Contacts of the helix formed by residues 154 - 169 (chain A) in PDB entry 4GTU
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* 4.0 21.1 - - + -
76A LEU* 4.1 23.7 - - + +
77A CYS* 4.5 12.8 - - - -
80A ALA* 3.6 23.1 - - + -
85A LEU* 3.0 22.6 + - - +
86A CYS* 4.3 15.7 - - - -
96A VAL* 3.5 31.6 - - + -
100A GLU* 3.3 34.5 - - + -
153A THR* 1.3 72.5 - - - +
155A VAL* 1.3 71.4 + - + +
156A ASP 2.9 6.6 + - - -
157A PHE* 2.9 24.9 + - - +
158A LEU* 3.3 13.4 + - + +
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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 VAL* 3.5 35.7 - - + +
99A LEU* 3.3 27.7 - - + +
100A GLU* 3.9 9.0 - - + +
147A PHE* 4.8 3.8 - - + -
148A VAL* 3.4 19.5 - - + -
153A THR* 3.2 20.9 - - - +
154A PHE* 1.3 97.0 - - + +
156A ASP* 1.3 59.0 + - - +
158A LEU* 3.6 8.0 - - - +
159A ALA* 3.0 28.2 + - - +
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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* 3.3 17.3 - - - +
147A PHE* 3.2 20.4 + - - +
148A VAL 4.9 0.7 + - - -
152A ILE* 3.3 26.4 - - + +
153A THR* 3.1 32.8 + - - +
154A PHE 2.9 1.2 + - - -
155A VAL* 1.3 74.7 - - - +
157A PHE* 1.3 62.2 + - - +
159A ALA* 3.2 3.8 + - - +
160A TYR* 2.8 30.1 + - - +
183A PHE* 3.1 32.2 - - + -
187A PHE* 4.0 7.6 - - + -
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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 ALA* 4.3 18.5 - - + +
18A LEU* 3.7 12.4 - - + +
19A LEU* 3.6 50.7 - - + -
22A TYR* 3.7 40.8 - + + -
76A LEU* 5.9 1.6 - - + -
85A LEU* 4.2 3.8 - - + -
152A ILE* 4.1 15.9 - - + -
153A THR 3.6 14.8 - - - -
154A PHE 2.9 14.2 + - - +
156A ASP* 1.3 75.3 - - - +
158A LEU* 1.3 63.0 + - - +
160A TYR* 3.1 6.3 + - - +
161A ASP* 2.9 22.9 + - - +
187A PHE* 3.3 33.4 - + - -
190A LEU* 5.8 0.2 - - + -
193A ILE* 4.5 3.1 - - + -
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Residues in contact with LEU 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 ALA* 4.3 14.5 - - + +
73A ASN* 4.5 2.9 - - - +
76A LEU* 4.3 24.9 - - + -
99A LEU* 5.3 0.2 - - + -
100A GLU* 3.6 45.1 - - + +
103A ALA* 3.6 29.2 - - + +
104A MET* 4.4 14.8 - - + -
107A SER* 5.9 0.4 - - - +
154A PHE* 3.3 7.4 + - + +
155A VAL* 3.6 17.3 - - - +
157A PHE* 1.3 78.5 - - - +
159A ALA* 1.3 63.9 + - - +
161A ASP* 3.0 17.1 + - - +
162A VAL* 3.1 21.9 + - + +
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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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99A LEU* 3.8 17.4 - - + +
103A ALA* 4.8 6.5 - - - -
137A PHE* 5.9 3.1 - - + -
147A PHE* 3.9 29.2 - - + -
155A VAL 3.0 16.3 + - - +
156A ASP 3.5 4.3 - - - +
158A LEU* 1.3 79.6 - - - +
160A TYR* 1.3 57.3 + - - +
162A VAL* 3.3 4.0 + - - +
163A LEU* 2.8 37.3 + - + +
183A PHE* 4.1 2.7 - - + -
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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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14A HIS* 4.6 8.9 + + - -
18A LEU* 3.8 24.7 - - + -
156A ASP 2.8 19.8 + - - +
157A PHE 3.4 3.4 - - - +
159A ALA* 1.3 72.4 - - - +
161A ASP* 1.3 60.4 + - - +
163A LEU* 3.7 2.8 - - - +
164A ASP* 2.9 44.0 + - + +
183A PHE* 4.0 11.2 - - + -
184A ILE* 3.9 24.7 - - + -
187A PHE* 3.3 46.0 - + + -
188A GLU* 3.5 25.4 + - + +
193A ILE* 5.8 0.4 - - + -
197A MET* 3.2 32.8 - - - +
202A PHE* 5.0 3.2 - + - -
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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* 2.9 37.6 + - - +
11A GLY 4.4 6.8 - - - +
12A LEU* 4.9 4.5 - - - +
14A HIS* 3.1 28.8 - - + +
15A ALA* 4.5 12.9 + - + +
18A LEU* 5.7 0.2 - - + -
107A SER* 6.0 1.0 - - - -
157A PHE 2.9 11.7 + - - +
158A LEU* 3.1 15.6 - - - +
160A TYR* 1.3 80.9 - - + +
162A VAL* 1.3 63.1 + - - +
164A ASP* 3.3 0.4 + - - -
165A LEU* 3.0 33.8 + - - +
