Contacts of the helix formed by residues 127 - 142 (chain D) in PDB entry 2P2N
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 ASP 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D SER* 3.4 7.9 - - - -
118D GLN* 2.8 26.1 + - - +
119D ILE 3.0 23.6 + - - -
125D ARG 3.6 0.8 + - - -
126D SER* 1.3 72.0 - - - +
128D GLY* 1.3 62.6 + - - +
129D GLN 3.5 1.3 - - - -
130D ILE* 3.7 14.8 + - + +
131D ASN* 3.1 39.5 + - - +
151D PHE* 3.7 6.4 - - - -
169D PHE* 3.4 30.9 - - + -
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLY 4.5 3.4 - - - -
117D SER* 3.5 20.4 - - - -
121D LEU* 3.5 13.7 - - - -
126D SER* 2.9 14.8 + - - -
127D ASP* 1.3 75.3 - - - +
129D GLN* 1.3 64.0 + - - +
131D ASN* 4.2 0.3 - - - +
132D LEU* 2.9 28.9 + - - +
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Residues in contact with GLN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 3.5 34.7 + - - +
38D MET* 3.6 33.9 - - + +
40D GLU* 3.8 21.4 - - - +
41D PHE* 3.4 9.9 - - - -
121D LEU* 3.2 29.0 + - + +
123D GLU 5.7 0.4 + - - -
126D SER* 4.4 17.9 + - - +
127D ASP 3.5 0.4 - - - -
128D GLY* 1.3 73.0 - - - +
130D ILE* 1.3 60.1 + - + +
133D LEU* 2.9 32.7 + - - +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 4.1 27.8 - - + +
126C SER 4.9 6.5 - - - +
130C ILE* 6.0 9.2 - - + -
169C PHE* 6.5 0.4 - - + -
40D GLU* 6.5 0.2 - - - -
126D SER 5.3 1.8 + - - +
127D ASP* 3.7 20.4 + - + +
129D GLN* 1.3 79.1 - - + +
131D ASN* 1.3 66.4 + - - +
133D LEU* 4.4 11.2 - - + -
134D ASN* 3.0 60.9 + - - +
153D ASN* 5.0 5.4 - - - +
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Residues in contact with ASN 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D THR* 3.4 16.1 + - - +
116D GLY 2.9 29.0 + - - +
127D ASP* 3.1 29.4 + - - +
128D GLY 4.2 0.4 - - - +
130D ILE* 1.3 81.2 - - - +
132D LEU* 1.3 57.8 + - - +
134D ASN* 5.3 0.3 + - - -
135D ALA* 3.0 28.1 + - - +
150D PHE* 3.9 11.3 - - - +
151D PHE* 3.4 32.3 - - - -
152D ASN* 3.1 25.9 + - - +
153D ASN 4.7 0.3 + - - -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 4.6 7.0 - - + -
31D LEU* 5.4 2.7 - - + -
35D LEU* 3.6 35.9 - - + -
41D PHE* 3.8 15.7 - - + -
49D PHE* 5.7 0.7 - - + -
86D VAL* 3.9 26.7 - - + -
88D LEU* 3.9 34.1 - - + -
115D THR* 4.3 4.9 - - + +
121D LEU* 5.9 1.8 - - + -
128D GLY 2.9 17.2 + - - +
129D GLN 4.2 1.3 - - - +
131D ASN* 1.3 73.6 - - - +
133D LEU* 1.3 68.0 + - - +
135D ALA 3.3 0.3 + - - -
136D LEU* 3.0 38.4 + - + +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 4.0 10.1 - - + -
125C ARG* 3.9 33.0 - - + +
40D GLU* 3.6 45.8 - - + +
41D PHE* 3.7 13.6 - - + -
46D MET* 3.5 33.7 - - + +
129D GLN 2.9 21.4 + - - +
130D ILE* 4.0 9.9 - - + +
132D LEU* 1.3 77.4 - - - +
134D ASN* 1.3 58.6 + - - +
136D LEU* 3.5 2.4 + - - +
137D TYR* 3.0 26.4 + - + +
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Residues in contact with ASN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 3.2 35.2 + - - +
169C PHE* 5.9 0.8 - - - -
130D ILE* 3.0 42.5 + - - +
131D ASN* 5.3 0.6 + - - -
133D LEU* 1.3 72.5 - - - +
135D ALA* 1.3 61.8 + - - +
137D TYR* 3.7 3.7 - - - +
138D VAL* 2.8 37.3 + - + +
150D PHE* 3.3 36.4 - - + -
153D ASN* 3.7 16.0 + - - +
183D ALA* 5.0 4.5 - - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D VAL* 4.0 15.3 - - + -
