Contacts of the helix formed by residues 155 - 170 (chain E) in PDB entry 1GUL
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 LEU 155 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 3.6 34.5 - - + -
72E LEU* 4.2 28.0 - - + +
73E HIS* 4.5 13.0 - - + -
76E ALA* 4.0 20.4 - - + -
81E LEU* 2.7 22.3 + - + +
82E PHE* 4.8 7.9 - - + -
92E ILE* 4.2 6.1 - - + -
96E VAL* 3.9 21.1 - - + -
154E SER* 1.3 75.8 - - - +
156E ALA* 1.3 62.4 + - - +
158E VAL* 3.2 5.7 + - + -
159E ILE* 3.2 33.4 + - + +
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Residues in contact with ALA 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ILE* 3.9 13.1 - - + +
95E TYR* 3.8 31.4 - - + +
96E VAL* 3.7 16.6 - - + +
99E THR* 5.3 1.6 + - - -
148E LEU* 4.1 14.5 - - + +
154E SER* 3.0 11.7 + - - +
155E LEU* 1.3 79.3 - - - +
157E ASP* 1.3 62.1 + - - +
159E ILE* 4.0 1.4 - - - +
160E LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E PHE* 3.6 10.1 - - - +
148E LEU* 2.8 29.4 + - - +
152E GLN 3.5 5.5 - - - +
153E LEU* 3.3 22.9 - - + -
154E SER* 2.9 33.0 + - - +
156E ALA* 1.3 76.9 - - - +
158E VAL* 1.3 60.1 + - - +
160E LEU* 3.9 0.3 - - - +
161E LEU* 2.8 31.6 + - - +
184E TYR* 2.6 32.6 + - - +
188E LEU* 3.9 9.0 - - + +
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Residues in contact with VAL 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TRP* 3.5 50.0 - - + +
22E VAL* 4.1 14.6 - - + +
25E ALA* 4.0 20.2 - - + -
81E LEU* 5.2 5.6 - - + -
153E LEU* 4.6 14.1 - - + -
154E SER 3.3 14.5 + - - +
155E LEU* 3.2 8.6 + - - +
157E ASP* 1.3 78.2 - - - +
159E ILE* 1.3 53.8 + - + +
161E LEU* 3.3 7.1 + - + +
162E GLN* 2.7 32.9 + - - +
194E ILE* 5.5 3.8 - - + -
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Residues in contact with ILE 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER* 3.8 28.5 - - - +
22E VAL* 4.4 7.9 - - + -
72E LEU* 4.3 7.6 - - + -
96E VAL* 4.5 14.6 - - + +
99E THR* 3.8 22.0 - - + -
100E LEU* 3.9 23.6 - - + -
103E LEU* 4.8 0.4 - - + -
155E LEU* 3.2 37.1 + - + +
156E ALA 4.1 2.7 - - - +
158E VAL* 1.3 77.7 - - + +
160E LEU* 1.3 55.7 + - - +
162E GLN* 3.3 11.0 + - - +
163E THR* 2.6 41.2 + - - +
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Residues in contact with LEU 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E THR* 4.1 18.1 - - + +
102E LEU* 6.0 1.6 - - + -
133E PHE* 4.6 8.3 - - + -
136E PHE* 3.8 48.5 - - + -
148E LEU* 3.8 18.6 - - + -
156E ALA 3.0 18.1 + - - +
157E ASP 3.9 2.7 - - - +
159E ILE* 1.3 75.6 - - - +
161E LEU* 1.3 66.1 + - - +
163E THR* 3.1 4.3 + - + -
164E ILE* 2.8 49.1 + - + +
181E LEU* 4.6 4.0 - - + -
184E TYR* 4.0 15.9 - - + +
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Residues in contact with LEU 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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21E TRP* 3.4 29.4 - - + -
157E ASP 2.8 18.8 + - - +
158E VAL* 3.5 4.7 - - - +
160E LEU* 1.3 77.0 - - - +
162E GLN* 1.3 66.0 + - - +
164E ILE* 3.7 6.5 - - + +
165E LEU* 3.0 47.5 + - + +
184E TYR* 5.2 0.6 - - - -
185E THR* 4.0 23.3 - - + +
188E LEU* 4.0 23.9 - - + +
189E SER* 4.0 15.7 - - - +
194E ILE* 3.9 23.6 - - + -
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Residues in contact with GLN 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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17E GLU* 3.8 22.0 - - - +
18E SER* 2.7 41.1 + - - +
21E TRP* 3.7 41.4 + - + +
103E LEU* 3.8 22.8 - - + +
158E VAL 2.7 21.1 + - - +
159E ILE* 3.5 12.6 - - - +
161E LEU* 1.3 74.7 - - - +
163E THR* 1.3 61.5 + - - +
165E LEU* 3.6 2.8 + - - +
166E ALA* 3.1 26.8 + - + +
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Residues in contact with THR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E THR* 3.4 18.8 - - + +
