Contacts of the helix formed by residues 140 - 148 (chain D) in PDB entry 3TWI
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 ILE 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LYS 4.0 14.8 - - - +
111D SER* 4.8 4.4 - - - -
133D TRP* 4.0 22.2 - - + -
134D ASP 3.5 18.4 + - - +
135D CYS* 4.0 23.3 - - - +
137D CYS* 3.0 23.4 + - - +
138D SER 3.0 0.8 - - - -
139D ASP* 1.3 79.0 - - - +
141D LEU* 1.3 69.0 + - + +
143D LEU* 3.0 32.8 + - + +
144D LYS* 3.2 11.5 + - + +
174D VAL* 4.3 10.3 - - + -
177D VAL* 4.2 9.6 - - + -
182D THR* 4.1 17.3 - - + -
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Residues in contact with LEU 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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138D SER* 3.5 18.8 - - - +
139D ASP 3.1 1.2 - - - -
140D ILE* 1.3 85.1 - - + +
142D TYR* 1.3 62.0 + - - +
144D LYS* 3.7 21.3 - - + +
145D ASN* 3.0 38.1 + - - +
177D VAL* 4.7 2.5 - - + +
178D THR 4.7 1.6 - - - -
179D GLU* 4.0 43.3 - - + +
182D THR* 4.4 18.6 - - + +
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Residues in contact with TYR 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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112D ILE* 3.5 36.3 - - + +
113D PRO 3.8 6.3 - - - -
114D MET* 4.1 27.8 - - - -
115D GLY* 3.3 30.0 - - - -
116D VAL* 3.7 8.7 - - + -
117D PHE* 3.1 29.0 + + - +
118D ASP* 2.8 24.8 + - - -
139D ASP 3.7 10.0 + - - +
140D ILE 3.2 1.4 + - - -
141D LEU* 1.3 77.3 - - - +
143D LEU* 1.3 56.6 + - - +
145D ASN* 3.7 7.4 + - + +
146D TRP* 3.0 40.4 + + + +
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Residues in contact with LEU 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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112D ILE* 3.9 28.5 - - + +
117D PHE* 4.4 4.7 - - + -
128D LEU* 4.0 17.5 - - + -
133D TRP* 3.6 46.9 - - + -
139D ASP 4.5 1.2 + - - +
140D ILE* 3.0 22.4 + - + +
142D TYR* 1.3 80.4 - - - +
144D LYS* 1.3 61.3 + - - +
146D TRP* 3.2 2.9 + - + -
147D ILE* 2.9 51.4 + - + +
165D VAL* 4.1 11.7 - - + -
174D VAL* 4.3 6.3 - - + -
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Residues in contact with LYS 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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140D ILE* 3.2 10.8 + - + +
141D LEU* 3.7 21.3 - - + +
143D LEU* 1.3 78.8 - - - +
145D ASN* 1.3 81.0 + - - +
147D ILE* 3.3 6.4 - - - +
148D VAL* 3.2 33.7 + - + +
174D VAL* 3.8 31.9 - - + +
175D ARG* 3.1 26.5 + - - +
176D ALA 4.3 1.2 - - - -
177D VAL* 2.5 32.3 + - + +
178D THR* 4.8 2.0 - - - +
179D GLU 5.6 0.2 - - - +
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Residues in contact with ASN 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 LEU* 3.0 28.3 + - - +
142D TYR* 4.0 7.7 - - + +
144D LYS* 1.3 98.1 - - - +
146D TRP* 1.3 60.5 + - - +
148D VAL* 3.9 5.5 + - - +
149D GLN* 2.8 38.5 + - - +
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Residues in contact with TRP 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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117D PHE* 3.7 43.4 + + + +
118D ASP* 4.5 5.1 + - - +
120D LEU 6.0 0.4 - - - -
123D LEU* 4.1 14.6 - - + -
126D ILE* 4.0 35.2 - - + -
128D LEU* 4.7 1.8 - - + -
142D TYR* 3.0 45.5 + + + +
143D LEU* 3.7 5.4 - - + +
144D LYS 3.2 0.2 - - - -
145D ASN* 1.3 76.5 - - - +
147D ILE* 1.3 78.0 + - + +
149D GLN* 3.1 8.9 + - - +
150D HIS* 2.9 60.4 + + + -
153D ILE* 4.2 10.5 - - + -
154D VAL* 3.9 20.9 - - + -
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Residues in contact with ILE 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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128D LEU* 4.1 12.8 - - + -
143D LEU* 2.9 35.2 + - + +
144D LYS 3.3 14.4 - - - +
146D TRP* 1.3 88.0 - - + +
148D VAL* 1.3 64.0 + - + +
150D HIS 3.1 12.5 + - - -
151D ALA* 3.4 14.9 + - - -
154D VAL* 4.3 16.4 - - + -
162D VAL* 3.7 30.4 - - + +
165D VAL* 4.2 13.2 - - + -
174D VAL* 3.9 28.3 - - + -
175D ARG 4.0 9.6 - - - +
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Residues in contact with VAL 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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144D LYS* 3.2 25.0 + - + +
145D ASN* 4.1 6.3 - - - +
146D TRP 3.2 1.0 - - - -
147D ILE* 1.3 76.7 - - - +
149D GLN* 1.3 64.6 + - + +
150D HIS 3.4 0.2 - - - -
151D ALA* 4.6 8.7 + - - +
162D VAL* 5.4 2.9 - - + -
175D ARG* 3.7 35.7 - - + +
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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