Contacts of the helix formed by residues 166 - 187 (chain H) in PDB entry 5TWV
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 GLN 166 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 3.8 31.9 - - + -
162H ILE* 3.9 11.4 - - + -
163H GLY 5.1 1.8 - - - +
164H PHE 3.2 5.5 - - - +
165H SER* 1.3 79.8 - - - +
167H LEU* 1.3 62.9 + - - +
168H ARG* 4.5 1.3 - - + +
169H PHE* 3.9 12.3 - - + +
170H CYS* 3.6 15.4 + - - +
344H TYR 3.7 11.9 - - - +
346H VAL* 3.5 9.0 - - - +
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Residues in contact with LEU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLU* 4.5 15.7 - - + +
166H GLN* 1.3 70.1 - - - +
168H ARG* 1.3 65.1 + - - +
169H PHE 3.2 1.1 - - - -
170H CYS* 3.8 8.4 - - - +
171H LEU* 3.4 19.9 + - - +
344H TYR* 3.3 11.3 + - + -
345H PHE 3.2 28.0 - - - +
346H VAL* 3.2 12.1 - - - +
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Residues in contact with ARG 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLU* 5.5 2.9 - - - -
157H PHE* 6.0 4.0 - - + -
166H GLN* 3.4 2.4 - - + -
167H LEU* 1.3 77.4 - - - +
169H PHE* 1.3 58.1 + - - +
171H LEU* 3.3 7.9 + - - +
172H THR* 2.9 28.0 + - - -
343H VAL* 5.7 4.0 - - + -
344H TYR* 3.9 24.8 + - + +
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Residues in contact with PHE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H PHE* 3.9 33.2 - + - -
157H PHE* 3.8 39.2 - + + -
163H GLY 4.1 17.5 - - - -
164H PHE* 5.9 0.9 - - - -
166H GLN* 3.9 23.2 - - + +
168H ARG* 1.3 78.0 - - - +
170H CYS* 1.3 60.1 + - - +
172H THR* 3.5 8.8 - - - -
173H GLY* 2.7 40.3 + - - -
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Residues in contact with CYS 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H GLN 3.6 10.6 + - - +
167H LEU* 3.6 11.8 + - - +
168H ARG 3.3 0.4 - - - -
169H PHE* 1.3 83.5 - - + +
171H LEU* 1.3 62.5 + - - +
173H GLY* 3.3 2.3 + - - -
174H LEU* 3.1 23.7 + - - +
346H VAL* 5.8 2.7 - - + -
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Residues in contact with LEU 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 5.1 8.0 - - - +
87H CYS* 4.9 9.2 - - + +
88H GLU* 4.2 31.4 - - + +
91H GLU* 5.8 1.8 - - + -
167H LEU 3.4 9.2 + - - +
168H ARG* 3.3 10.2 + - - +
169H PHE 3.2 0.2 - - - -
170H CYS* 1.3 77.7 - - - +
172H THR* 1.3 63.9 + - - +
174H LEU* 3.4 5.9 + - - +
175H LEU* 3.1 23.6 + - - +
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Residues in contact with THR 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LYS* 5.7 4.2 - - - +
153H LYS* 4.8 25.4 - - - -
154H PHE* 6.1 0.9 - - - -
168H ARG 2.9 16.1 + - - -
169H PHE* 3.5 12.1 - - - -
171H LEU* 1.3 78.0 - - - +
173H GLY* 1.3 57.5 + - - +
175H LEU* 3.2 7.2 + - - +
176H VAL* 2.9 30.2 + - - +
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Residues in contact with GLY 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H PHE* 2.7 29.4 + - - -
170H CYS* 3.8 2.0 - - - -
172H THR* 1.3 74.1 - - - +
174H LEU* 1.3 60.8 + - - +
176H VAL* 3.3 15.8 + - - +
177H ILE* 3.4 12.1 + - - +
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Residues in contact with LEU 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 4.6 16.6 - - + +
170H CYS 3.1 16.7 + - - +
171H LEU* 3.7 6.5 - - - +
172H THR 3.3 0.2 - - - -
173H GLY* 1.3 75.8 - - - +
175H LEU* 1.3 61.4 + - - +
177H ILE* 3.3 16.3 + - - +
178H LEU* 3.5 9.5 + - - +
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 4.9 10.0 - - + +
150H LYS* 6.2 0.4 - - + -
171H LEU 3.1 17.6 + - - +
172H THR* 3.5 8.3 - - - +
174H LEU* 1.3 75.1 - - - +
176H VAL* 1.3 63.7 + - - +
178H LEU* 3.1 22.4 + - - +
179H TYR* 3.4 26.6 + - + +
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Residues in contact with VAL 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 5.6 2.3 - - - -
150H LYS* 5.1 10.3 - - + +
172H THR 2.9 14.5 + - - +
173H GLY* 3.5 12.3 - - - +
174H LEU 3.3 0.2 - - - -
175H LEU* 1.3 77.6 - - - +
177H ILE* 1.3 60.3 + - - +
179H TYR* 3.2 16.0 + - - +
180H GLY* 3.2 17.3 + - - -
