Contacts of the helix formed by residues 154 - 169 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.7 26.7 - - + -
73E ASN* 5.8 0.2 - - - -
76E LEU* 3.9 23.2 - - + +
77E CYS* 3.7 22.4 - - - -
80E ALA* 3.6 12.6 - - + -
85E LEU* 3.2 28.1 + - + +
86E CYS* 4.1 12.3 - - + -
96E VAL* 3.8 21.5 - - + -
100E GLU* 3.6 31.6 - - + -
153E THR* 1.3 71.9 - - - +
155E VAL* 1.3 72.5 + - + +
156E ASP 3.0 4.9 - - - -
157E PHE* 2.7 42.5 + - - +
158E LEU* 3.3 12.9 + - + +
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Residues in contact with VAL 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 3.0 44.0 - - + +
99E LEU* 4.1 22.2 - - + +
100E GLU* 4.1 8.7 - - + +
148E VAL* 3.4 17.7 - - + -
153E THR* 2.9 26.7 - - - +
154E PHE* 1.3 95.4 - - + +
156E ASP* 1.3 60.5 + - - +
158E LEU* 3.3 9.3 + - + +
159E ALA* 2.8 29.5 + - - +
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Residues in contact with ASP 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E TRP* 3.4 22.6 - - + +
147E PHE* 3.9 13.9 - - - +
148E VAL* 3.7 7.1 - - - +
151E LYS 4.3 0.2 - - - +
152E ILE* 3.2 23.4 - - + +
153E THR* 3.2 29.9 + - - +
154E PHE 3.0 0.2 + - - -
155E VAL* 1.3 88.5 - - - +
157E PHE* 1.3 61.2 + - + +
159E ALA* 3.3 7.3 + - - +
160E TYR* 2.8 30.5 + - - +
183E PHE* 3.7 15.8 - - + -
187E PHE* 5.2 4.2 - - + -
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Residues in contact with PHE 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA* 4.0 20.2 - - + +
18E LEU* 3.5 16.1 - - + +
19E LEU* 3.5 55.0 - - + -
22E TYR* 3.9 27.4 - + + -
76E LEU* 5.8 1.3 - - + -
85E LEU* 4.6 4.3 - - + -
152E ILE* 4.1 14.8 - - + -
153E THR 3.2 24.0 - - - -
154E PHE* 2.7 15.2 + - + +
156E ASP* 1.3 78.7 - - + +
158E LEU* 1.3 60.6 + - - +
160E TYR* 3.3 11.2 + - - +
161E ASP* 3.2 20.1 + - - +
187E PHE* 3.6 30.3 - + + -
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU 5.8 2.0 - - - +
15E ALA* 3.7 17.0 - - + +
73E ASN* 4.5 4.9 - - - +
76E LEU* 3.5 33.7 - - + -
99E LEU 6.1 0.2 - - - -
100E GLU* 4.0 39.0 - - + +
103E ALA* 4.5 11.7 - - + -
104E MET* 5.6 10.5 - - + +
154E PHE* 3.3 9.5 + - + +
155E VAL* 3.5 16.4 - - - +
157E PHE* 1.3 76.3 - - - +
159E ALA* 1.3 66.5 + - - +
161E ASP* 2.8 18.4 + - + +
162E VAL* 3.0 17.2 + - + +
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Residues in contact with ALA 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 5.2 7.6 - - + -
103E ALA* 4.6 6.4 - - + +
137E PHE* 4.8 6.5 - - + -
147E PHE* 4.5 20.4 - - + -
155E VAL 2.8 17.5 + - - +
156E ASP* 3.5 8.7 - - - +
158E LEU* 1.3 73.1 - - - +
160E TYR* 1.3 64.2 + - - +
162E VAL* 3.0 11.2 + - - +
163E LEU* 2.9 29.3 + - + +
183E PHE* 4.1 14.4 - - + -
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Residues in contact with TYR 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E HIS* 5.0 7.0 - - - -
18E LEU* 4.1 19.1 - - + -
156E ASP 2.8 14.6 + - - +
157E PHE 3.4 8.3 - - - +
158E LEU 3.1 0.2 - - - -
159E ALA* 1.3 76.3 - - - +
161E ASP* 1.3 60.1 + - - +
163E LEU* 3.7 3.4 - - - +
164E ASP* 2.9 53.5 + - + +
167E ARG* 4.6 1.2 + - - -
183E PHE* 4.1 10.7 - + + -
184E ILE* 3.5 42.2 - - + -
187E PHE* 3.3 43.3 - + + -
188E GLU* 3.0 20.8 + - + -
197E MET* 3.9 17.6 - - + +
202E PHE* 6.0 0.7 - - - -
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Residues in contact with ASP 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG* 2.9 36.9 + - - +
11E GLY 4.7 5.0 - - - +
12E LEU* 5.3 5.5 - - - +
14E HIS* 4.1 20.4 - - + +
15E ALA* 4.7 10.7 + - + +
107E SER* 4.9 5.0 + - - -
157E PHE 3.2 10.2 + - - +
158E LEU* 2.8 16.4 + - - +
160E TYR* 1.3 75.8 - - + +
