Contacts of the helix formed by residues 158 - 167 (chain B) in PDB entry 3JTC
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 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B PHE* 3.5 7.4 - - - -
130B ARG* 2.7 28.1 + - - +
131B ALA* 2.8 27.3 + - + +
132B LEU* 3.5 21.2 - - - +
133B TRP* 5.1 0.7 - - + -
151B LEU 3.5 15.3 - - - +
152B ASN* 3.4 28.8 + - - +
153B ALA 5.0 0.7 - - - -
154B TYR 3.1 20.3 + - - +
157B THR* 1.4 77.2 - - - +
159B TYR* 1.3 97.6 + - + +
160B GLU 3.5 0.2 - - - -
161B LEU* 3.5 1.2 + - - +
162B ARG* 2.9 27.5 + - - +
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Residues in contact with TYR 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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130B ARG 4.3 2.5 + - - -
131B ALA* 4.2 5.8 - - + -
155B ASN* 3.0 29.4 + - + +
158B ARG* 1.3 119.1 + - + +
160B GLU* 1.3 63.0 + - + +
162B ARG* 3.3 38.1 + - - +
163B GLU* 2.8 43.3 + - - +
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Residues in contact with GLU 160 (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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155B ASN* 3.0 19.8 + - + +
156B ARG* 2.8 64.4 + - - +
159B TYR* 1.3 76.9 - - + +
161B LEU* 1.3 57.0 + - - +
163B GLU* 3.3 19.7 + - - +
164B PHE 2.9 24.1 + - - -
607B PTY 3.4 22.8 + - - +
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Residues in contact with LEU 161 (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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114B PHE* 3.7 37.2 - - + -
126B PHE* 3.7 28.7 - - + -
133B TRP* 3.7 28.9 - - + -
156B ARG 3.3 6.8 + - - +
157B THR* 3.6 21.8 - - - +
158B ARG 3.7 1.1 - - - +
160B GLU* 1.3 74.5 - - - +
162B ARG* 1.3 66.5 + - - +
164B PHE* 3.1 14.3 + - + +
165B LEU* 3.1 18.1 + - + +
607B PTY 4.1 39.5 - - + +
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Residues in contact with ARG 162 (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 ARG* 6.1 1.1 - - - -
112B VAL* 5.8 0.2 - - + -
126B PHE* 3.9 15.5 - - + -
128B PRO* 2.9 31.8 + - + -
129B GLU 3.0 19.2 + - - -
130B ARG* 3.9 2.4 - - - +
131B ALA* 3.5 22.2 - - - +
158B ARG 2.9 14.2 + - - +
159B TYR* 3.4 32.9 - - - +
161B LEU* 1.3 75.4 - - - +
163B GLU* 1.3 58.0 + - + +
165B LEU* 3.0 7.3 + - - +
166B GLU* 2.9 54.8 + - + +
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Residues in contact with GLU 163 (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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159B TYR* 2.8 29.0 + - - +
160B GLU* 3.4 17.0 - - - +
162B ARG* 1.3 70.4 - - + +
164B PHE* 1.3 67.7 + - - +
166B GLU* 4.6 1.8 - - - +
167B ASP* 2.8 42.3 + - + +
168B THR* 3.2 1.7 + - - -
607B PTY 3.1 29.5 + - - -
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Residues in contact with PHE 164 (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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13B MET* 3.9 15.7 - - + -
69B LEU* 4.9 4.9 - - + -
99B LEU* 3.8 24.0 - - + -
114B PHE* 6.1 0.9 - + - -
160B GLU 2.9 7.9 + - - +
161B LEU* 3.1 9.8 + - + +
163B GLU* 1.3 75.6 - - - +
165B LEU* 1.3 68.5 - - + +
168B THR* 3.3 19.9 - - + -
169B CYS* 2.8 33.6 + - + +
607B PTY 3.3 111.6 - - + +
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Residues in contact with LEU 165 (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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13B MET* 5.2 0.9 - - + -
99B LEU* 4.1 10.5 - - + -
100B GLY* 3.9 20.4 - - - +
101B CYS* 3.5 3.8 - - - +
112B VAL* 3.5 39.9 - - + +
113B PHE 3.8 27.8 - - - +
114B PHE* 4.2 3.4 - - + -
126B PHE* 4.0 25.4 - - + -
161B LEU* 3.1 21.9 + - + +
162B ARG 3.0 7.0 + - - +
164B PHE* 1.3 93.6 - - + +
166B GLU* 1.3 61.1 + - - +
169B CYS* 3.1 23.0 - - + +
170B VAL* 3.6 1.7 - - - +
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Residues in contact with GLU 166 (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 ARG* 3.1 44.7 + - + +
110B ALA* 5.1 5.4 - - + +
112B VAL* 3.8 22.6 - - + +
128B PRO* 3.7 23.0 - - - +
162B ARG* 2.9 42.6 + - + +
163B GLU* 5.0 1.6 - - - -
165B LEU* 1.3 72.1 - - - +
167B ASP* 1.3 59.4 + - - +
170B VAL* 3.3 25.1 - - - +
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Residues in contact with ASP 167 (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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163B GLU* 2.8 24.7 + - + +
165B LEU 3.4 0.2 - - - -
166B GLU* 1.3 80.0 - - + +
168B THR* 1.3 66.5 + - - +
169B CYS 3.4 0.7 - - - -
170B VAL* 3.9 0.6 - - - +
171B GLN* 2.8 54.6 + - - +
607B PTY 6.1 0.7 - - - -
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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