Contacts of the helix formed by residues 147 - 158 (chain B) in PDB entry 3P8P
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 ASN 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ASN 3.2 15.8 + - - -
124B ALA 3.8 0.2 - - - -
125B THR* 2.9 36.8 + - - +
142B LEU* 3.3 13.6 - - - +
146B THR* 1.3 77.6 - - - +
148B GLN* 1.3 65.2 + - + +
149B ARG* 3.2 8.2 + - - +
150B GLY 2.6 33.3 + - - -
151B ALA 3.1 15.8 + - - -
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Residues in contact with GLN 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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142B LEU* 3.4 28.6 - - + +
147B ASN* 1.3 74.6 - - + +
149B ARG* 1.3 52.3 + - + +
151B ALA* 3.3 3.8 + - - +
152B GLU* 2.8 71.6 + - - +
165B THR* 5.0 9.5 + - - +
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Residues in contact with ARG 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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121B ASP* 3.1 23.0 + - - +
123B ASN* 3.7 17.5 - - + +
124B ALA* 3.5 14.8 - - + -
147B ASN* 3.1 10.1 + - - +
148B GLN* 1.3 75.6 - - + +
150B GLY* 1.3 61.0 + - - +
152B GLU* 2.8 44.0 + - - +
153B ILE* 2.8 67.2 + - - +
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Residues in contact with GLY 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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119B MET* 3.2 26.5 - - - +
124B ALA* 3.6 6.6 - - - +
125B THR 3.3 20.2 - - - -
126B LEU* 3.4 12.0 - - - +
147B ASN* 2.6 15.4 + - - -
149B ARG* 1.3 72.4 - - - +
151B ALA* 1.3 59.5 + - - +
154B LEU 3.0 16.6 + - - -
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Residues in contact with ALA 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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126B LEU* 4.0 9.9 - - - +
140B VAL* 3.9 24.5 - - + -
142B LEU* 4.2 1.8 - - + -
146B THR* 4.4 0.2 - - - +
147B ASN 3.1 12.7 + - - +
148B GLN* 3.6 9.4 - - - +
150B GLY* 1.3 75.8 - - - +
152B GLU* 1.3 63.8 + - + +
154B LEU* 2.9 7.2 + - - +
155B ALA* 2.9 24.7 + - - +
163B VAL* 4.5 2.9 - - + +
165B THR* 4.0 22.9 - - + -
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Residues in contact with GLU 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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148B GLN* 2.8 50.5 + - - +
149B ARG* 2.8 59.2 + - - +
151B ALA* 1.3 76.8 - - - +
153B ILE* 1.3 54.4 + - - +
155B ALA* 3.5 6.0 + - - +
156B ASP* 2.9 28.8 + - - +
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Residues in contact with ILE 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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89B LEU* 4.9 5.6 - - + -
117B VAL* 5.4 5.4 - - + -
118B GLU 5.5 1.3 - - - +
119B MET* 3.9 32.3 - - + -
121B ASP* 3.8 12.1 - - + +
124B ALA* 3.5 28.3 - - + -
149B ARG* 2.8 48.9 + - - +
152B GLU* 1.3 70.3 - - - +
154B LEU* 1.3 52.9 + - - +
156B ASP* 3.1 19.4 - - + +
157B THR* 2.4 34.1 + - - +
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Residues in contact with LEU 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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82B VAL* 4.5 7.2 - - + -
89B LEU* 4.0 21.8 - - + -
119B MET* 4.6 0.2 - - - +
126B LEU* 3.9 10.8 - - + -
131B VAL* 3.5 39.7 - - + -
138B PHE* 4.2 12.3 - - + -
140B VAL* 3.9 8.3 - - + -
150B GLY 3.0 12.3 + - - +
151B ALA* 2.9 8.8 + - - +
153B ILE* 1.3 74.2 - - - +
155B ALA* 1.3 66.8 + - - +
156B ASP 3.0 1.3 - - - -
157B THR* 3.0 13.1 + - - -
158B PHE* 3.1 33.3 + - + -
163B VAL* 3.5 30.1 - - + -
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Residues in contact with ALA 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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151B ALA 2.9 11.9 + - - +
152B GLU* 3.9 6.3 - - - +
154B LEU* 1.3 77.0 - - - +
156B ASP* 1.3 62.8 + - - +
157B THR 3.3 0.7 + - - -
158B PHE 3.5 9.7 + - - +
159B LYS* 3.5 14.0 + - - +
161B TYR 4.8 1.1 - - - +
163B VAL* 3.2 44.5 - - + +
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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 GLU 2.9 20.2 + - - +
153B ILE* 3.1 22.5 - - - +
155B ALA* 1.3 76.9 - - - +
157B THR* 1.3 55.3 + - - +
159B LYS* 3.3 38.7 + - - +
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Residues in contact with THR 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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87B THR* 5.1 9.7 + - - +
88B ALA 5.4 1.3 - - - +
89B LEU* 4.1 11.5 - - + +
117B VAL* 3.1 52.7 - - + +
153B ILE* 2.4 29.3 + - - +
154B LEU* 3.0 6.5 + - - -
156B ASP* 1.3 77.9 - - - +
158B PHE* 1.3 71.9 + - + +
159B LYS* 3.2 10.1 + - - +
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Residues in contact with PHE 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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82B VAL* 3.7 33.0 - - + -
84B CYS* 3.2 31.2 - - + -
87B THR* 3.0 40.8 - - - -
88B ALA 4.8 0.2 - - - -
89B LEU* 4.0 21.3 - - + -
138B PHE* 3.7 30.5 - + + -
154B LEU* 3.1 34.5 + - + +
155B ALA 3.5 4.8 + - - +
157B THR* 1.3 82.9 - - + +
159B LYS* 1.3 53.3 + - - +
160B ASP* 3.0 5.8 - - - +
161B TYR* 2.7 36.8 + + + +
163B VAL* 4.8 1.6 - - + +
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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