Contacts of the helix formed by residues 148 - 160 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 4.1 20.6 - - - +
144A ASP* 3.2 18.7 + - - +
145A LEU 3.4 6.9 + - - +
147A GLY* 1.3 86.3 - - - +
149A PRO* 1.3 67.2 - - - +
150A ASP* 2.5 46.4 + - - +
151A LEU* 2.9 53.0 + - + +
152A ARG 3.0 9.0 + - - -
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU 4.3 0.6 - - - +
146A ALA 5.0 3.4 - - - +
147A GLY* 3.8 6.3 - - - +
148A ARG* 1.3 86.0 - - - +
150A ASP* 1.3 63.7 + - - +
152A ARG* 3.6 10.0 - - + +
153A ALA* 3.1 26.0 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR* 5.6 2.5 - - - +
148A ARG* 2.5 40.4 + - + +
149A PRO* 1.3 79.9 - - + +
151A LEU* 1.3 63.7 + - - +
153A ALA* 4.0 3.5 - - - +
154A SER* 3.3 21.3 + - - -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR 3.6 24.2 - - - +
110A GLN* 4.9 0.2 - - - -
111A ALA* 3.7 14.7 - - + +
114A ARG* 3.6 42.2 - - - +
144A ASP* 4.0 7.2 - - - +
145A LEU* 3.6 17.2 - - + +
148A ARG* 2.9 51.2 + - + +
150A ASP* 1.3 77.1 - - - +
152A ARG* 1.3 67.8 + - - +
153A ALA 3.2 1.1 - - - -
154A SER* 3.8 5.4 - - - -
155A PHE* 3.0 27.0 + - - +
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 4.3 4.8 + - - -
145A LEU* 3.5 42.3 - - - +
146A ALA* 5.3 2.8 - - - +
148A ARG 3.0 6.4 + - - +
149A PRO* 3.6 14.6 - - + +
151A LEU* 1.3 76.9 - - - +
153A ALA* 1.3 57.5 + - + +
155A PHE* 3.7 13.5 - - - +
156A ASP* 2.8 63.7 + - - +
210A MET* 2.9 40.6 - - - +
211A ALA 3.8 17.9 + - - +
212A GLY* 4.4 11.7 - - - -
213A THR* 3.0 19.1 + - - -
635A SAH 3.3 20.6 + - - -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO 3.1 15.2 + - - +
150A ASP* 4.0 4.3 - - - +
152A ARG* 1.3 78.9 - - + +
154A SER* 1.3 63.1 + - - +
156A ASP* 3.6 7.8 + - - +
157A SER* 3.2 28.1 + - - -
189A LYS* 5.3 0.3 - - - -
216A THR* 5.9 2.7 - - - +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR 5.6 0.2 - - - -
110A GLN* 3.4 28.6 - - - +
111A ALA* 2.7 33.3 + - - +
150A ASP 3.3 15.8 + - - -
151A LEU* 4.2 3.2 - - - -
152A ARG 3.4 0.6 - - - -
153A ALA* 1.3 75.2 - - - +
155A PHE* 1.3 61.2 + - - +
157A SER* 3.5 4.8 + - - -
158A LEU* 3.0 33.9 + - - +
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.7 16.8 - - + -
112A VAL* 4.5 10.8 - - + -
141A PHE* 3.5 26.9 - + - -
142A TYR* 3.9 18.6 - + - -
145A LEU* 3.8 16.4 - - + -
151A LEU 3.0 18.9 + - - +
152A ARG* 3.7 7.9 - - - +
154A SER* 1.3 75.9 + - - +
156A ASP* 1.3 78.1 + - - +
158A LEU* 3.3 5.9 + - - +
159A LEU* 3.1 42.1 + - + +
600A ERT 3.6 46.2 - + - -
635A SAH 4.4 8.1 - + + -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 2.8 48.7 + - - +
153A ALA* 4.0 7.0 - - - +
154A SER 3.5 0.2 - - - -
155A PHE* 1.3 79.4 - - - +
157A SER* 1.3 56.6 + - - +
159A LEU* 3.7 3.4 + - - +
160A ALA* 3.1 31.5 + - - +
188A GLY* 5.9 0.8 - - - -
189A LYS* 4.0 21.6 - - + +
212A GLY 4.7 0.3 - - - -
213A THR* 2.7 39.5 + - + +
216A THR* 5.0 3.3 - - + +
635A SAH 4.4 2.4 + - - -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 5.8 1.3 - - - -
153A ALA 3.2 18.8 + - - -
154A SER* 3.9 5.8 - - - -
155A PHE 3.2 0.2 - - - -
156A ASP* 1.3 74.1 - - - +
158A LEU* 1.3 66.1 + - - +
160A ALA* 3.5 1.3 - - - +
161A CYS* 3.1 23.7 + - - +
189A LYS* 3.0 26.1 + - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 5.5 1.8 - - + -
104A ALA* 3.4 39.9 - - + +
105A TRP* 3.3 40.9 - - + +
110A GLN* 3.9 11.7 - - + +
111A ALA 4.5 5.2 - - - +
112A VAL* 3.4 43.1 - - + +
154A SER 3.0 22.8 + - - +
155A PHE* 3.3 5.4 + - - +
157A SER* 1.3 77.2 - - - +
159A LEU* 1.3 62.2 + - + +
161A CYS* 3.1 27.3 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.3 31.4 - - + -
112A VAL* 5.1 0.7 - - + -
155A PHE* 3.1 32.9 + - + +
156A ASP* 4.2 4.5 - - - +
158A LEU* 1.3 80.5 - - + +
160A ALA* 1.3 58.1 + - + +
161A CYS 3.4 0.7 - - - -
162A ASP* 4.8 0.9 + - - +
163A GLN 5.3 0.2 + - - -
167A PHE* 5.5 1.0 - - - -
600A ERT 3.4 101.4 + - + +
635A SAH 3.6 23.7 - - + +
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP 3.1 20.3 + - - +
157A SER* 3.5 4.3 - - - +
159A LEU* 1.3 77.3 - - + +
161A CYS* 1.3 58.0 + - - +
162A ASP 3.0 7.1 + - - +
163A GLN* 3.3 49.5 + - + +
167A PHE* 6.1 2.7 - - + -
189A LYS* 4.1 18.3 + - + +
635A SAH 5.6 2.0 - - - +
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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