162E VAL* 1.3 69.6 + - + +
164E ASP* 4.5 2.2 - - - -
165E LEU* 3.0 45.9 + - - +
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Residues in contact with VAL 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ALA* 3.3 35.0 - - + +
106E VAL* 3.5 24.0 - - + -
107E SER* 4.6 10.8 - - - +
133E MET* 6.0 0.4 - - + -
134E MET* 6.0 0.7 - - - -
137E PHE* 4.0 18.8 - - + -
158E LEU* 3.0 13.9 + - + +
159E ALA* 3.4 8.5 - - - +
161E ASP* 1.3 79.4 - - + +
163E LEU* 1.3 59.9 + - + +
165E LEU* 4.2 6.7 - - - +
166E HIS* 2.7 46.2 + - + +
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E MET* 4.0 20.2 - - + -
137E PHE* 3.6 30.7 - - + -
147E PHE* 4.8 3.6 - - + -
159E ALA 2.9 15.9 + - - +
160E TYR 3.7 0.4 - - - +
162E VAL* 1.3 75.4 - - - +
164E ASP* 1.3 59.3 + - - +
165E LEU 3.0 1.4 + - - -
166E HIS* 3.1 7.9 + - - +
167E ARG* 2.9 27.0 + - - +
174E LEU* 4.4 10.2 - - + +
180E LEU* 4.3 24.2 - - + +
183E PHE* 3.5 37.0 - - + -
184E ILE* 3.4 24.7 - - + -
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Residues in contact with ASP 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG* 2.9 30.9 + - - +
14E HIS* 5.3 0.5 + - - -
160E TYR* 2.9 49.3 + - + +
161E ASP 4.0 2.5 - - - +
163E LEU* 1.3 73.7 - - - +
165E LEU* 1.3 57.7 + - - +
167E ARG* 2.9 40.8 + - - +
168E ILE* 3.4 18.5 - - - +
184E ILE* 4.2 1.9 - - + +
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG* 3.5 28.7 - - - +
107E SER* 4.6 13.9 - - - +
110E LEU* 4.6 14.4 - - + -
161E ASP* 3.0 41.4 + - - +
162E VAL* 4.2 6.5 - - - +
164E ASP* 1.3 71.7 - - - +
166E HIS* 1.3 67.6 + - + +
168E ILE* 3.0 17.4 + - + +
169E PHE* 3.1 12.9 + - - +
207E LEU* 3.6 31.9 - - + +
208E TYR* 4.9 13.0 - - + +
214E TRP* 4.9 4.5 - - + -
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Residues in contact with HIS 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E VAL* 4.7 7.4 - - + -
107E SER* 6.0 0.7 - - - -
110E LEU* 3.7 28.0 - - + +
126E TYR* 2.8 37.4 + + - -
130E LEU* 4.1 13.0 - - + -
133E MET* 4.1 11.4 - - + -
134E MET* 4.4 11.0 - - + +
162E VAL* 2.7 39.0 + - + +
163E LEU 3.1 6.8 + - - +
165E LEU* 1.3 79.0 - - + +
167E ARG* 1.3 57.4 + - - +
169E PHE* 2.9 9.9 + + - -
170E GLU 2.7 36.5 + - - +
173E CYS* 3.9 17.9 - - - -
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Residues in contact with ARG 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E TYR* 4.6 1.6 + - - -
163E LEU 2.9 9.5 + - - +
164E ASP* 2.9 39.6 + - - +
166E HIS* 1.3 76.7 - - - +
168E ILE* 1.3 57.8 + - + +
170E GLU 4.4 3.8 - - - -
171E PRO* 3.1 27.5 - - - +
173E CYS* 4.6 0.2 - - - -
174E LEU* 3.5 34.8 - - + +
181E LYS* 4.9 6.5 + - - +
184E ILE* 3.1 40.1 - - - +
185E SER* 4.6 8.1 + - - -
188E GLU* 3.7 13.5 + - - -
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG* 5.3 2.0 - - - +
164E ASP* 3.4 29.4 - - - +
165E LEU* 3.0 6.6 + - - +
167E ARG* 1.3 78.7 - - + +
169E PHE* 1.3 68.1 + - - +
170E GLU 3.4 0.2 - - - -
171E PRO* 3.8 11.6 - - - +
207E LEU* 4.5 31.2 - - + -
214E TRP* 5.1 6.3 - - + -
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Residues in contact with PHE 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU* 3.5 34.8 - - + -
113E VAL* 5.7 3.4 - - + -
114E CYS* 4.7 1.8 - - - -
119E PHE* 4.2 9.6 - + - -
123E LYS* 3.6 49.6 + - + -
126E TYR* 4.5 8.1 - + + -
127E LEU* 4.4 20.0 - - + +
130E LEU* 5.7 0.7 - - + -
165E LEU 3.1 11.8 + - - +
166E HIS* 2.9 15.4 + + - +
168E ILE* 1.3 78.8 - - - +
170E GLU* 1.3 59.4 + - + +
171E PRO* 3.9 3.5 - - - +
214E TRP* 3.1 51.5 - + + -
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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