Contacts of the helix formed by residues 154 - 175 (chain B) in PDB entry 6WB0
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 LYS 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASN* 3.1 40.3 - - + +
88B TRP* 3.3 52.7 - - + +
152B GLY 5.6 0.4 + - - -
153B TRP* 1.3 75.4 - - - +
155B GLY* 1.3 60.5 + - - +
156B SER 3.6 0.4 - - - -
157B PRO* 3.6 10.4 - - - +
158B ALA* 3.2 23.9 + - - +
183B TYR* 4.4 39.7 - - + +
184B MET* 5.6 2.5 - - + -
386B THR* 5.4 5.0 + - - +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 4.6 10.3 - - - -
88B TRP* 4.8 5.1 - - - -
153B TRP* 3.5 30.6 - - - +
154B LYS* 1.3 79.2 - - - +
156B SER* 1.3 65.0 + - - +
158B ALA* 3.1 7.5 + - - +
159B ILE* 2.9 31.5 + - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 3.9 11.4 - - - -
149B LEU* 3.8 28.7 - - - +
150B PRO 3.9 13.5 - - - -
153B TRP* 3.2 18.6 - - - -
155B GLY* 1.3 75.2 - - - +
157B PRO* 1.3 63.0 - - - +
159B ILE* 3.0 17.1 - - - +
160B PHE* 2.9 27.4 + - - +
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Residues in contact with PRO 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 3.4 34.3 - - + +
153B TRP 3.2 26.5 - - - +
154B LYS* 3.6 11.4 - - - +
156B SER* 1.3 90.9 - - - +
158B ALA* 1.3 64.7 + - - +
160B PHE* 4.2 3.6 - - + -
161B GLN* 2.9 26.5 + - - +
182B GLN* 4.8 14.6 - - + +
183B TYR 4.5 4.5 - - - +
184B MET* 4.4 14.4 - - - -
185B ASP 5.6 0.2 - - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 5.3 1.1 - - + -
88B TRP* 3.9 11.2 - - + -
92B LEU* 3.3 37.7 - - + +
154B LYS 3.2 20.9 + - - +
155B GLY* 3.1 10.9 + - - +
157B PRO* 1.3 77.5 - - - +
159B ILE* 1.3 61.3 + - + +
161B GLN* 3.1 24.1 + - - +
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Residues in contact with ILE 159 (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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8B VAL* 5.6 19.3 - - + +
87B PHE* 4.2 25.4 - - + -
91B GLN* 6.1 0.7 - - - +
92B LEU* 4.9 5.6 - - + -
118B VAL* 5.9 7.2 - - + -
120B LEU* 6.3 4.0 - - + -
149B LEU* 5.9 4.5 - - + -
153B TRP* 5.7 3.1 - - + -
155B GLY 2.9 19.1 + - - +
156B SER* 3.0 24.9 - - - +
158B ALA* 1.3 77.4 - - + +
160B PHE* 1.3 61.2 + - + +
161B GLN* 3.3 1.4 + - - +
162B SER* 3.2 20.7 + - - -
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA* 4.8 24.7 - - + -
115B TYR* 4.6 25.8 - + + -
118B VAL* 4.6 23.8 - - + -
156B SER 2.9 18.7 + - - +
157B PRO* 3.2 5.6 + - + +
159B ILE* 1.3 75.3 - - + +
161B GLN* 1.3 64.2 + - - +
162B SER* 3.0 4.7 - - - -
163B SER* 3.1 31.3 + - - -
164B MET* 2.9 33.8 + - + +
182B GLN* 5.3 4.5 - - - -
214B LEU* 4.9 18.2 - - + -
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 5.4 4.5 - - + +
93B GLY 5.1 8.6 - - - +
94B ILE* 5.8 2.4 - - - +
157B PRO 2.9 13.0 + - - +
158B ALA* 3.1 22.9 + - - +
159B ILE 4.7 1.0 + - - -
160B PHE* 1.3 77.0 - - - +
162B SER* 1.3 86.0 + - - +
164B MET* 3.8 10.0 - - - +
165B THR* 2.9 28.4 + - - -
182B GLN* 4.8 7.6 - - - +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE 3.2 16.0 + - - -
160B PHE* 4.2 0.9 + - - -
161B GLN* 1.3 99.1 - - - +
163B SER* 1.3 70.4 + - - +
165B THR* 3.8 12.5 + - - -
166B LYS* 4.1 6.2 + - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 3.1 29.0 + - - -
162B SER* 1.3 82.6 + - - +
164B MET* 1.3 61.3 + - - +
165B THR 3.1 2.2 - - - -
166B LYS* 2.9 47.0 + - - +
167B ILE* 2.9 13.7 + - - +
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 2.9 30.1 + - + +
161B GLN* 3.2 11.4 + - - +
163B SER* 1.3 76.9 - - - +
165B THR* 1.3 56.5 + - - +
167B ILE* 3.6 8.7 - - - +
168B LEU* 2.9 32.6 + - - +
182B GLN* 3.9 23.6 - - - +
