues in contact with MET 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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22B ALA* 3.9 14.8 - - + +
25B ALA* 3.9 11.0 - - + -
26B MET* 3.6 32.3 - - + -
29B MET* 3.8 19.5 - - + -
120B LEU* 3.7 23.1 - - + +
125B LEU* 3.8 20.2 - - + -
179B PHE* 3.0 21.4 + - + +
180B VAL 3.2 4.2 + - - +
182B MET* 1.3 98.2 - - + +
184B GLN* 1.3 58.5 + - - +
186B ILE* 3.8 3.3 - - + +
187B CYS* 2.9 40.8 + - - +
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Residues in contact with GLN 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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36A LEU* 5.8 0.2 - - - +
180B VAL* 2.8 26.2 + - + +
181B GLU* 3.0 27.7 + - - +
183B MET* 1.3 76.5 - - - +
185B LYS* 1.3 56.6 + - + +
188B ASP* 2.9 24.1 + - - -
189B VAL* 3.1 32.5 + - - +
190B LYS* 3.7 10.2 - - + +
191B VAL* 2.8 42.5 + - + +
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Residues in contact with LYS 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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164B GLN 5.1 0.8 + - - -
165B GLU* 2.7 38.3 + - - +
181B GLU* 3.0 48.2 + - - +
182B MET* 3.8 4.5 - - - +
184B GLN* 1.3 74.1 - - + +
186B ILE* 1.3 68.5 + - + +
188B ASP* 3.5 9.7 + - - +
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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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18B SER* 3.7 24.7 - - - -
19B GLN* 4.4 0.4 - - + +
22B ALA* 3.9 22.4 - - + -
26B MET* 4.4 5.2 - - - -
165B GLU* 3.5 28.0 - - - +
182B MET* 2.9 22.9 + - + +
183B MET* 3.3 8.0 + - + +
185B LYS* 1.3 77.1 - - + +
187B CYS* 1.3 68.6 + - - +
188B ASP* 3.8 0.5 + - - +
199B GOL 2.8 47.3 + - - +
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Residues in contact with CYS 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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26B MET* 3.8 32.3 - - - -
116B LYS* 3.7 38.6 - - + +
120B LEU* 3.9 17.5 - - + -
183B MET* 2.9 19.8 + - - +
186B ILE* 1.3 82.4 - - - +
188B ASP* 1.3 70.1 + - - +
189B VAL* 3.4 10.4 + - + +
199B GOL 4.2 4.9 - - - -
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Residues in contact with ASP 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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184B GLN 2.9 13.0 + - - -
185B LYS* 3.5 5.5 + - - +
186B ILE 3.5 3.4 - - - +
187B CYS* 1.3 78.7 - - - +
189B VAL* 1.3 61.5 + - - +
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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