Contacts of the helix formed by residues 139 - 148 (chain D) in PDB entry 3F7G
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 ASP 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D LEU* 5.8 2.1 - - - +
137D GLY 3.5 4.7 + - - +
138D ASP* 1.3 72.5 - - - +
140D PRO* 1.3 70.0 - - - +
141D TRP* 3.6 15.2 + - - +
142D THR* 2.6 38.7 + - - +
143D GLU* 3.0 26.9 + - - +
162D PHE* 4.9 1.6 - - - -
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Residues in contact with PRO 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 4.0 20.4 - - + -
107D LEU* 3.7 35.2 - - + +
108D LEU* 4.0 15.9 - - + -
111D ALA* 3.5 21.8 - - + -
113D PHE* 3.7 6.9 - - + -
134D TRP* 3.8 13.0 - - + -
138D ASP 3.5 10.1 - - - +
139D ASP* 1.3 89.6 - - - +
141D TRP* 1.3 61.9 + - + +
143D GLU* 3.8 1.0 - - - +
144D HIS* 2.9 24.3 + - - +
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Residues in contact with TRP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU 5.8 0.7 - - - -
110D ALA* 3.2 25.7 + - + +
111D ALA* 3.7 26.8 - - + +
139D ASP* 3.3 15.1 + - - +
140D PRO* 1.3 78.8 - - + +
142D THR* 1.3 58.2 + - - +
144D HIS* 3.2 7.6 - - - +
145D ALA* 3.0 27.2 + - - +
153D PHE* 3.5 27.4 - + - -
154D LEU* 3.8 27.7 - - + +
157D SER* 3.6 17.0 - - - -
158D LYS* 3.5 50.6 - - + +
162D PHE* 3.8 15.1 - - + -
161E ASP* 4.6 3.7 + - - -
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Residues in contact with THR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ASP* 2.6 34.4 + - - +
141D TRP* 1.3 73.4 - - - +
143D GLU* 1.3 67.4 + - - +
145D ALA* 3.3 1.0 + - - -
146D LYS* 2.8 29.6 + - + +
162D PHE* 4.0 17.6 - - - -
166D VAL* 3.6 23.2 - - + +
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 4.2 8.7 - - - -
73A ALA* 3.3 29.8 + - + +
131D LEU* 3.7 19.9 - - + +
134D TRP* 3.7 19.5 - - + -
138D ASP* 4.4 9.7 - - + +
139D ASP 3.0 22.3 + - - +
140D PRO 3.8 3.8 - - - +
142D THR* 1.3 80.4 - - - +
144D HIS* 1.3 66.5 + - - +
146D LYS* 3.3 14.2 + - - +
147D TRP* 3.0 51.0 + - - +
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Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA 2.9 28.0 + - - -
113D PHE* 3.6 13.2 - + + -
124D CYS* 3.4 17.2 - - + +
127D CYS* 3.7 0.6 - - - -
131D LEU* 4.4 0.8 - - - +
140D PRO 2.9 13.9 + - - +
141D TRP* 3.2 17.9 - - - +
143D GLU* 1.3 76.7 - - - +
145D ALA* 1.3 53.9 + - - +
148D PHE* 2.8 54.3 + + + -
151D CYS* 3.6 5.0 - - - -
153D PHE* 4.3 7.0 - + - -
154D LEU* 3.9 20.2 - - + -
1001D ZN 2.1 37.4 - - - -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TRP 3.0 15.8 + - - +
142D THR 3.8 4.0 - - - +
143D GLU 3.3 0.2 - - - -
144D HIS* 1.3 74.5 - - - +
146D LYS* 1.3 61.3 + - - +
147D TRP 3.6 0.3 + - - -
149D PRO* 3.9 12.0 - - - +
154D LEU* 3.6 12.5 - - + +
162D PHE* 3.9 20.2 - - + -
163D VAL* 4.0 19.2 - - + +
166D VAL* 3.9 15.9 - - + -
167D GLN* 3.0 21.5 - - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 5.2 8.3 - - - -
73A ALA 5.1 2.4 + - - -
150A SER* 5.5 0.9 - - - -
142D THR* 2.8 20.4 + - + +
143D GLU* 3.3 20.3 + - - +
145D ALA* 1.3 77.9 - - - +
147D TRP* 1.3 100.4 + - + +
149D PRO* 4.5 0.3 - - - +
166D VAL* 3.6 16.1 - - + +
167D GLN* 3.0 17.4 + - - +
169D THR 5.9 0.9 - - - +
170D HIS 4.4 18.1 + - - +
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Residues in contact with TRP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.6 17.5 + - - -
74A THR* 5.1 0.9 - - + -
75A LEU* 3.8 33.7 - - + -
149A PRO* 5.3 0.3 - - - +
150A SER* 2.5 41.8 + - - -
160A ARG* 6.2 2.5 - - - -
131D LEU* 3.4 20.1 - - + +
143D GLU* 3.0 45.2 + - - +
146D LYS* 1.3 113.4 - - + +
148D PHE* 1.3 78.8 + - + +
149D PRO* 3.3 12.2 - - - +
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.4 34.8 - - + -
127A CYS* 6.5 1.3 - - + -
150A SER* 3.9 5.4 - - - -
113D PHE* 4.8 2.0 - + - -
127D CYS* 3.7 21.5 - - + -
129D GLY* 3.4 38.8 - - - -
130D GLY 3.4 10.1 - - - -
131D LEU* 3.7 21.3 - - + -
144D HIS* 2.8 35.6 + + + +
147D TRP* 1.3 86.6 - - + +
149D PRO* 1.3 64.3 - - - +
150D SER* 3.3 2.7 - - - -
151D CYS* 3.2 13.2 + - + +
154D LEU* 3.3 12.3 - - - +
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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