Contacts of the helix formed by residues 153 - 170 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LYS 3.5 16.6 - - - +
82A LEU* 3.0 20.9 - - - +
84A PRO* 4.5 4.3 - - + -
93A VAL* 3.9 22.3 - - + +
148A ALA* 4.3 9.3 - - + +
151A ASP* 3.5 14.8 - - + +
152A LEU* 1.3 78.4 - - - +
154A ILE* 1.3 59.9 + - - +
155A ALA* 3.2 22.7 + - - +
156A ASP* 2.8 35.1 + - - +
157A LEU* 3.3 7.5 + - - +
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Residues in contact with ILE 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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18A THR* 3.8 21.8 - - + +
69A GLN* 2.9 47.0 + - + +
70A ILE* 5.0 1.8 - - + +
73A ALA* 3.9 13.0 - - + -
82A LEU* 3.1 52.7 + - + +
83A TYR* 4.4 9.4 - - + -
93A VAL* 5.2 0.9 - - + -
97A LEU* 3.9 15.5 - - + -
153A THR* 1.3 75.8 - - - +
155A ALA* 1.3 62.2 + - - +
157A LEU* 3.1 7.0 + - + -
158A SER* 2.9 19.9 + - - -
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Residues in contact with ALA 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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93A VAL* 3.9 19.1 - - + +
96A ARG* 3.7 32.5 - - + -
97A LEU* 3.6 14.0 - - + +
147A ALA* 4.7 4.0 - - + -
148A ALA* 4.9 1.3 - - + -
153A THR* 3.0 13.6 + - - +
154A ILE* 1.3 78.9 - - - +
156A ASP* 1.3 57.8 + - - +
158A SER* 3.2 2.1 + - - -
159A LEU* 2.8 35.6 + - - +
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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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146A TYR* 3.3 23.3 - - - +
147A ALA* 2.8 30.6 + - - +
148A ALA 4.8 0.9 + - - -
151A ASP 3.7 0.7 - - - +
152A LEU* 3.2 21.1 - - + -
153A THR* 2.8 31.7 + - - +
155A ALA* 1.3 76.6 - - - +
157A LEU* 1.3 58.3 + - - +
159A LEU* 3.8 6.8 - - - +
160A ALA* 2.8 32.5 + - - +
182A TRP* 2.9 22.0 + - - +
186A CYS* 4.4 2.8 - - - -
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Residues in contact with LEU 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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14A ALA* 4.0 6.3 - - - +
17A MET* 3.2 31.2 - - + +
18A THR* 3.5 37.9 - - - +
21A ALA* 4.3 12.1 - - + -
69A GLN* 3.7 8.5 - - - +
82A LEU* 4.6 5.8 - - + -
152A LEU* 4.8 7.2 - - + -
153A THR 3.8 9.9 - - - +
154A ILE* 3.1 17.0 + - + +
156A ASP* 1.3 78.9 - - - +
158A SER* 1.3 60.9 + - - +
160A ALA* 3.5 3.1 + - + -
161A ALA* 3.1 18.7 + - - +
190A ALA* 3.9 27.6 - - + -
191A PRO* 4.4 10.3 - - + -
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Residues in contact with SER 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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14A ALA* 3.9 14.0 - - - +
66A ARG* 3.1 18.5 + - - +
69A GLN* 3.4 19.3 + - - +
97A LEU* 3.8 11.0 - - - -
100A ASP* 2.4 34.9 + - - +
154A ILE 2.9 9.3 + - - -
155A ALA 3.6 7.4 - - - -
157A LEU* 1.3 78.5 - - - +
159A LEU* 1.3 63.0 + - - +
161A ALA* 3.2 14.0 + - - +
162A THR* 3.2 9.7 + - - -
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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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96A ARG* 4.4 13.9 - - + +
99A PHE* 4.1 17.7 - - + -
100A ASP* 3.7 23.1 - - + +
104A LEU* 3.5 26.0 - - + -
137A LEU* 4.1 16.4 - - + -
147A ALA* 3.3 33.9 - - + -
155A ALA 2.8 19.5 + - - +
158A SER* 1.3 78.6 - - - +
160A ALA* 1.3 56.1 + - - +
162A THR* 3.4 1.7 + - - -
163A ILE* 2.9 34.8 + - - +
182A TRP* 3.6 19.3 - - + -
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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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17A MET* 4.2 11.0 - - + -
156A ASP 2.8 23.3 + - - +
157A LEU* 3.7 7.2 - - + +
159A LEU* 1.3 71.1 - - - +
161A ALA* 1.3 66.6 + - - +
163A ILE* 4.1 2.1 - - - +
164A ALA* 3.0 21.1 + - - +
182A TRP* 3.9 7.6 - - + -
183A PHE* 4.3 5.2 - - + -
186A CYS* 4.4 17.3 - - + -
193A TYR* 4.3 16.2 - - + -
196A ASN* 3.3 10.0 + - - -
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Residues in contact with ALA 161 (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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10A ALA* 3.3 29.7 - - - +
13A ARG* 2.9 10.8 + - - +
14A ALA* 3.7 15.5 - - + +
17A MET* 3.8 1.3 - - + +
157A LEU 3.1 11.3 + - - +
158A SER 3.4 9.6 - - - +
160A ALA* 1.3 80.1 - - - +
162A THR* 1.3 59.4 + - - +
164A ALA 3.8 0.2 + - - -
165A THR* 2.9 22.5 + - - -
196A ASN* 3.3 19.1 - - - +
