Contacts of the helix formed by residues 166 - 187 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F PHE* 3.8 32.3 - - + -
162F ILE* 3.9 11.4 - - + -
163F GLY 5.1 0.9 - - - +
164F PHE* 3.2 5.0 - - - +
165F SER* 1.3 78.8 - - - +
167F LEU* 1.3 61.3 + - - +
168F ARG* 3.4 1.8 - - + +
169F PHE* 3.9 13.5 - - + +
170F CYS* 3.6 16.1 + - - +
344F TYR 3.7 11.9 - - - +
346F VAL* 3.5 8.1 - - - +
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU* 4.5 15.9 - - + +
166F GLN* 1.3 69.9 - - - +
168F ARG* 1.3 67.2 + - - +
169F PHE 3.2 1.6 - - - -
170F CYS* 3.6 7.7 + - - +
171F LEU* 3.4 19.2 + - - +
344F TYR* 3.3 11.1 + - + -
345F PHE 3.2 27.6 - - - +
346F VAL* 3.2 14.0 - - - +
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Residues in contact with ARG 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU* 5.5 2.7 - - - -
157F PHE* 6.0 4.0 - - + -
166F GLN* 3.4 2.6 - - + -
167F LEU* 1.3 78.1 - - - +
169F PHE* 1.3 57.9 + - - +
171F LEU* 3.3 7.8 + - - +
172F THR* 2.9 28.8 + - - -
343F VAL* 5.7 3.6 - - + -
344F TYR* 3.9 24.8 + - + +
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Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F PHE* 3.9 33.7 - + - -
157F PHE* 3.8 38.0 - + + -
163F GLY 4.1 17.9 - - - -
164F PHE* 5.9 0.9 - - - -
166F GLN* 3.9 23.2 - - + +
168F ARG* 1.3 77.9 - - - +
170F CYS* 1.3 59.8 + - - +
172F THR* 3.2 9.5 + - - -
173F GLY* 2.7 39.9 + - - -
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Residues in contact with CYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F GLN 3.6 10.9 + - - +
167F LEU* 3.6 12.0 + - - +
168F ARG 3.3 0.6 - - - -
169F PHE* 1.3 83.8 - - + +
171F LEU* 1.3 62.4 + - - +
173F GLY* 3.3 1.6 + - - -
174F LEU* 3.1 24.6 + - - +
346F VAL* 5.8 2.7 - - + -
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL* 5.1 7.2 - - - +
87F CYS* 4.9 9.6 - - + +
88F GLU* 4.2 31.2 - - + +
91F GLU* 5.8 1.3 - - + -
167F LEU 3.4 9.8 + - - +
168F ARG* 3.3 10.7 + - - +
169F PHE 3.2 0.4 - - - -
170F CYS* 1.3 79.2 - - - +
172F THR* 1.3 62.4 + - - +
174F LEU* 3.4 6.5 + - - +
175F LEU* 3.1 24.0 + - - +
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Residues in contact with THR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F LYS* 5.7 5.3 - - - +
153F LYS* 4.8 24.2 - - - -
154F PHE* 6.1 1.1 - - - -
168F ARG 2.9 16.8 + - - -
169F PHE* 3.2 12.1 + - - -
171F LEU* 1.3 77.4 - - - +
173F GLY* 1.3 57.8 + - - +
175F LEU* 3.2 7.9 + - - +
176F VAL* 2.9 29.3 + - - +
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Residues in contact with GLY 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F PHE* 2.7 28.8 + - - -
170F CYS* 3.8 2.2 - - - -
172F THR* 1.3 74.2 - - - +
174F LEU* 1.3 59.4 + - - +
176F VAL* 3.3 15.2 + - - +
177F ILE* 3.4 12.3 + - - +
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Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL* 4.6 16.8 - - + +
170F CYS 3.1 17.0 + - - +
171F LEU* 3.7 6.3 - - - +
173F GLY* 1.3 75.1 - - - +
175F LEU* 1.3 62.6 + - - +
177F ILE* 3.3 16.5 + - - +
178F LEU* 3.5 9.0 + - - +
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL* 4.9 10.5 - - + +
150F LYS* 6.2 0.9 - - + -
171F LEU 3.1 17.6 + - - +
172F THR* 3.5 9.0 - - - +
174F LEU* 1.3 75.5 - - - +
176F VAL* 1.3 64.5 + - - +
178F LEU* 3.1 22.5 + - - +
179F TYR* 3.4 26.2 + - + +
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 5.6 2.5 - - - -
150F LYS* 5.1 9.4 - - + +
172F THR 2.9 12.8 + - - +
173F GLY* 3.5 13.2 - - - +
174F LEU 3.3 0.4 - - - -
175F LEU* 1.3 78.7 - - - +
177F ILE* 1.3 60.9 + - - +
179F TYR* 3.2 16.5 + - - +
180F GLY* 3.2 17.3 + - - -
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Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F GLY 3.4 7.5 + - - +
174F LEU* 3.3 13.3 + - - +
175F LEU 3.2 0.4 - - - -
