Contacts of the helix formed by residues 158 - 173 (chain B) in PDB entry 3GTU
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.4 9.6 - - + -
77B ASN* 5.1 0.9 - - - -
80B LEU* 4.1 23.3 - - + +
81B ARG* 3.5 25.4 - - + -
84B ALA* 3.7 20.4 - - + -
89B MET* 3.0 18.7 + - - +
90B CYS* 3.8 23.1 - - + -
100B VAL* 3.6 30.3 - - + -
104B GLU* 3.3 28.5 - - - -
157B THR* 1.3 76.5 - - - +
159B VAL* 1.3 73.4 + - + +
161B PHE* 3.0 25.7 + - - +
162B LEU* 3.3 25.8 + - + +
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Residues in contact with VAL 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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99B ARG 5.7 0.2 - - - -
100B VAL* 3.4 50.3 - - + +
103B ILE* 3.5 23.3 - - + +
104B GLU* 4.0 6.3 - - + +
151B PHE* 4.6 13.5 - - + -
152B ALA* 4.7 3.8 - - + +
157B THR* 2.9 27.1 + - - +
158B PHE* 1.3 90.4 - - + +
160B ASP* 1.3 55.6 + - - +
162B LEU* 3.3 9.8 + - - +
163B THR* 2.8 37.1 + - - -
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Residues in contact with ASP 160 (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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150B TRP* 3.4 22.6 - - + +
151B PHE* 3.0 29.3 + - - +
152B ALA 4.8 0.3 + - - -
155B LYS 3.9 0.3 - - - +
156B LEU* 3.3 18.2 - - + +
157B THR* 3.1 35.3 + - - +
158B PHE 3.1 0.8 - - - -
159B VAL* 1.3 74.4 - - - +
161B PHE* 1.3 60.5 + - + +
163B THR* 4.4 2.2 - - - -
164B TYR* 2.9 31.9 + - - +
187B PHE* 3.5 25.5 - - + -
191B PHE* 4.5 4.9 - - + -
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Residues in contact with PHE 161 (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 ALA* 3.9 22.8 - - + +
22B LEU* 4.0 7.9 - - + +
23B LEU* 3.7 40.6 - - + -
26B PHE* 3.7 37.5 - + + -
80B LEU* 5.1 2.7 - - + -
89B MET* 3.5 17.9 - - + -
156B LEU* 3.7 10.8 - - + -
157B THR 3.3 21.5 - - - -
158B PHE* 3.0 12.3 + - - +
160B ASP* 1.3 76.4 - - - +
162B LEU* 1.3 61.5 + - - +
164B TYR* 3.8 3.8 - - - +
165B ASP* 3.2 23.0 + - - +
191B PHE* 3.5 34.3 - + + -
197B ILE* 4.2 1.6 - - + -
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Residues in contact with LEU 162 (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 ALA* 4.3 7.4 - - + -
76B SER* 6.3 0.4 - - - -
77B ASN* 4.3 14.1 - - - +
80B LEU* 3.5 29.4 - - + -
104B GLU* 4.3 11.4 - - + -
107B VAL* 4.0 24.4 - - + +
111B ARG* 3.4 30.9 + - - +
158B PHE* 3.3 32.3 + - + +
159B VAL* 3.3 12.7 + - + +
160B ASP 3.2 0.2 - - - -
161B PHE* 1.3 77.1 - - - +
163B THR* 1.3 65.3 + - - +
165B ASP* 3.3 6.1 + - - +
166B ILE* 3.2 22.5 + - - +
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Residues in contact with THR 163 (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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103B ILE* 3.5 19.9 - - - +
107B VAL* 3.9 2.9 - - - +
141B PHE* 4.1 13.9 - - + -
151B PHE* 3.5 45.2 - - + -
159B VAL 2.8 24.3 + - - -
160B ASP* 3.8 3.8 - - - -
162B LEU* 1.3 70.1 - - - +
164B TYR* 1.3 67.3 + - - +
166B ILE* 3.2 8.0 - - + +
167B LEU* 2.9 43.0 + - + +
187B PHE* 4.5 1.1 - - + -
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Residues in contact with TYR 164 (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 HIS* 4.1 10.9 + - - -
22B LEU* 3.9 22.2 - - + -
160B ASP 2.9 18.6 + - - +
161B PHE 3.8 2.9 - - - +
163B THR* 1.3 77.8 - - - +
165B ASP* 1.3 55.8 + - - +
167B LEU* 3.8 0.5 - - - +
168B ASP* 2.8 55.5 + - + +
171B ARG* 4.1 11.2 + - - -
187B PHE* 4.0 12.7 - - + -
188B MET* 3.7 18.8 - - + -
191B PHE* 3.3 40.4 - + + -
192B GLU* 3.2 44.8 + - + +
201B LEU* 3.6 17.4 - - + +
206B PHE* 5.8 0.3 - - - -
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Residues in contact with ASP 165 (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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14B ARG* 3.2 29.7 + - - +
15B GLY 4.3 8.6 - - - +
16B LEU* 5.7 0.7 - - - +
18B HIS* 3.2 25.7 - - + +
19B ALA* 4.6 8.8 + - + +
111B ARG* 3.5 24.1 + - - -
161B PHE 3.2 11.8 + - - +
162B LEU* 3.3 10.5 + - - +
164B TYR* 1.3 83.0 - - - +
166B ILE* 1.3 55.8 + - - +
169B GLN* 3.0 44.9 + - - +