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Residues in contact with THR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLN* 2.9 19.4 + - - -
162B SER* 3.8 8.1 - - - -
163B SER 3.1 0.2 - - - -
164B MET* 1.3 78.0 - - - +
166B LYS* 1.3 57.7 + - - +
168B LEU* 3.3 2.0 + - - -
169B GLU* 2.9 29.7 + - - +
172B LYS* 3.7 7.7 + - - +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER 4.1 3.1 + - - +
163B SER* 2.9 46.8 + - - +
165B THR* 1.3 76.6 - - - +
167B ILE* 1.3 65.8 + - - +
169B GLU* 4.0 6.6 - - - +
170B PRO* 3.2 21.5 - - - +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 6.1 2.7 - - + -
163B SER 2.9 17.2 + - - +
164B MET* 3.2 11.2 + - - +
166B LYS* 1.3 79.7 - - + +
168B LEU* 1.3 56.4 + - - +
170B PRO* 5.6 0.2 - - - -
208B HIS* 2.8 27.9 + - - +
209B LEU* 5.6 4.3 - - - -
214B LEU* 5.5 11.4 - - + -
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Residues in contact with LEU 168 (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 MET 2.9 15.6 + - - +
165B THR* 4.9 0.2 - - - -
167B ILE* 1.3 76.1 - - - +
169B GLU* 1.3 65.2 + - - +
170B PRO* 3.3 4.5 - - - -
171B PHE* 3.0 15.1 + - - +
172B LYS* 3.3 28.0 + - + +
180B ILE* 6.0 9.0 - - + -
208B HIS* 3.4 5.4 - - - -
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Residues in contact with GLU 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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165B THR 2.9 16.8 + - - +
166B LYS* 4.0 7.0 - - - +
168B LEU* 1.3 75.0 - - - +
170B PRO* 1.3 70.7 - - + +
171B PHE 3.1 0.2 + - - -
172B LYS* 3.2 18.2 - - - +
173B LYS* 2.9 28.6 + - + +
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Residues in contact with PRO 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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166B LYS 3.2 18.8 - - - +
168B LEU 3.3 3.8 - - - -
169B GLU* 1.3 91.8 - - + +
171B PHE* 1.3 58.7 + - - +
173B LYS* 3.9 10.7 + - + +
174B GLN* 3.9 10.9 + - - +
208B HIS* 3.3 24.7 - - + +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.0 4.9 + - - +
170B PRO* 1.3 76.4 - - - +
172B LYS* 1.3 64.4 + - - +
173B LYS 3.1 1.3 - - - -
174B GLN* 3.1 13.9 + - - +
175B ASN* 3.2 20.4 + - - +
205B LEU* 5.3 10.1 - - + -
208B HIS* 3.0 32.6 - - + +
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Residues in contact with LYS 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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165B THR* 3.7 9.4 + - - +
168B LEU* 3.3 20.8 + - - +
169B GLU* 3.2 37.2 - - - +
171B PHE* 1.3 76.6 - - - +
173B LYS* 1.3 67.8 + - - +
175B ASN* 3.3 27.2 - - - +
176B PRO* 3.4 8.6 - - + +
178B ILE* 5.2 2.7 - - - +
180B ILE* 4.4 25.2 - - + +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 2.9 19.8 + - + +
170B PRO* 3.9 8.7 - - + +
171B PHE 3.1 0.2 - - - -
172B LYS* 1.3 79.7 - - - +
174B GLN* 1.3 57.4 + - - +
176B PRO* 4.4 6.4 - - - +
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PRO 3.9 7.6 + - - +
171B PHE* 3.1 10.4 + - - +
173B LYS* 1.3 80.0 - - - +
175B ASN* 1.3 71.8 + - - +
176B PRO* 3.5 8.3 - - - +
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Residues in contact with ASN 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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171B PHE* 3.2 16.3 + - - +
172B LYS* 3.3 12.4 - - - +
174B GLN* 1.3 91.7 + - - +
176B PRO* 1.3 66.4 - - - +
177B ASP* 3.2 3.8 - - + -
178B ILE* 3.3 43.6 + - + +
201B LYS* 5.5 4.4 - - - +
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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
------------------------------------------------------------
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