Contacts of the helix formed by residues 120 - 131 (chain C) in PDB entry 2HNK
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 SER 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C VAL* 4.2 6.2 - - - +
119C GLY* 1.3 71.1 - - - -
121C ALA* 1.3 57.9 + - - +
122C LEU* 3.6 9.2 + - - +
123C GLU* 3.3 38.5 + - - +
124C THR* 2.9 27.3 + - - -
2003C SAH 4.2 9.3 + - - -
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Residues in contact with ALA 121 (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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67C ILE* 3.7 25.4 - - + -
91C CYS* 4.2 12.6 - - + -
119C GLY 3.5 1.1 + - - -
120C SER* 1.3 70.2 + - - +
122C LEU* 1.3 67.1 + - - +
124C THR* 4.1 7.6 - - - -
125C LEU* 2.9 31.7 + - + +
163C TYR* 3.7 8.3 - - + -
2003C SAH 3.1 34.4 + - + +
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Residues in contact with LEU 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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120C SER* 3.4 7.4 + - - +
121C ALA* 1.3 78.1 - - - +
123C GLU* 1.3 56.9 + - - +
126C GLN* 3.1 29.0 + - - +
159C ASN* 3.9 27.1 - - - +
162C ASN* 4.0 23.8 - - + +
163C TYR* 3.6 33.9 + - + +
166C LEU* 3.9 24.5 - - + +
2003C SAH 5.5 0.6 + - - +
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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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120C SER* 3.3 27.4 + - - +
121C ALA 3.2 0.2 - - - -
122C LEU* 1.3 77.8 - - + +
124C THR* 1.3 66.1 + - - +
126C GLN* 3.2 4.7 + - - +
127C VAL* 2.9 36.8 + - + +
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Residues in contact with THR 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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89C LEU* 4.7 4.3 - - + -
91C CYS* 3.8 25.1 - - - +
117C LYS* 3.7 40.8 + - + +
119C GLY 4.5 4.7 + - - -
120C SER 2.9 18.8 + - - -
121C ALA* 3.2 9.3 + - - -
123C GLU* 1.3 75.2 - - - +
125C LEU* 1.3 63.5 + - + +
127C VAL* 3.7 2.3 + - - +
128C LEU* 3.3 21.7 + - - +
137C TRP* 3.8 22.0 - - + -
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Residues in contact with LEU 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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65C ILE* 4.1 18.4 - - + -
67C ILE* 3.9 25.4 - - + -
91C CYS* 4.5 9.2 - - - -
121C ALA* 2.9 22.2 + - + +
122C LEU 4.0 2.9 - - - +
124C THR* 1.3 77.0 - - - +
126C GLN* 1.3 58.4 + - - +
128C LEU* 3.3 8.2 + - + +
129C ILE* 3.0 33.2 + - - +
151C PHE* 4.1 17.3 - - + -
163C TYR* 4.1 16.4 - - + -
166C LEU* 4.0 23.8 - - + -
167C ILE* 4.8 3.4 - - + -
170C LEU* 3.8 22.5 - - + +
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Residues in contact with GLN 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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122C LEU 3.1 18.9 + - - +
123C GLU* 3.2 6.3 + - - +
125C LEU* 1.3 74.7 - - - +
127C VAL* 1.3 60.0 + - + +
129C ILE* 3.2 14.8 + - - +
130C ASP* 2.8 72.8 + - - +
166C LEU* 3.5 24.6 - - + +
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Residues in contact with VAL 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* 2.9 29.2 + - + +
124C THR* 4.0 5.2 - - - +
126C GLN* 1.3 76.9 - - + +
128C LEU* 1.3 53.6 + - - +
130C ASP* 4.2 4.4 - - - +
131C SER* 2.6 46.6 + - - +
135C PRO* 4.9 4.5 - - + -
137C TRP* 4.1 21.5 - - + -
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Residues in contact with LEU 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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65C ILE* 3.7 30.3 - - + -
89C LEU* 3.8 16.6 - - + -
124C THR 3.3 11.8 + - - +
125C LEU* 3.4 12.6 - - + +
126C GLN 3.2 0.4 - - - -
127C VAL* 1.3 77.7 - - - +
129C ILE* 1.3 63.1 + - - +
131C SER* 3.7 8.1 + - - -
135C PRO* 4.3 6.1 - - + -
137C TRP* 3.7 24.0 - - + -
138C ALA* 3.8 19.5 - - + -
141C PHE* 5.0 1.8 - - + -
142C ALA 3.8 13.9 - - - +
143C PHE* 3.9 8.9 - - + -
144C GLY 2.8 26.6 + - - -
148C ILE* 5.2 2.5 - - + -
170C LEU* 4.3 12.8 - - + -
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Residues in contact with ILE 129 (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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125C LEU 3.0 20.5 + - - +
126C GLN* 3.2 14.1 + - - +
128C LEU* 1.3 79.8 - - - +
130C ASP* 1.3 70.9 + - - +
131C SER 3.5 1.6 + - - +
132C LYS* 5.4 2.1 + - - -
144C GLY* 3.7 5.6 - - - -
145C PRO* 3.5 23.0 - - + +
166C LEU* 3.8 47.8 - - + +
169C LYS* 4.2 29.4 - - + -
170C LEU* 3.6 21.3 - - + -
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Residues in contact with ASP 130 (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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126C GLN* 2.8 50.9 + - - +
127C VAL* 4.2 5.2 - - - +
129C ILE* 1.3 80.9 - - - +
131C SER* 1.3 65.0 + - - +
132C LYS* 3.4 23.8 + - - +
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Residues in contact with SER 131 (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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127C VAL* 2.6 31.1 + - - +
128C LEU* 3.8 9.2 - - - -
129C ILE 3.4 6.6 - - - +
130C ASP* 1.3 77.8 - - - +
132C LYS* 1.3 61.8 + - - +
133C SER 3.3 17.7 + - - -
135C PRO* 3.6 20.5 - - - +
143C PHE* 3.4 20.5 - - - -
144C GLY* 4.4 3.5 - - - -
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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
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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