Contacts of the helix formed by residues 148 - 160 (chain B) in PDB entry 1TW2
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 ARG 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ARG* 3.7 27.1 - - - +
144B ASP* 3.2 20.0 + - - +
145B LEU 3.1 7.7 + - - +
146B ALA 3.2 0.8 - - - -
147B GLY* 1.3 82.8 - - - +
149B PRO* 1.3 70.1 - - - +
150B ASP* 3.0 38.1 + - - +
151B LEU* 3.0 40.7 + - + +
152B ARG 3.0 9.9 + - - -
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU 4.1 0.6 - - - +
146B ALA 4.8 4.7 - - - +
147B GLY 3.8 6.1 - - - +
148B ARG* 1.3 87.6 - - + +
150B ASP* 1.3 57.8 + - - +
152B ARG* 3.6 8.6 - - + +
153B ALA* 3.1 28.1 + - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR 4.7 5.6 - - - +
148B ARG* 3.0 46.1 + - - +
149B PRO* 1.3 73.0 - - - +
151B LEU* 1.3 64.2 + - - +
153B ALA* 3.6 4.9 + - - +
154B SER* 3.0 29.7 + - - -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR 3.6 24.2 - - - +
110B GLN* 4.4 0.4 - - - -
111B ALA* 3.5 18.2 - - + +
114B ARG* 3.4 48.2 - - - +
133B TYR* 4.5 0.4 - - - +
144B ASP* 3.9 10.1 - - - +
145B LEU* 3.9 19.3 - - + -
148B ARG* 3.0 41.1 + - + +
150B ASP* 1.3 75.8 + - - +
152B ARG* 1.3 66.4 + - - +
154B SER* 3.4 4.1 + - - -
155B PHE* 3.0 26.5 + - - +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 4.0 6.1 + - - -
145B LEU* 3.4 44.2 + - - +
146B ALA* 5.1 4.2 - - - +
148B ARG 3.0 5.4 + - - +
149B PRO* 3.6 13.0 - - + +
151B LEU* 1.3 76.7 - - - +
153B ALA* 1.3 57.6 + - - +
155B PHE* 3.4 18.4 + - - +
156B ASP* 2.6 62.9 + - - +
210B MET* 3.1 37.4 - - - +
211B ALA 3.6 17.7 - - - +
212B GLY* 4.4 10.5 - - - -
213B THR* 2.8 21.8 + - - +
1635B SAH 3.2 19.2 + - - -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO 3.1 14.7 + - - +
150B ASP* 3.9 5.2 - - - +
152B ARG* 1.3 81.0 - - - +
154B SER* 1.3 59.0 + - - +
156B ASP* 4.0 7.9 - - - +
157B SER* 3.1 31.6 + - - +
189B LYS* 5.2 0.3 + - - -
216B THR* 5.7 5.4 - - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR 4.8 0.2 + - - -
110B GLN* 3.4 35.5 - - - +
111B ALA 3.0 26.7 + - - -
150B ASP 3.0 19.4 + - - -
151B LEU* 3.3 4.9 + - - -
153B ALA* 1.3 75.2 - - - +
155B PHE* 1.3 64.9 + - - +
157B SER* 4.1 4.1 - - - -
158B LEU* 3.1 32.5 + - - +
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 3.7 8.9 - - + +
112B VAL* 4.2 13.9 - - + -
141B PHE* 3.9 14.6 - + - -
142B TYR* 4.1 16.6 - + - -
145B LEU* 3.6 15.9 - - + -
151B LEU 3.0 18.2 + - - +
152B ARG* 3.7 27.4 - - - +
154B SER* 1.3 76.1 + - - +
156B ASP* 1.3 66.6 + - - +
158B LEU* 3.3 6.1 + - - +
159B LEU* 3.1 56.6 + - + +
1600B ERT 3.4 45.5 - + - -
1635B SAH 4.2 7.0 - + - -
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 2.6 50.9 + - - +
153B ALA* 4.0 7.3 + - - +
155B PHE* 1.3 80.6 - - - +
157B SER* 1.3 56.0 + - - +
159B LEU* 3.5 3.8 + - - +
160B ALA* 3.1 30.8 + - - +
188B GLY* 5.9 1.6 - - - -
189B LYS* 3.7 20.8 - - + +
212B GLY 4.7 0.3 - - - -
213B THR* 2.7 37.1 + - + +
216B THR* 4.7 4.5 - - + +
1635B SAH 4.5 2.3 + - - -
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ALA* 3.1 20.0 + - - +
154B SER* 4.1 4.7 - - - -
155B PHE 3.2 0.2 - - - -
156B ASP* 1.3 74.1 - - - +
158B LEU* 1.3 64.4 + - - +
160B ALA* 3.9 1.7 - - - +
161B CYS* 3.3 18.4 + - - -
189B LYS* 3.2 25.2 + - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA* 5.3 2.9 - - + -
104B ALA* 3.7 35.9 - - + +
105B TRP* 3.6 49.0 - - + +
110B GLN* 4.6 8.1 - - + +
111B ALA 4.7 3.1 - - - +
112B VAL* 3.7 36.1 - - + +
154B SER 3.1 29.1 + - - +
155B PHE* 3.7 4.3 - - - +
157B SER* 1.3 75.4 - - - +
159B LEU* 1.3 66.3 + - + +
161B CYS* 3.3 25.7 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TRP* 4.1 22.4 - - + -
112B VAL* 5.3 0.4 - - + -
155B PHE* 3.1 50.4 + - + +
156B ASP* 4.0 4.3 - - - +
158B LEU* 1.3 78.6 - - + +
160B ALA* 1.3 56.5 - - - +
161B CYS* 3.2 6.5 + - - +
162B ASP 5.0 0.5 + - - -
167B PHE* 5.8 0.9 - - - -
252B PHE* 6.1 0.4 - - + -
1600B ERT 3.0 64.3 + - + +
1635B SAH 3.4 44.2 - - + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP 3.1 18.6 + - - +
157B SER* 3.8 3.1 + - - +
159B LEU* 1.3 74.3 - - - +
161B CYS* 1.3 65.5 + - - +
162B ASP 3.4 2.5 - - - -
163B GLN* 2.9 50.9 + - - +
167B PHE* 5.9 1.8 - - + -
189B LYS* 3.8 23.1 - - + +
1635B SAH 5.8 0.9 - - - -
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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