Contacts of the helix formed by residues 113 - 129 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ALA 4.1 6.5 - - - +
95C MET 3.0 16.6 - - - +
97C CYS* 3.6 24.5 - - - -
98C LYS* 3.7 5.6 - - + +
103C CYS* 3.6 7.4 - - - -
111C CYS* 3.6 2.6 - - - -
112C ILE* 1.3 78.2 - - - +
114C LEU* 1.3 65.1 + - - +
115C LEU* 3.7 5.4 - - - -
116C CYS* 3.1 24.4 + - - +
117C LEU* 2.8 25.5 + - - +
175C ZN 2.2 36.6 - - - -
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MET* 2.8 59.4 + - + +
96C TYR* 3.8 12.1 - - + +
112C ILE 5.7 0.4 - - - +
113C CYS* 1.3 70.1 - - - +
115C LEU* 1.3 59.9 + - - +
117C LEU* 2.8 9.7 + - + -
118C LEU* 2.5 51.5 + - + +
160C TRP* 4.1 4.0 - - + -
164C ILE* 3.4 33.2 - - + -
168C THR* 5.0 8.1 - - + -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR 3.0 17.9 + - - +
97C CYS* 4.0 21.1 - - + -
103C CYS 4.4 15.0 - - - +
104C ALA* 4.2 13.5 - - + +
113C CYS* 3.7 6.5 - - - -
114C LEU* 1.3 80.4 - - - +
116C CYS* 1.3 68.1 + - - +
118C LEU* 4.0 1.3 - - - +
119C ARG* 3.2 23.0 + - + +
141C PHE* 3.2 51.5 + - + +
142C ASP* 5.8 1.3 - - - +
157C LEU* 4.3 12.3 - - + -
160C TRP* 3.3 14.7 - - + -
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Residues in contact with CYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C CYS* 3.5 15.3 - - - -
106C LYS* 5.8 0.2 - - - -
108C SER* 3.7 7.9 - - - -
111C CYS* 3.3 22.9 - - + +
113C CYS* 3.1 8.5 - - - +
114C LEU 3.1 0.4 - - - -
115C LEU* 1.3 84.0 - - - +
117C LEU* 1.3 61.6 + - - +
119C ARG* 3.1 42.1 + - - +
120C MET* 3.3 5.7 + - - +
175C ZN 2.3 35.2 - - - -
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C CYS 4.8 7.9 - - - +
112C ILE* 3.8 35.4 - - + +
113C CYS 2.8 23.8 + - - +
114C LEU* 2.8 6.6 + - + +
116C CYS* 1.3 69.8 - - - +
118C LEU* 1.3 65.9 + - + +
120C MET* 3.0 39.4 + - + +
121C LYS* 3.1 11.3 + - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LEU* 2.5 41.2 + - + +
115C LEU* 4.0 3.6 - - - +
117C LEU* 1.3 70.9 - - + +
119C ARG* 1.3 64.0 + - - +
121C LYS* 3.3 22.1 + - + +
122C HIS 3.1 14.9 + - - -
138C CYS* 4.8 2.0 - - - -
139C TYR* 3.5 27.6 - - + +
140C CYS* 3.7 20.0 - - - +
160C TRP* 3.4 30.1 - - + -
164C ILE* 4.4 7.6 - - + -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C CYS 3.2 26.7 + - - -
104C ALA* 3.8 10.7 + - - +
105C LYS* 4.4 0.4 - - - +
106C LYS* 3.0 56.1 - - - +
108C SER 5.9 0.2 + - - -
115C LEU* 3.2 19.0 + - + +
116C CYS* 3.1 34.3 + - - +
118C LEU* 1.3 73.2 - - - +
120C MET* 1.3 63.2 + - - +
122C HIS* 2.7 27.7 + - + +
123C GLU* 2.7 27.0 + - + +
140C CYS* 4.2 8.9 - - + +
141C PHE 6.1 0.2 - - - +
142C ASP* 4.6 17.7 + - - +
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Residues in contact with MET 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C CYS 3.3 5.8 + - - +
117C LEU* 3.0 34.9 + - + +
119C ARG* 1.3 77.9 - - - +
121C LYS* 1.3 73.3 + - - +
123C GLU* 3.1 16.9 + - + +