176F VAL* 1.3 77.4 - - - +
178F LEU* 1.3 58.0 + - - +
180F GLY* 3.1 3.3 + - - +
181F MET* 2.8 30.9 + - - +
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Residues in contact with LEU 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LEU* 5.3 11.2 - - + +
80F ILE* 6.3 2.2 - - + -
81F LEU* 5.3 14.8 - - + +
143F TRP* 5.1 8.1 - - + -
174F LEU 3.5 6.0 + - - +
175F LEU* 3.1 14.9 + - - +
177F ILE* 1.3 79.2 - - - +
179F TYR* 1.3 56.4 + - + +
181F MET* 3.5 6.7 - - - +
182F LEU* 2.6 38.9 + - - +
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Residues in contact with TYR 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F TYR* 5.7 0.4 - + - -
143F TRP* 3.7 32.8 - + - +
146F ALA* 3.0 51.1 + - + +
147F PHE* 3.9 27.3 - + + -
149F THR* 4.6 2.8 + - - -
150F LYS* 3.8 22.0 - - + -
175F LEU* 3.5 28.8 - - + +
176F VAL* 3.2 10.0 + - - +
178F LEU* 1.3 77.4 - - + +
180F GLY* 1.3 63.4 + - - +
182F LEU* 3.2 17.5 + - - +
183F LEU* 3.3 9.2 + - - +
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Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 5.4 4.2 - - - -
176F VAL 3.2 6.6 + - - -
177F ILE* 3.1 7.2 + - - -
179F TYR* 1.3 79.7 - - - +
181F MET* 1.3 60.8 + - - +
182F LEU 3.5 0.2 + - - -
183F LEU* 3.6 15.2 + - - +
184F LEU* 4.6 1.7 + - - +
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Residues in contact with MET 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU* 5.3 10.8 - - + -
177F ILE 2.8 16.7 + - - +
178F LEU* 3.5 8.3 - - - +
180F GLY* 1.3 74.0 - - - +
182F LEU* 1.3 62.7 + - - +
183F LEU 3.3 0.9 + - - -
184F LEU* 3.5 17.2 + - - +
185F VAL* 4.3 3.5 + - - +
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Residues in contact with LEU 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F TRP* 3.6 51.5 + - + -
178F LEU 2.6 21.6 + - - +
179F TYR* 3.2 9.8 + - - +
181F MET* 1.3 73.8 - - - +
183F LEU* 1.3 62.0 + - - +
184F LEU 3.3 0.5 + - - -
185F VAL* 3.3 17.2 + - - +
186F GLU* 3.5 10.3 + - - +
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Residues in contact with LEU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 6.0 1.3 - - - -
143F TRP* 6.2 0.9 - - - -
179F TYR 3.3 9.6 + - - +
180F GLY* 3.9 11.9 - - - +
181F MET 3.2 1.2 - - - -
182F LEU* 1.3 76.4 - - - +
184F LEU* 1.3 62.8 + - - +
186F GLU* 2.9 20.2 + - - +
187F VAL* 3.0 13.7 + - - +
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Residues in contact with LEU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F GLY 4.6 1.7 + - - +
181F MET 3.5 10.8 + - - +
182F LEU 3.4 1.0 - - - -
183F LEU* 1.3 76.7 - - - +
185F VAL* 1.3 61.9 + - - +
187F VAL* 3.0 23.7 + - - +
188F ASN* 3.7 6.9 - - - +
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Residues in contact with VAL 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F PRO 5.0 5.4 - - - +
70F GLY* 5.5 9.2 - - - +
74F ARG* 5.6 3.6 - - + -
124F TYR* 3.7 22.6 + - - +
136F LEU* 5.8 2.8 - - - +
143F TRP* 6.0 3.4 - - + +
181F MET 4.3 2.1 + - - +
182F LEU* 3.3 13.8 + - - +
183F LEU 3.2 0.6 - - - -
184F LEU* 1.3 77.1 - - - +
186F GLU* 1.3 57.5 + - - +
187F VAL 3.2 0.2 - - - -
188F ASN* 3.0 32.2 + - - +
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LEU* 5.1 10.1 - - - +
140F LEU* 3.5 46.7 - - + +
143F TRP* 5.4 6.5 - - + -
182F LEU 3.5 7.5 + - - +
183F LEU* 2.9 13.1 + - - +
185F VAL* 1.3 77.9 - - - +
187F VAL* 1.3 53.6 + - - +
188F ASN* 3.3 7.5 + - - +
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Residues in contact with VAL 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F LEU 3.0 9.5 + - - +
184F LEU* 3.0 18.8 + - - +
186F GLU* 1.3 75.0 - - - +
188F ASN* 1.3 67.0 + - - +
189F VAL* 3.4 10.2 + - - +
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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