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Residues in contact with ILE 166 (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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107B VAL* 4.3 16.4 - - + +
110B PHE* 3.7 34.1 - - + -
111B ARG* 3.7 39.5 - - + +
114B LEU* 3.7 25.1 - - + -
141B PHE* 5.3 1.6 - - + -
162B LEU 3.2 10.8 + - - +
163B THR* 3.2 17.3 - - + +
165B ASP* 1.3 78.5 - - - +
167B LEU* 1.3 72.8 + - + +
169B GLN* 3.5 8.5 + - - +
170B ASN* 3.1 31.7 + - - +
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Residues in contact with LEU 167 (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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110B PHE* 4.8 9.9 - - + -
138B LEU* 3.4 32.3 - - + -
141B PHE* 5.0 7.9 - - + -
151B PHE* 4.8 0.2 - - + -
163B THR* 2.9 39.0 + - + +
166B ILE* 1.3 77.0 - - + +
168B ASP* 1.3 59.3 + - - +
170B ASN* 3.4 4.4 + - - +
171B ARG* 2.8 28.8 + - - +
178B LEU* 4.4 9.1 - - + +
184B LEU* 4.2 26.5 - - + -
187B PHE* 4.1 21.3 - - + -
188B MET* 3.6 19.8 - - + +
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Residues in contact with ASP 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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14B ARG* 2.9 29.9 + - - +
18B HIS* 4.6 1.2 + - - -
164B TYR* 2.8 38.5 + - + +
165B ASP* 3.5 4.9 - - - +
167B LEU* 1.3 74.2 - - - +
169B GLN* 1.3 65.3 + - - +
171B ARG* 3.0 32.7 + - - +
172B ILE* 2.9 29.1 + - - +
188B MET* 3.4 11.6 - - + +
206B PHE* 5.4 2.8 - - - -
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Residues in contact with GLN 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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14B ARG* 3.8 16.6 - - - +
15B GLY* 5.0 7.6 - - - +
111B ARG* 5.0 6.2 + - - +
114B LEU* 3.7 28.3 - - + +
115B ILE* 6.0 3.2 - - - +
165B ASP* 3.0 43.3 + - - +
166B ILE* 3.7 11.5 - - - +
167B LEU 3.4 0.2 - - - -
168B ASP* 1.3 74.9 - - - +
170B ASN* 1.3 58.4 + - - +
172B ILE* 3.2 12.7 + - - +
173B PHE* 3.0 26.3 + - - +
211B ILE* 4.0 25.4 - - + +
212B ASN* 4.3 9.3 + - - +
218B TRP* 3.9 10.2 - - + -
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Residues in contact with ASN 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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110B PHE* 3.3 22.5 - - + -
114B LEU* 4.4 6.7 - - - +
130B TYR* 2.8 40.0 + - - -
134B LEU* 3.3 19.3 - - + +
138B LEU* 5.3 4.3 - - + -
166B ILE* 3.1 27.9 + - - +
167B LEU* 3.7 6.5 - - - +
169B GLN* 1.3 73.4 - - - +
171B ARG* 1.3 54.6 + - - +
173B PHE* 3.1 8.3 + - - +
174B ASP* 2.8 35.0 + - - +
177B CYS* 3.6 13.5 - - - -
178B LEU* 5.5 0.9 - - + -
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Residues in contact with ARG 171 (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 TYR* 4.1 1.6 + - - -
167B LEU 2.8 15.0 + - - +
168B ASP* 3.1 34.3 + - - +
170B ASN* 1.3 74.4 - - - +
172B ILE* 1.3 59.7 + - - +
174B ASP 4.0 0.2 - - - -
175B PRO* 2.9 45.3 - - + +
177B CYS* 3.8 11.6 - - - -
178B LEU* 4.6 12.8 - - + +
188B MET* 3.2 37.6 - - + +
192B GLU* 3.0 37.8 + - - -
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Residues in contact with ILE 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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14B ARG* 3.8 26.2 - - - +
168B ASP* 2.9 28.3 + - - +
169B GLN* 3.4 12.1 - - - +
171B ARG* 1.3 78.5 - - - +
173B PHE* 1.3 64.3 + - - +
174B ASP 3.5 0.2 + - - -
175B PRO* 4.2 8.3 - - - +
211B ILE* 3.9 22.7 - - + -
218B TRP* 3.9 17.7 - - + -
223B VAL* 5.1 12.8 - - + -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 5.0 4.9 - - + -
117B LEU* 3.7 17.5 - - + -
118B CYS* 5.0 1.8 - - - -
123B HIS* 3.7 18.2 - + - -
127B LYS* 3.7 44.5 + - + -
130B TYR* 4.1 24.5 - + - -
131B LEU* 3.7 32.1 - - + -
134B LEU* 5.6 0.4 - - + -
169B GLN 3.0 12.6 + - - +
170B ASN* 3.1 13.9 + - - +
172B ILE* 1.3 77.0 - - - +
174B ASP* 1.3 61.2 + - + +
175B PRO* 4.1 2.2 - - - +
218B TRP* 3.5 40.8 - + + +
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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