Contacts of the helix formed by residues 153 - 169 (chain B) in PDB entry 1PN9
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 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS 5.0 0.9 - - - +
82B LEU* 3.2 23.3 - - - +
84B PRO* 4.4 9.2 - - + -
93B VAL* 3.8 24.2 - - + +
148B ALA* 4.5 8.2 - - + +
151B ASP* 3.3 21.8 - - + +
152B LEU* 1.3 84.2 - - - +
154B ILE* 1.3 59.2 + - - +
155B ALA* 2.9 23.5 + - - +
156B ASP* 2.9 29.0 + - - +
157B LEU* 3.3 7.3 + - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 3.8 28.3 - - + +
69B GLN* 3.0 22.4 - - + +
70B ILE* 3.7 34.3 - - + +
73B ALA* 4.4 8.1 - - + -
82B LEU* 3.0 32.9 + - + +
83B TYR* 3.5 30.7 - - + -
93B VAL* 4.0 5.8 - - + -
97B LEU* 3.8 9.8 - - + +
153B THR* 1.3 69.7 - - - +
155B ALA* 1.3 59.5 + - - +
156B ASP 3.3 0.2 - - - -
157B LEU* 3.3 8.7 + - + -
158B SER* 2.9 25.3 + - - -
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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
----------------------------------------------------------
93B VAL* 3.8 16.8 - - + +
96B ARG* 3.7 32.3 - - + -
97B LEU* 3.6 12.3 - - + +
147B ALA* 4.6 4.7 - - + -
148B ALA* 4.9 1.1 - - + -
153B THR* 2.9 14.2 + - - +
154B ILE* 1.3 82.0 - - - +
156B ASP* 1.3 57.4 + - - +
158B SER* 3.2 2.1 + - - -
159B LEU* 2.9 36.7 + - - +
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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
----------------------------------------------------------
146B TYR* 3.4 25.5 - - - +
147B ALA* 2.9 21.8 + - - +
148B ALA 4.8 0.9 + - - -
151B ASP 3.8 0.5 - - - +
152B LEU* 3.4 13.6 - - + -
153B THR* 2.9 34.2 + - - +
155B ALA* 1.3 78.1 - - - +
157B LEU* 1.3 57.7 + - - +
159B LEU* 3.7 1.1 - - - -
160B ALA* 2.8 33.5 + - - +
182B TRP* 2.8 35.1 + - - +
186B CYS* 4.3 6.7 - - - -
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Residues in contact with LEU 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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14B ALA* 4.2 2.6 - - - +
17B MET* 3.2 37.5 - - + +
18B THR* 3.5 36.8 - - - +
21B ALA* 4.3 11.2 - - + -
69B GLN* 4.0 6.5 - - - +
82B LEU* 4.5 8.3 - - + -
152B LEU* 4.0 12.1 - - + -
153B THR 3.3 9.3 + - - +
154B ILE* 3.6 17.0 - - + +
155B ALA 3.2 0.4 - - - -
156B ASP* 1.3 78.5 - - - +
158B SER* 1.3 62.0 + - - +
160B ALA* 4.4 1.1 - - - -
161B ALA* 3.1 17.8 + - - +
190B ALA* 3.6 32.3 - - + -
191B PRO* 4.4 3.1 - - + -
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Residues in contact with SER 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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14B ALA* 3.9 13.1 - - - +
66B ARG* 3.2 14.4 + - - -
69B GLN* 3.5 21.5 + - - -
97B LEU* 3.9 10.5 - - - -
100B ASP* 2.4 29.6 + - - -
154B ILE 2.9 13.3 + - - -
155B ALA 3.7 3.6 - - - -
157B LEU* 1.3 78.1 - - - +
159B LEU* 1.3 63.1 + - - +
161B ALA* 3.1 13.7 + - - +
162B THR* 3.1 14.7 + - - -
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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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96B ARG* 4.3 15.5 - - + +
99B PHE* 4.1 13.9 - - + -
100B ASP* 3.5 34.3 - - + +
104B LEU* 3.6 19.3 - - + -
137B LEU* 4.1 15.5 - - + -
147B ALA* 3.4 32.5 - - + -
155B ALA 2.9 20.2 + - - +
158B SER* 1.3 76.3 - - - +
160B ALA* 1.3 57.1 + - - +
162B THR* 3.4 1.7 + - - -
163B ILE* 2.8 34.7 + - - +
182B TRP* 3.6 19.7 - - + -
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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
----------------------------------------------------------
17B MET* 4.5 5.4 - - + -
156B ASP 2.8 23.5 + - - +
157B LEU* 3.9 6.1 - - - +
159B LEU* 1.3 70.5 - - - +
161B ALA* 1.3 61.5 + - - +
163B ILE* 4.4 2.7 - - - -
164B ALA* 2.9 30.5 + - - +
182B TRP* 3.7 7.6 - - + -
183B PHE* 4.2 4.8 - - + -
186B CYS* 4.2 26.2 - - + -
190B ALA* 5.6 2.0 - - + -
193B TYR* 4.5 12.1 - - + -
196B ASN* 3.2 3.5 + - - -
