Contacts of the helix formed by residues 113 - 126 (chain D) in PDB entry 2PKG
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 CYS 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ALA 3.7 9.6 - - - +
95D MET 2.9 16.8 - - - +
97D CYS* 3.6 28.3 - - - -
98D LYS* 3.8 2.2 - - + +
103D CYS* 3.7 1.6 - - - -
111D CYS* 3.8 3.3 - - - -
112D ILE* 1.3 78.5 - - - +
114D LEU* 1.3 59.7 - - - +
115D LEU* 3.7 4.5 - - - -
116D CYS* 3.2 18.2 + - - -
117D LEU* 2.8 31.0 + - - +
175D ZN 2.3 36.6 - - - -
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Residues in contact with LEU 114 (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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95D MET* 2.8 40.0 + - + +
96D TYR* 3.8 17.7 - - + +
112D ILE 5.4 0.7 - - - +
113D CYS* 1.3 72.3 - - - +
115D LEU* 1.3 60.9 + - - +
117D LEU* 4.4 8.1 - - + -
118D LEU* 2.6 54.3 + - + +
160D TRP* 3.9 5.2 - - + -
164D ILE* 3.5 31.2 - - + -
168D THR* 5.2 7.2 - - + -
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Residues in contact with LEU 115 (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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96D TYR 2.8 21.7 + - - +
97D CYS* 3.9 21.3 - - + -
100D TRP* 4.5 2.2 - - + -
103D CYS 4.3 18.8 - - - +
104D ALA* 4.4 11.2 - - - +
113D CYS* 3.3 6.3 - - - -
114D LEU* 1.3 76.4 - - - +
116D CYS* 1.3 64.5 + - - +
118D LEU* 4.1 1.0 - - - +
119D ARG* 3.2 24.0 + - + +
141D PHE* 3.3 50.3 + - + +
142D ASP* 5.5 2.2 - - - +
157D LEU* 4.1 15.5 - - + -
160D TRP* 3.4 11.6 - - + -
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Residues in contact with CYS 116 (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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103D CYS* 3.6 16.8 - - - -
106D LYS* 5.7 0.2 - - - -
108D SER* 4.6 6.3 - - - -
111D CYS* 3.3 23.3 - - + +
113D CYS* 3.2 7.7 - - - +
115D LEU* 1.3 79.3 - - - +
117D LEU* 1.3 63.6 + - - +
119D ARG* 3.1 45.0 + - - +
120D MET* 3.3 5.9 + - - +
175D ZN 2.1 35.4 - - - -
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Residues in contact with LEU 117 (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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111D CYS 4.7 7.9 - - - +
112D ILE* 4.1 31.2 - - + +
113D CYS 2.8 24.4 + - - +
114D LEU* 3.9 5.8 - - + +
116D CYS* 1.3 71.8 - - - +
118D LEU* 1.3 59.1 + - + +
120D MET* 2.8 50.9 + - + +
121D LYS* 3.0 10.1 + - - +
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Residues in contact with LEU 118 (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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114D LEU* 2.6 50.1 + - + +
115D LEU* 4.1 2.9 - - - +
117D LEU* 1.3 73.7 - - + +
119D ARG* 1.3 59.6 + - - +
121D LYS* 3.4 24.3 - - + +
122D HIS 3.3 13.5 + - - -
138D CYS* 5.0 1.9 - - - -
139D TYR* 3.8 33.9 - - + +
140D CYS* 3.7 17.1 - - - +
160D TRP* 3.9 16.4 - - + -
164D ILE* 4.6 8.1 - - + -
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Residues in contact with ARG 119 (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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103D CYS 3.2 27.1 + - - -
104D ALA* 3.8 12.1 + - - +
105D LYS* 4.5 0.4 - - - +
106D LYS* 3.2 54.2 - - - +
115D LEU* 3.2 18.7 + - + +
116D CYS* 3.1 33.0 + - - +
117D LEU 3.0 1.0 - - - -
118D LEU* 1.3 75.2 - - - +
120D MET* 1.3 59.2 + - - +
122D HIS* 2.6 37.6 + - + +
123D GLU* 2.9 20.6 + - + -
140D CYS* 4.1 10.3 - - + +
141D PHE 6.1 0.4 - - - +
142D ASP* 4.7 17.1 + - - +
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Residues in contact with MET 120 (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 CYS 3.3 5.4 + - - +
117D LEU* 2.8 39.4 + - + +
119D ARG* 1.3 77.3 - - - +
121D LYS* 1.3 71.2 + - + +
123D GLU* 3.0 17.4 + - + +
124D ASN* 2.7 37.7 + - + +
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Residues in contact with LYS 121 (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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117D LEU 3.0 8.8 + - - +
118D LEU* 3.4 28.0 - - + +
119D ARG 3.1 0.2 - - - -
120D MET* 1.3 77.9 - - + +
122D HIS* 1.3 55.6 + - - +
124D ASN* 3.5 7.2 - - - +
125D ARG* 2.6 61.4 + - + +
138D CYS* 6.3 0.7 - - - -
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Residues in contact with HIS 122 (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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118D LEU 3.3 4.2 + - - +
119D ARG* 2.6 26.8 + - + +
121D LYS* 1.3 76.1 - - - +
123D GLU* 1.3 65.9 - - + -
125D ARG* 3.6 4.0 - - - +
126D LYS* 2.9 43.9 + - + +
133D LEU* 3.2 33.1 + - + +
138D CYS* 3.1 8.4 - - - -
140D CYS* 3.2 4.0 - - + -
142D ASP* 6.2 0.2 - - + -
143D CYS* 3.2 13.5 - - - -
176D ZN 1.8 39.8 - - - -
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Residues in contact with GLU 123 (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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106D LYS* 3.1 37.6 + - - -
119D ARG* 2.9 25.9 + - + +
120D MET* 3.5 14.0 - - + +
122D HIS* 1.3 78.0 - - + +
124D ASN* 1.3 59.7 + - - +
126D LYS* 2.5 35.4 + - - +
127D LEU* 3.4 9.7 + - - +
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Residues in contact with ASN 124 (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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120D MET* 2.7 30.9 + - + +
121D LYS* 3.6 6.8 + - - +
123D GLU* 1.3 74.8 - - - +
125D ARG* 1.3 62.6 + - - +
126D LYS 3.3 0.3 + - - -
127D LEU* 3.4 31.3 + - - +
128D TYR* 4.3 2.6 + - - +
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Residues in contact with ARG 125 (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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121D LYS* 2.6 47.9 + - + +
122D HIS* 3.6 4.6 - - - +
124D ASN* 1.3 76.2 - - - +
126D LYS* 1.3 58.3 + - - +
127D LEU 3.2 2.3 + - - -
128D TYR* 3.9 6.3 + - - +
129D ARG* 3.8 32.1 + - - +
133D LEU* 3.8 33.0 - - - +
137D ASP* 3.2 42.0 + - - +
138D CYS* 4.8 6.1 - - - +
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Residues in contact with LYS 126 (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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100B GLU* 3.7 33.6 + - - -
122D HIS* 2.9 34.9 + - + +
123D GLU* 2.5 23.3 + - - +
125D ARG* 1.3 71.6 - - - +
127D LEU* 1.3 57.9 + - - +
129D ARG* 2.6 29.5 - - - +
130D LYS 5.4 4.0 - - - +
131D ASP 4.8 12.3 - - - +
133D LEU* 4.8 10.3 - - + +
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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
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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