Contacts of the helix formed by residues 154 - 169 (chain A) 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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 16.6 - - + -
73A ASN* 6.0 0.2 - - - -
76A LEU* 4.0 20.8 - - + +
77A ARG* 3.7 27.8 - - + -
80A ALA* 3.7 25.6 - - + -
85A LEU* 3.0 19.0 + - - +
86A CYS* 4.1 8.5 - - - -
96A GLU* 3.1 42.8 - - + -
100A GLU* 3.6 22.4 - - + -
153A THR* 1.3 73.7 - - - +
155A VAL* 1.3 68.3 + - + +
157A PHE* 3.0 30.2 + - - +
158A ILE* 3.5 21.7 + - + +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.7 36.1 - - + +
99A LEU* 3.6 39.0 - - + -
100A GLU 4.5 4.5 - - - +
103A PHE* 4.2 10.1 - - + -
147A PHE* 5.1 2.0 - - + -
148A LEU* 3.8 22.7 - - + -
153A THR* 3.1 4.2 - - - +
154A PHE* 1.3 84.8 - - + +
156A ASP* 1.3 58.4 + - - +
158A ILE* 3.1 15.2 + - + +
159A ALA* 3.0 24.3 + - - +
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TRP* 3.6 16.8 - - + +
147A PHE* 3.0 38.4 + - - +
148A LEU 4.8 0.7 + - - -
151A LYS 4.3 0.3 - - - +
152A ILE* 3.5 19.9 - - + -
153A THR* 3.0 36.4 + - - +
155A VAL* 1.3 77.6 - - - +
157A PHE* 1.3 57.7 + - - +
159A ALA* 3.4 7.3 - - - +
160A TYR* 2.9 30.1 + - - +
183A PHE* 3.4 16.0 - - + -
187A PHE* 4.3 3.3 - - + -
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 2.9 31.6 + - - +
18A LEU* 3.9 8.1 - - + +
19A LEU* 3.7 51.8 - - + -
22A TYR* 3.8 31.4 - + + -
76A LEU* 5.2 2.7 - - + -
85A LEU* 5.0 2.9 - - + -
152A ILE* 4.0 22.7 - - + -
153A THR* 3.3 24.2 - - - -
154A PHE* 3.0 14.1 + - - +
156A ASP* 1.3 75.8 - - - +
158A ILE* 1.3 64.4 + - + +
160A TYR* 4.2 3.9 - - - +
161A ASP* 3.5 13.0 + - - +
187A PHE* 3.5 29.4 - + - -
193A ILE* 4.4 1.8 - - + -
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 3.6 6.5 - - - +
73A ASN* 4.4 12.6 - - - +
76A LEU* 3.7 25.6 - - + -
100A GLU* 4.4 17.9 - - + +
103A PHE* 3.7 26.9 - - + -
107A ARG* 3.7 24.9 - - - +
154A PHE* 3.8 33.2 - - + +
155A VAL* 3.1 13.6 + - + +
157A PHE* 1.3 74.0 - - - +
159A ALA* 1.3 65.8 + - - +
161A ASP* 3.3 4.2 + - - +
162A VAL* 3.1 23.7 + - + +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.7 17.9 - - + -
147A PHE* 3.7 30.1 - - + -
155A VAL 3.0 12.6 + - - +
156A ASP* 3.4 11.7 - - - +
158A ILE* 1.3 72.8 - - - +
160A TYR* 1.3 66.7 + - - +
161A ASP 3.2 0.3 + - - -
162A VAL* 3.2 9.3 - - - +
163A LEU* 2.9 32.1 + - + +
183A PHE* 3.9 3.8 - - + -
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.9 0.7 - - - -
14A HIS* 3.8 16.1 + + - -
18A LEU* 3.6 34.5 - - + -
156A ASP 2.9 20.4 + - - +
157A PHE 4.2 2.9 - - - +
159A ALA* 1.3 71.8 - - - +
161A ASP* 1.3 61.9 + - - +
163A LEU* 4.8 2.0 - - - -
164A GLU* 2.8 64.7 + - + +
183A PHE* 3.9 10.0 - - + -
184A ILE* 3.9 14.1 - - + -
187A PHE* 3.5 34.1 - + + -
188A GLU* 3.0 40.0 + - + -
193A ILE* 5.9 0.2 - - + -
197A MET* 3.7 14.2 - - + +
202A PHE* 4.7 3.7 - + - -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.1 29.8 + - - +
11A GLY 4.1 4.3 - - - +
12A LEU* 5.5 0.5 - - - -
14A HIS* 3.5 17.0 - - + +
15A SER* 3.3 23.7 + - - +
107A ARG* 3.0 21.9 + - - +
157A PHE 3.5 2.8 + - - +
158A ILE 3.3 6.2 + - - +
159A ALA 3.2 0.6 - - - -
160A TYR* 1.3 83.0 - - + +
162A VAL* 1.3 57.5 + - - +