102E LEU* 4.0 32.5 - - + -
103E LEU* 3.8 30.1 - - + +
106E LEU* 4.8 1.1 - - + -
133E PHE* 5.8 0.2 - - + -
159E ILE* 2.6 25.6 + - - +
160E LEU* 3.5 5.2 - - + -
162E GLN* 1.3 76.7 - - - +
164E ILE* 1.3 66.9 + - + +
166E ALA* 3.1 6.5 + - - +
167E LEU* 2.9 34.4 + - + +
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Residues in contact with ILE 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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133E PHE* 3.8 24.9 - - + -
160E LEU* 2.8 40.0 + - + +
161E LEU* 3.7 5.6 - - - +
163E THR* 1.3 76.2 - - - +
165E LEU* 1.3 69.5 + - + +
167E LEU* 3.0 11.4 + - - +
168E GLU* 2.7 37.7 + - + +
174E ILE* 5.7 0.2 - - + -
175E LEU* 4.2 26.0 - - + -
181E LEU* 4.4 17.3 - - + -
184E TYR* 4.9 3.4 - - + -
185E THR* 3.9 21.3 - - + +
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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
----------------------------------------------------------
21E TRP* 3.8 31.9 - - + -
161E LEU* 3.0 24.2 + - + +
162E GLN 3.8 3.6 - - - +
164E ILE* 1.3 82.1 - - + +
166E ALA* 1.3 62.4 + - - +
168E GLU* 3.3 23.2 + - - +
169E GLU* 3.1 25.8 + - - +
185E THR* 4.1 22.9 - - + -
189E SER* 5.1 3.1 - - - +
198E LEU* 4.1 19.1 - - + -
204E LYS* 5.6 1.8 - - - -
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Residues in contact with ALA 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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13E ARG* 4.9 7.4 - - - +
103E LEU* 5.0 5.4 - - + -
106E LEU* 4.1 23.0 - - + +
162E GLN* 3.1 16.9 + - + +
163E THR* 3.1 11.4 + - - +
165E LEU* 1.3 74.4 - - - +
167E LEU* 1.3 67.3 + - - +
169E GLU* 3.2 32.4 + - - +
170E LYS* 3.7 9.0 + - - +
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Residues in contact with LEU 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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102E LEU* 4.1 14.6 - - + -
106E LEU* 3.9 21.1 - - + -
124E MET* 3.9 35.0 - - + +
128E ALA* 4.3 4.7 - - + -
133E PHE* 3.8 26.5 - - + -
163E THR* 2.9 31.7 + - + +
164E ILE* 3.3 6.3 - - - +
166E ALA* 1.3 76.9 - - - +
168E GLU* 1.3 53.2 + - - +
170E LYS* 2.6 27.5 + - - +
171E ILE* 2.7 20.5 + - + +
174E ILE* 4.3 20.6 - - + -
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Residues in contact with GLU 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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164E ILE* 2.7 29.6 + - + +
165E LEU* 3.7 24.0 - - - +
166E ALA 3.2 0.2 - - - -
167E LEU* 1.3 79.0 - - - +
169E GLU* 1.3 62.9 + - - +
170E LYS 3.2 0.3 + - - -
171E ILE 3.5 9.6 - - - +
172E PRO* 3.3 36.7 - - + +
174E ILE* 3.7 15.5 - - + -
175E LEU* 3.8 26.5 - - - +
185E THR* 5.2 3.2 - - - +
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Residues in contact with GLU 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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13E ARG* 2.8 45.4 + - - -
165E LEU* 3.1 21.6 + - - +
166E ALA* 3.4 13.9 - - - +
167E LEU 2.9 1.0 - - - -
168E GLU* 1.3 81.2 - - - +
170E LYS* 1.3 63.5 + - + +
172E PRO* 4.8 3.6 - - - +
204E LYS* 4.6 3.5 + - - -
207E PRO* 3.9 16.7 - - + +
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Residues in contact with LYS 170 (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 LEU* 4.2 23.1 + - + -
109E HIS* 2.7 37.1 + - + +
110E PRO* 5.5 1.8 - - - +
121E VAL* 4.4 26.1 - - + +
124E MET* 4.5 6.7 - - + -
166E ALA 4.0 10.8 - - - +
167E LEU* 2.6 12.5 + - - +
169E GLU* 1.3 80.2 - - + +
171E ILE* 1.3 69.6 + - + +
172E PRO* 3.3 8.7 - - - +
208E PRO* 6.3 0.6 - - - +
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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