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Residues in contact with ILE 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H GLY 3.4 7.3 + - - +
174H LEU* 3.3 12.5 + - - +
175H LEU 3.2 0.4 - - - -
176H VAL* 1.3 77.1 - - - +
178H LEU* 1.3 57.7 + - - +
180H GLY* 3.1 3.8 + - - +
181H MET* 2.8 30.6 + - - +
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H LEU* 5.3 11.3 - - + +
80H ILE* 6.3 2.9 - - + -
81H LEU* 5.3 15.0 - - + -
143H TRP* 4.9 8.4 - - + -
174H LEU 3.5 5.3 + - - +
175H LEU* 3.1 15.9 + - - +
177H ILE* 1.3 79.0 - - - +
179H TYR* 1.3 54.7 + - + +
181H MET* 3.2 7.7 + - - +
182H LEU* 2.6 38.0 + - - +
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Residues in contact with TYR 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H TYR* 5.7 1.1 - + - -
143H TRP* 3.7 32.8 - + - +
146H ALA* 3.0 50.9 + - + +
147H PHE* 3.9 27.7 - + + -
149H THR* 4.6 2.3 + - - -
150H LYS* 3.8 22.0 - - + -
175H LEU* 3.5 28.9 - - + +
176H VAL* 3.2 10.0 + - - +
178H LEU* 1.3 78.0 - - + +
180H GLY* 1.3 62.7 + - - +
182H LEU* 3.2 17.8 + - - +
183H LEU* 3.3 9.2 + - - +
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Residues in contact with GLY 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 5.4 4.4 - - - -
176H VAL 3.2 6.8 + - - -
177H ILE* 3.1 7.4 + - - -
179H TYR* 1.3 80.1 - - - +
181H MET* 1.3 60.5 + - - +
183H LEU* 3.6 14.8 + - - +
184H LEU* 4.6 1.6 + - - +
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Residues in contact with MET 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H LEU 6.1 0.4 - - - +
77H LEU* 5.3 11.0 - - + -
177H ILE 2.8 16.5 + - - +
178H LEU* 3.5 7.2 - - - +
180H GLY* 1.3 75.6 - - - +
182H LEU* 1.3 64.2 + - - +
183H LEU 3.3 1.0 + - - -
184H LEU* 3.5 17.4 + - - +
185H VAL* 4.3 3.1 + - - +
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Residues in contact with LEU 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H TRP* 3.6 52.8 + - + -
178H LEU 2.6 21.0 + - - +
179H TYR 3.2 9.6 + - - +
181H MET* 1.3 73.5 - - - +
183H LEU* 1.3 61.4 + - - +
184H LEU 3.3 0.7 + - - -
185H VAL* 3.3 17.1 + - - +
186H GLU* 3.5 9.4 + - - +
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Residues in contact with LEU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 6.0 1.1 - - - -
143H TRP* 6.2 0.9 - - - -
179H TYR 3.3 9.6 + - - +
180H GLY* 3.9 11.9 - - - +
181H MET 3.2 1.2 - - - -
182H LEU* 1.3 76.8 - - - +
184H LEU* 1.3 62.8 + - - +
186H GLU* 2.9 19.6 + - - +
187H VAL* 3.0 13.9 + - - +
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Residues in contact with LEU 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H GLY 4.6 1.5 + - - +
181H MET 3.5 9.9 + - - +
182H LEU 3.4 0.8 - - - -
183H LEU* 1.3 76.8 - - - +
185H VAL* 1.3 64.6 + - - +
187H VAL* 3.0 24.0 + - - +
188H ASN* 3.7 6.9 - - - +
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Residues in contact with VAL 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H PRO 5.0 5.6 - - - +
70H GLY* 5.5 8.1 - - - +
73H LEU 6.5 0.2 - - - -
74H ARG* 5.6 4.5 - - + -
124H TYR* 3.7 23.9 + - - +
136H LEU* 5.8 2.6 - - - +
143H TRP* 6.0 3.1 - - + +
181H MET 4.3 2.3 + - - +
182H LEU* 3.3 14.4 + - - +
183H LEU 3.2 0.6 - - - -
184H LEU* 1.3 78.5 - - - +
186H GLU* 1.3 57.0 + - - +
188H ASN* 3.0 32.0 + - - +
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Residues in contact with GLU 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H LEU* 5.1 10.2 - - - +
140H LEU* 3.5 47.1 - - + +
143H TRP* 5.4 5.8 - - + -
182H LEU 3.5 7.9 + - - +
183H LEU* 2.9 12.7 + - - +
185H VAL* 1.3 78.8 - - - +
187H VAL* 1.3 54.2 + - - +
188H ASN* 3.3 8.3 + - - +
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Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H LEU 3.0 9.9 + - - +
184H LEU* 3.0 17.9 + - - +
186H GLU* 1.3 75.2 - - - +
188H ASN* 1.3 66.4 + - - +
189H VAL* 3.4 9.9 + - - +
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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