113D ILE* 3.5 18.8 - - + +
115D THR* 3.8 21.1 - - + -
131D ASN 3.0 20.8 + - - +
132D LEU 3.3 4.5 + - - +
134D ASN* 1.3 76.5 - - - +
136D LEU* 1.3 53.6 + - - +
138D VAL* 4.5 4.0 - - - -
139D ALA* 2.8 36.6 + - - +
150D PHE* 4.4 8.2 - - + -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.7 27.6 - - + +
8D VAL* 3.9 20.4 - - + -
41D PHE* 3.9 25.4 - - + -
46D MET* 3.9 12.8 - - + -
47D PRO* 3.7 9.2 - - + +
49D PHE* 3.9 35.7 - - + -
86D VAL* 4.2 8.1 - - + -
132D LEU* 3.0 30.0 + - + +
133D LEU 3.7 3.1 - - - +
135D ALA* 1.3 74.5 - - - +
137D TYR* 1.3 59.1 + - - +
139D ALA* 3.3 3.4 + - - +
140D ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 3.5 30.3 - - + -
125C ARG* 4.4 12.1 - - - -
45D GLU* 3.7 19.5 - - + -
46D MET* 4.3 8.7 - - - -
47D PRO* 4.5 6.5 - - + -
133D LEU* 3.0 20.4 + - + +
134D ASN* 3.7 6.3 - - - +
136D LEU* 1.3 76.9 - - - +
138D VAL* 1.3 61.6 + - + +
140D ALA 3.4 0.7 + - - -
141D ASN* 2.9 61.3 + - + +
142D TYR* 4.5 3.1 - + - -
187D ILE* 3.4 34.3 - - + -
9011D EDO 5.9 1.1 - - - -
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ILE* 3.7 16.2 - - + -
134D ASN* 2.8 25.9 + - + +
135D ALA* 3.8 4.0 - - - +
137D TYR* 1.3 71.2 - - + +
139D ALA* 1.3 62.0 + - - +
142D TYR* 2.7 45.5 + - + +
150D PHE* 4.1 21.8 - - + -
155D LEU* 4.1 11.9 - - + -
181D LEU* 3.8 34.1 - - + -
187D ILE* 4.8 14.1 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.0 19.6 - - + +
83D ASP* 4.7 2.4 - - - +
85D PHE 4.9 4.0 - - - +
86D VAL* 4.2 13.9 - - + -
111D PRO* 3.4 30.9 - - + +
113D ILE* 3.5 17.4 - - + +
135D ALA 2.8 22.7 + - - +
136D LEU 3.7 4.0 - - - +
138D VAL* 1.3 72.9 - - - +
140D ALA* 1.3 61.8 + - - +
143D PRO* 4.1 6.9 - - - +
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2D GLY* 5.5 0.3 - - - -
-1D SER 4.4 1.0 - - - +
4D LYS* 3.5 42.0 + - + +
6D ILE* 4.0 5.3 - - + +
47D PRO* 3.8 28.0 - - + -
83D ASP* 6.2 0.7 - - - -
136D LEU 2.9 16.9 + - - +
139D ALA* 1.3 77.2 - - - +
141D ASN* 1.3 75.3 + - - +
142D TYR 3.8 0.2 - - - -
143D PRO* 4.4 6.6 - - - +
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Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3D ARG* 3.9 0.3 - - - -
-2D GLY* 2.9 30.5 + - - +
-1D SER 4.4 2.1 - - - +
0D HIS* 4.3 23.2 - - - +
4D LYS* 5.2 1.4 + - - +
45D GLU 4.9 2.6 + - - -
47D PRO* 5.6 0.6 - - - +
137D TYR* 2.9 59.8 + - + +
140D ALA* 1.3 88.9 - - - +
142D TYR* 1.3 83.4 + - + +
143D PRO* 3.5 6.7 - - - -
9011D EDO 4.8 5.4 + - - -
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Residues in contact with TYR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-5D VAL* 5.2 0.4 - - + -
-4D PRO 3.3 20.4 - - - +
-3D ARG* 4.2 15.5 - - + -
111D PRO* 5.1 1.0 - - - +
113D ILE* 5.6 0.5 - - - +
137D TYR* 4.5 3.0 - + - -
138D VAL* 2.7 33.0 + - + +
139D ALA* 5.0 0.5 - - - -
141D ASN* 1.3 95.0 - - + +
143D PRO* 1.3 53.9 - - - +
144D ILE* 2.8 26.7 + - + +
155D LEU* 5.2 0.2 - - - +
181D LEU* 3.8 22.7 - - + -
187D ILE* 3.5 60.7 + - + +
189D ARG* 4.9 15.3 - - + -
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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
------------------------------------------------------------
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