124C ASN* 2.8 34.1 + - + +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU 3.1 10.0 + - - +
118C LEU* 3.4 26.0 - - + +
119C ARG 3.1 0.2 - - - -
120C MET* 1.3 79.3 - - + +
122C HIS* 1.3 56.0 + - - +
124C ASN* 4.3 6.5 - - + +
125C ARG* 2.6 62.9 + - + +
138C CYS* 5.8 3.6 - - - -
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Residues in contact with HIS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 5.6 2.8 + - - -
118C LEU 3.1 6.2 + - - +
119C ARG* 2.7 21.5 + - + +
121C LYS* 1.3 79.3 - - - +
123C GLU* 1.3 69.9 + - + +
125C ARG* 3.3 3.6 + - - +
126C LYS* 2.9 42.2 + - + +
133C LEU* 3.1 32.0 + - + +
138C CYS* 3.2 6.1 - - - -
140C CYS* 3.2 5.3 - - + -
142C ASP* 6.3 0.4 - - + -
143C CYS* 3.0 15.5 - - - -
176C ZN 1.7 40.7 - - - -
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Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS* 3.0 41.4 + - - -
119C ARG* 2.7 35.5 + - + +
120C MET* 3.7 16.3 - - + +
122C HIS* 1.3 74.8 - - + +
124C ASN* 1.3 57.8 + - - +
126C LYS* 2.6 36.5 + - - +
127C LEU* 3.4 8.5 + - - +
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C MET* 2.8 31.2 + - + +
121C LYS* 3.4 7.2 + - - +
123C GLU* 1.3 72.6 - - - +
125C ARG* 1.3 57.6 + - - +
126C LYS 2.7 13.0 + - - -
127C LEU* 2.8 36.6 + - - +
128C TYR* 4.2 1.9 + - - +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LYS* 2.6 47.2 + - + +
122C HIS* 3.6 5.1 - - - +
124C ASN* 1.3 77.4 - - - +
126C LYS* 1.3 58.2 + - - +
127C LEU 3.3 1.1 + - - -
128C TYR* 4.2 5.3 + - - +
129C ARG* 3.8 31.8 + - - +
133C LEU* 3.7 32.0 - - - +
137C ASP* 2.8 42.3 + - - +
138C CYS* 4.6 7.7 - - - -
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 4.1 30.1 + - - +
122C HIS* 2.9 33.3 + - + +
123C GLU* 2.6 23.0 + - - +
124C ASN 2.7 0.2 + - - -
125C ARG* 1.3 70.6 - - - +
127C LEU* 1.3 57.0 + - - +
129C ARG* 2.5 30.2 - - - +
130C LYS 5.4 5.2 - - - +
131C ASP 4.9 11.2 - - - +
132C PRO* 5.9 0.9 - - - -
133C LEU* 4.6 9.2 - - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLU 4.0 6.7 - - - +
124C ASN* 2.8 30.8 + - - +
126C LYS* 1.3 76.2 - - - +
128C TYR* 1.3 67.3 + - - +
129C ARG 3.1 7.5 + - - +
130C LYS* 5.5 1.9 - - - +
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Residues in contact with TYR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN 4.2 1.9 + - - +
125C ARG* 4.2 5.7 + - - +
127C LEU* 1.3 79.2 - - - +
129C ARG* 1.3 58.2 + - + +
130C LYS* 5.5 2.0 - - - +
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Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 3.8 33.7 + - - +
126C LYS* 2.5 30.2 - - - +
127C LEU 3.1 4.4 - - - +
128C TYR* 1.3 83.2 - - + +
130C LYS* 1.3 67.5 + - - +
131C ASP* 3.4 41.3 + - + +
132C PRO 4.0 9.5 + - - -
133C LEU* 3.9 26.4 - - - +
137C ASP* 4.3 24.2 + - - +
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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