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Residues in contact with ALA 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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10B ALA* 3.4 28.5 - - + +
13B ARG* 2.8 11.2 + - + -
14B ALA* 3.8 15.3 - - + +
17B MET* 3.8 2.2 - - + +
157B LEU 3.1 13.1 + - - +
158B SER 3.1 9.8 + - - +
160B ALA* 1.3 76.5 - - - +
162B THR* 1.3 60.4 + - - +
165B THR* 2.8 24.1 + - - -
196B ASN* 3.4 18.8 - - - +
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 4.2 7.7 - - - +
66B ARG* 4.4 1.4 + - - -
100B ASP* 2.7 32.6 + - - +
104B LEU* 3.6 29.2 - - + -
105B TYR* 3.8 29.3 - - + +
158B SER 3.1 4.5 + - - -
159B LEU 3.6 4.5 - - - -
160B ALA 3.2 0.2 - - - -
161B ALA* 1.3 78.0 - - - +
163B ILE* 1.3 57.7 + - - +
165B THR* 3.0 23.0 + - - -
166B TYR* 3.1 27.0 + - + -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.7 32.3 - - + -
134B VAL* 4.9 3.4 - - + -
137B LEU* 4.1 11.2 - - + -
159B LEU 2.8 21.3 + - - +
160B ALA 4.2 2.7 - - - +
162B THR* 1.3 71.5 - - - +
164B ALA* 1.3 60.6 + - - +
165B THR 3.0 1.8 - - - -
166B TYR* 3.0 10.9 + - + +
167B GLU* 2.8 26.7 + - - +
173B PHE* 3.7 30.7 - - + -
179B VAL* 4.6 2.5 - - + -
182B TRP* 3.6 22.4 - - + -
183B PHE* 3.7 29.6 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 4.1 3.4 - - - +
160B ALA 2.9 20.9 + - - +
161B ALA 3.9 4.5 - - - +
162B THR 3.3 0.2 - - - -
163B ILE* 1.3 77.5 - - - +
165B THR* 1.3 62.2 + - - +
167B GLU* 3.5 6.2 + - - +
168B VAL* 3.2 27.4 + - - +
183B PHE* 3.7 11.0 - - - -
193B TYR* 3.8 10.3 - - - +
196B ASN* 3.3 24.5 - - - +
197B GLN* 5.8 1.1 - - - -
200B ALA* 4.0 10.5 - - + +
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Residues in contact with THR 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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8B GLY 5.2 0.4 - - - +
10B ALA* 3.6 8.3 - - + +
13B ARG* 2.8 22.5 + - - +
105B TYR* 5.5 2.9 - - + -
108B PHE* 3.5 29.8 - - + -
161B ALA 2.8 17.2 + - - -
162B THR* 3.0 8.6 + - - -
164B ALA* 1.3 78.0 - - - +
166B TYR* 1.3 66.1 + - - +
168B VAL* 3.0 22.1 - - + +
169B ALA* 3.1 10.6 + - - +
200B ALA* 5.0 0.2 - - - -
203B PHE* 3.7 28.5 - - + -
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Residues in contact with TYR 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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104B LEU* 2.6 47.2 + - + +
108B PHE* 3.5 29.9 + + + -
130B MET* 3.3 40.2 + - + +
133B ALA* 4.2 1.4 - - - +
134B VAL* 3.5 21.8 - - + -
162B THR* 3.1 38.0 + - + -
163B ILE* 3.0 14.3 + - + +
165B THR* 1.3 76.3 - - - +
167B GLU* 1.3 62.1 + - - +
169B ALA* 3.0 17.2 + - - +
171B PHE* 3.1 40.1 + + + +
173B PHE* 3.8 11.4 - + + -
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Residues in contact with GLU 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 ILE 2.8 12.3 + - - +
164B ALA* 3.6 11.2 - - - +
166B TYR* 1.3 72.2 - - - +
168B VAL* 1.3 59.1 + - + +
169B ALA 2.9 4.0 - - - -
170B GLY* 2.7 27.0 + - - -
171B PHE 4.0 3.2 + - - +
173B PHE* 4.0 20.5 - - + -
183B PHE* 3.4 21.6 - - + -
187B LYS* 2.8 30.5 + - - -
193B TYR* 5.0 0.7 + - - -
197B GLN* 4.6 13.0 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA 3.2 13.9 + - - +
165B THR* 3.0 22.2 - - - +
167B GLU* 1.3 79.8 - - + +
169B ALA* 1.3 58.3 + - - +
170B GLY* 3.1 2.0 + - - -
197B GLN* 5.0 4.5 - - - +
200B ALA* 3.7 37.2 - - + +
201B ASP* 4.1 13.7 - - - +
203B PHE* 4.4 5.4 - - + -
204B LYS* 3.3 34.2 - - + +
207B PHE* 4.0 19.2 - - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.9 11.7 - - + -
112B HIS* 4.0 15.6 - - + +
165B THR 3.1 12.7 + - - +
166B TYR* 3.1 13.2 - - - +
167B GLU 2.9 0.8 - - - -
168B VAL* 1.3 78.7 - - - +
170B GLY* 1.3 59.2 + - - +
171B PHE* 3.5 2.1 + - + +
207B PHE* 3.4 32.5 - - + -
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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
------------------------------------------------------------
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