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Residues in contact with THR 162 (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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10A ALA* 4.4 7.5 - - - +
66A ARG* 4.5 1.4 + - - -
100A ASP* 2.8 30.3 + - - +
104A LEU* 3.6 18.6 - - + -
105A TYR* 3.8 27.3 - - + +
108A PHE* 5.2 0.4 - - + -
158A SER 3.2 2.3 + - - -
159A LEU 3.6 4.9 - - - -
160A ALA 3.1 0.2 - - - -
161A ALA* 1.3 77.7 - - - +
163A ILE* 1.3 60.7 + - - +
165A THR* 3.0 23.9 + - - -
166A TYR* 3.0 35.6 + - + -
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Residues in contact with ILE 163 (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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104A LEU* 3.9 28.5 - - + -
134A VAL* 5.2 2.5 - - + -
137A LEU* 4.1 12.1 - - + -
159A LEU 2.9 21.9 + - - +
160A ALA 4.1 2.5 - - - +
162A THR* 1.3 71.9 - - - +
164A ALA* 1.3 55.5 + - - +
166A TYR* 2.9 12.4 + - + +
167A GLU* 2.7 32.9 + - - +
173A PHE* 3.6 32.5 - - + -
179A VAL* 4.6 3.4 - - + -
182A TRP* 3.7 21.3 - - + -
183A PHE* 3.7 32.3 - - + -
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Residues in contact with ALA 164 (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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160A ALA 3.0 19.0 + - - +
161A ALA 4.0 4.0 - - - +
163A ILE* 1.3 76.0 - - - +
165A THR* 1.3 61.5 + - - +
167A GLU* 3.6 5.7 - - - +
168A VAL* 3.2 28.1 + - - +
183A PHE* 3.6 12.5 - - + -
193A TYR* 3.9 11.2 - - - +
196A ASN* 3.4 22.4 - - - +
197A GLN* 5.8 0.9 - - - -
200A ALA* 3.8 15.5 - - + +
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Residues in contact with THR 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLY 5.3 0.2 - - - +
10A ALA* 3.7 8.5 - - + +
13A ARG* 2.9 23.5 + - - +
105A TYR* 5.5 1.1 - - + -
108A PHE* 3.4 31.2 - - + -
113A TYR* 4.9 3.6 - - - +
161A ALA 2.9 17.5 + - - -
162A THR* 3.0 9.5 + - - -
164A ALA* 1.3 75.6 - - - +
166A TYR* 1.3 66.3 + - - +
168A VAL* 3.6 5.3 + - - +
169A ALA* 3.0 22.5 + - - +
200A ALA* 4.9 2.9 - - - +
203A PHE* 4.0 24.8 - - + -
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Residues in contact with TYR 166 (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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104A LEU* 2.7 36.3 + - + +
108A PHE* 3.5 37.2 + + + +
130A MET* 3.5 31.8 + - + +
133A ALA* 4.2 1.9 - - - +
134A VAL* 3.5 23.8 - - + -
162A THR* 3.0 41.5 + - + -
163A ILE* 3.0 13.2 - - + +
165A THR* 1.3 75.5 - - - +
167A GLU* 1.3 67.4 + - - +
169A ALA* 2.9 14.4 + - - +
170A GLY 3.1 7.1 + - - -
171A PHE* 3.2 33.1 + + + +
173A PHE* 3.6 12.3 - + + -
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Residues in contact with GLU 167 (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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163A ILE 2.7 17.3 + - - +
164A ALA* 3.6 7.1 - - - +
166A TYR* 1.3 73.0 - - - +
168A VAL* 1.3 63.7 + - + +
170A GLY* 2.8 22.7 + - - -
171A PHE 3.8 4.8 + - - +
173A PHE* 3.8 21.0 - - + -
183A PHE* 3.6 25.6 - - + -
187A LYS* 3.3 24.6 + - - -
193A TYR* 5.2 0.2 + - - -
197A GLN* 4.9 8.7 + - - +
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Residues in contact with VAL 168 (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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164A ALA 3.2 15.7 + - - +
165A THR* 3.9 5.2 - - - +
167A GLU* 1.3 86.0 - - + +
169A ALA* 1.3 60.2 + - - +
170A GLY* 3.0 2.0 + - - -
197A GLN* 5.7 2.0 - - - +
200A ALA* 3.7 28.5 - - + +
201A ASP* 4.3 10.1 - - - +
203A PHE* 4.6 2.7 - - + -
204A LYS* 3.1 57.0 + - + +
208A LEU* 3.2 18.5 - - + +
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Residues in contact with ALA 169 (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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108A PHE* 3.7 23.3 - - + -
112A HIS* 3.7 26.7 - - + +
116A ILE* 6.2 0.2 - - + -
165A THR 3.0 14.5 + - - +
166A TYR* 2.9 11.7 + - - +
168A VAL* 1.3 76.7 - - - +
170A GLY* 1.3 58.6 + - - +
171A PHE 3.7 0.7 - - - +
203A PHE* 5.7 0.2 - - + -
208A LEU* 3.9 17.9 - - + -
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Residues in contact with GLY 170 (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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167A GLU 2.8 14.3 + - - -
168A VAL 3.0 2.1 - - - -
169A ALA* 1.3 82.4 - - - +
171A PHE* 1.3 63.8 + - - +
172A ASP* 3.6 2.9 + - - +
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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