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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 ALA* 3.4 30.1 - - + +
106A VAL* 3.5 27.8 - - + -
107A SER* 4.0 17.5 - - - +
137A PHE* 5.3 6.5 - - + -
158A LEU* 3.1 18.2 + - + +
159A ALA* 3.9 7.2 - - - +
161A ASP* 1.3 81.2 - - - +
163A LEU* 1.3 60.3 + - + +
165A LEU* 3.4 10.4 - - + +
166A HIS* 2.7 47.4 - - + +
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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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134A MET* 4.8 10.5 - - + +
137A PHE* 4.8 25.1 - - + -
147A PHE* 5.1 3.4 - - + -
159A ALA* 2.8 18.8 + - - +
160A TYR 3.7 4.7 - - - +
162A VAL* 1.3 80.0 - - + +
164A ASP* 1.3 66.3 + - - +
166A HIS* 3.2 15.6 + - + +
167A ARG* 3.0 17.9 + - - +
173A CYS* 5.5 0.2 - - - -
174A LEU* 4.0 15.6 - - + +
180A LEU* 4.2 24.2 - - + +
183A PHE* 3.8 22.0 - - + -
184A ILE* 3.5 35.4 - - + -
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Residues in contact with ASP 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* 3.7 25.1 + - - +
14A HIS* 5.5 0.4 + - - -
160A TYR* 2.9 33.3 + - + +
161A ASP* 3.8 3.6 - - - +
163A LEU* 1.3 73.3 - - - +
165A LEU* 1.3 68.3 + - - +
167A ARG* 2.8 50.9 + - - +
168A ILE* 3.4 19.1 + - - +
188A GLU* 4.8 5.5 - - - +
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Residues in contact with LEU 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* 3.2 37.7 - - - +
11A GLY 6.0 0.7 - - - +
110A LEU* 3.9 22.7 - - + -
161A ASP* 3.0 19.2 + - - +
162A VAL* 3.4 16.2 - - + +
164A ASP* 1.3 78.0 - - - +
166A HIS* 1.3 64.6 + - + +
167A ARG 3.2 0.5 + - - -
168A ILE* 3.4 14.2 + - - +
169A PHE* 3.4 12.5 + - - +
207A LEU* 4.2 19.9 - - + +
208A TYR* 3.9 25.1 - - + +
214A TRP* 4.9 3.1 - - + -
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Residues in contact with HIS 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 VAL* 3.7 16.8 + - + +
107A SER* 5.8 0.2 - - - -
110A LEU* 3.8 21.8 - - + +
126A TYR* 3.0 44.8 + + - -
130A LEU* 3.8 15.9 - - + +
134A MET* 4.5 12.3 - - + -
162A VAL* 2.7 34.3 - - + +
163A LEU* 3.2 9.3 + - + +
164A ASP 3.2 0.6 - - - -
165A LEU* 1.3 78.8 - - + +
167A ARG* 1.3 56.0 + - - +
168A ILE 3.4 0.2 - - - -
169A PHE* 3.8 10.1 - - + +
170A GLU* 2.9 31.5 + - - +
173A CYS* 3.4 19.9 - - - -
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Residues in contact with ARG 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 16.4 - - - +
164A ASP* 2.8 40.9 + - - +
166A HIS* 1.3 78.6 - - - +
168A ILE* 1.3 62.4 + - + +
170A GLU 4.4 3.6 - - - -
171A PRO* 3.2 35.0 - - + +
173A CYS* 4.9 0.9 - - - -
174A LEU* 3.4 36.8 - - - +
181A LYS* 5.3 4.0 - - - +
184A ILE* 3.1 41.3 - - - +
188A GLU* 4.6 5.3 + - - -
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Residues in contact with ILE 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* 6.0 0.4 - - - +
164A ASP* 3.8 27.1 - - - +
165A LEU* 3.4 6.7 + - - +
167A ARG* 1.3 80.5 - - + +
169A PHE* 1.3 65.8 + - - +
171A PRO* 4.3 6.8 - - - +
205A LYS* 5.2 15.3 - - + -
207A LEU* 4.9 17.3 - - + -
214A TRP* 4.3 16.9 - - + -
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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* 4.1 28.9 - - + -
113A VAL* 5.1 3.1 - - + -
114A CYS* 4.4 0.4 - - - -
119A PHE* 3.5 34.5 - + - -
123A LYS* 3.1 39.8 + - + -
126A TYR* 4.2 11.0 - + - -
127A LEU* 3.7 20.6 - - + -
130A LEU* 5.0 2.2 - - + -
165A LEU 3.4 13.9 + - - +
166A HIS* 3.9 13.9 - - - +
168A ILE* 1.3 83.3 - - - +
170A GLU* 1.3 62.7 + - + +
171A PRO* 4.0 2.1 - - - +
214A TRP* 3.5 41.4 - + + -
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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
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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