Contacts of the helix formed by residues 136 - 148 (chain B) in PDB entry 3TNP
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 THR 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 1.3 76.5 - - - +
137B ASP* 1.3 65.6 + - - +
138B ASP* 3.5 8.0 + - - +
139B GLN* 2.9 42.2 + - - +
140B ARG* 3.0 20.4 + - - +
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Residues in contact with ASP 137 (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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135B LYS 3.7 1.0 + - - -
136B THR* 1.3 73.5 - - - +
138B ASP* 1.3 57.8 + - - +
140B ARG* 3.3 9.4 + - - +
141B ASN* 3.0 38.8 + - - +
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Residues in contact with ASP 138 (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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136B THR* 3.2 6.9 + - - +
137B ASP* 1.3 75.1 - - - +
139B GLN* 1.3 66.1 + - - +
140B ARG 3.0 1.6 - - - -
141B ASN* 3.1 12.0 + - - +
142B ARG* 2.7 63.4 + - - +
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Residues in contact with GLN 139 (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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135B LYS* 3.4 13.2 - - + +
136B THR* 2.9 47.7 + - - +
138B ASP* 1.3 75.9 - - - +
140B ARG* 1.3 57.8 + - - +
142B ARG* 3.8 16.9 - - - +
143B LEU* 3.0 30.7 + - - +
170B GLU* 5.1 6.7 + - - -
193B ASP* 3.5 31.6 + - - +
243B TRP* 3.6 28.5 + - + -
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Residues in contact with ARG 140 (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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132B ILE* 5.5 2.6 - - - +
133B HIS 4.9 3.0 + - - -
134B PRO* 6.0 0.4 - - - +
135B LYS* 4.2 33.2 + - + +
136B THR 3.0 16.8 + - - +
137B ASP* 3.6 9.0 - - - +
138B ASP 3.0 0.2 - - - -
139B GLN* 1.3 76.3 - - - +
141B ASN* 1.3 63.1 + - - +
143B LEU* 3.7 5.8 - - - +
144B GLN* 3.0 29.7 + - - +
162B SER* 3.6 23.0 + - - +
165B LEU* 3.7 29.8 - - + +
166B ASP* 2.6 37.4 + - - +
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Residues in contact with ASN 141 (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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137B ASP* 3.0 26.6 + - - +
138B ASP* 3.1 12.6 + - - +
140B ARG* 1.3 81.4 - - - +
142B ARG* 1.3 58.5 + - + +
144B GLN* 3.4 8.9 + - - +
145B GLU* 3.0 27.9 + - - +
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Residues in contact with ARG 142 (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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138B ASP* 2.7 55.2 + - - +
139B GLN* 3.8 17.9 - - - +
141B ASN* 1.3 74.4 - - + +
143B LEU* 1.3 60.7 + - - +
145B GLU* 3.3 7.3 + - - +
146B ALA* 2.9 29.3 + - - +
191B VAL* 6.1 0.2 - - - -
192B ILE 5.2 0.4 + - - -
193B ASP* 2.7 53.3 + - - +
194B ARG* 5.2 0.8 - - - +
215B ASN 5.4 0.2 + - - -
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Residues in contact with LEU 143 (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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135B LYS* 3.8 35.2 - - + -
139B GLN 3.0 15.9 + - - +
140B ARG* 3.7 4.9 - - - +
142B ARG* 1.3 77.9 - - - +
144B GLN* 1.3 60.9 + - - +
146B ALA* 3.4 4.3 + - - +
147B CYS* 3.2 29.8 + - - -
165B LEU* 3.8 19.1 - - + -
168B MET* 4.0 21.8 - - + -
191B VAL* 3.9 27.6 - - + -
243B TRP* 3.7 35.0 - - + +
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Residues in contact with GLN 144 (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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140B ARG* 3.0 19.6 + - - +
141B ASN* 3.5 10.1 - - - +
143B LEU* 1.3 78.4 - - - +
145B GLU* 1.3 61.6 + - - +
147B CYS* 3.2 12.1 + - - +
148B LYS* 3.2 15.8 + - + +
158B PRO* 6.2 0.6 - - - +
161B MET* 3.7 32.7 - - + +
165B LEU* 3.7 24.6 - - + +
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Residues in contact with GLU 145 (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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141B ASN 3.0 18.2 + - - +
142B ARG* 3.3 7.6 + - - +
144B GLN* 1.3 73.8 - - - +
146B ALA* 1.3 64.2 + - - +
148B LYS* 3.0 58.3 - - - +
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Residues in contact with ALA 146 (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 ARG 2.9 15.7 + - - +
143B LEU 3.7 6.3 - - - +
144B GLN 3.3 0.2 - - - -
145B GLU* 1.3 76.7 - - - +
147B CYS* 1.3 59.3 + - - +
148B LYS 3.5 0.4 + - - -
149B ASP 4.8 2.0 + - - -
150B ILE* 4.0 15.2 - - - +
191B VAL* 3.8 29.6 - - + -
217B GLY 5.7 2.5 - - - +
218B SER* 4.9 5.8 + - - -
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Residues in contact with CYS 147 (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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143B LEU* 3.2 22.6 + - - +
144B GLN 3.2 2.8 + - - -
146B ALA* 1.3 78.2 - - - +
148B LYS* 1.3 65.0 + - - +
149B ASP 3.3 2.5 - - - -
150B ILE* 3.2 12.5 + - - +
153B PHE* 3.2 52.1 - - + +
161B MET* 3.8 19.3 - - + -
165B LEU* 5.1 3.1 - - - -
168B MET* 5.0 6.3 - - - -
189B PHE* 4.2 14.1 - - - -
191B VAL* 4.2 11.2 - - - -
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Residues in contact with LYS 148 (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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144B GLN* 3.2 12.1 + - + +
145B GLU* 3.0 54.7 - - - +
146B ALA 3.5 0.2 - - - -
147B CYS* 1.3 78.8 - - - +
149B ASP* 1.3 87.4 + - - +
154B LYS* 2.9 26.6 - - - +
161B MET* 5.1 4.3 - - + -
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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