165A ARG* 2.9 63.5 + - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.5 48.7 - - + +
106A SER* 5.1 10.1 - - - -
107A ARG* 3.8 33.7 - - + +
110A LEU* 5.5 0.5 - - - +
133A MET* 6.5 0.7 - - + -
137A TYR* 5.8 0.9 - - + -
158A ILE* 3.1 14.3 + - + +
159A ALA 3.2 10.1 - - - +
161A ASP* 1.3 76.0 - - - +
163A LEU* 1.3 64.8 + - + +
165A ARG* 3.4 9.7 + - - +
166A ASN* 3.0 36.4 + - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 4.9 2.5 - - + -
133A MET* 6.0 1.1 - - + -
134A LEU* 3.7 28.7 - - + -
137A TYR* 4.4 18.6 - - + -
147A PHE* 4.4 13.2 - - + -
159A ALA* 2.9 31.3 + - + +
160A TYR 4.2 1.3 - - - +
162A VAL* 1.3 79.8 - - + +
164A GLU* 1.3 65.9 + - - +
166A ASN* 3.0 10.0 + - - +
167A GLN* 3.0 21.1 + - - +
174A LEU* 4.3 8.7 - - + +
180A LEU* 4.5 20.6 - - + +
183A PHE* 4.1 22.2 - - + -
184A ILE* 4.3 12.3 - - + -
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 2.9 33.8 + - - +
160A TYR* 2.8 56.7 + - + +
161A ASP 4.2 0.9 - - - +
163A LEU* 1.3 73.3 - - - +
165A ARG* 1.3 55.6 + - - +
167A GLN* 3.1 12.8 + - - +
168A VAL* 3.0 40.3 + - - +
184A ILE* 3.8 22.5 - - + +
188A GLU* 4.4 4.7 - - - +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.9 13.8 - - - +
11A GLY* 3.3 28.0 + - - -
107A ARG* 4.3 23.7 + - - +
110A LEU* 3.7 26.0 - - + -
161A ASP* 2.9 53.8 + - - +
162A VAL* 3.5 9.4 - - - +
164A GLU* 1.3 79.4 + - - +
166A ASN* 1.3 62.3 + - - +
168A VAL* 3.0 30.1 - - + +
169A PHE* 3.1 8.2 + - - +
207A VAL* 3.8 26.6 - - + +
208A PHE* 3.7 24.4 - - - -
214A TRP* 4.8 2.0 - - + -
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 5.5 1.9 - - - +
110A LEU* 4.1 14.0 - - - +
126A TYR* 2.7 36.3 + - - -
130A LEU* 3.7 15.7 - - + +
133A MET* 3.5 20.7 - - - +
134A LEU* 5.5 3.3 - - + +
162A VAL* 3.0 20.8 + - - +
163A LEU* 3.0 11.3 + - - +
165A ARG* 1.3 76.1 - - - +
167A GLN* 1.3 56.9 + - - +
169A PHE* 3.0 8.1 + - - +
170A GLU* 2.9 27.4 + - - +
173A CYS* 3.7 13.5 - - - -
174A LEU* 5.2 1.8 - - + -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU 3.0 11.9 + - - +
164A GLU* 3.1 19.0 + - - +
166A ASN* 1.3 78.6 - - - +
168A VAL* 1.3 57.1 + - - +
170A GLU 3.0 0.7 - - - -
171A PRO* 2.9 53.9 - - + +
173A CYS* 3.6 15.0 - - - -
174A LEU* 3.9 22.6 - - + +
175A ASP* 5.5 0.5 - - - +
181A LYS* 4.3 13.7 - - - +
184A ILE* 4.0 23.2 - - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.7 5.6 - - - +
164A GLU* 3.0 38.8 + - - +
165A ARG* 3.0 25.1 - - + +
167A GLN* 1.3 78.8 - - + +
169A PHE* 1.3 60.1 + - - +
171A PRO* 4.3 8.1 - - - +
205A ARG* 3.5 35.4 + - - +
207A VAL* 4.8 6.7 - - + -
214A TRP* 4.0 22.1 - - + -
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.2 9.2 - - + -
113A LEU* 3.8 22.7 - - + -
114A CYS* 4.2 1.1 - - - -
119A PHE* 3.7 30.5 - + - -
123A LYS* 4.0 28.1 + - + -
126A TYR* 3.9 31.6 - + - -
127A LEU* 4.0 20.0 - - + -
130A LEU* 5.7 1.1 - - + -
165A ARG 3.1 11.9 + - - +
166A ASN* 3.0 15.5 + - - +
168A VAL* 1.3 79.0 - - - +
170A GLU* 1.3 62.1 + - + +
171A PRO* 4.2 2.5 - - - +
214A TRP* 3.5 42.9 + + + -
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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
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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