Contacts of the helix formed by residues 129 - 141 (chain C) in PDB entry 4K81
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ASP 4.2 4.3 - - - +
128C ILE* 1.3 77.8 - - - +
130C ALA* 1.3 64.1 + - - +
131C ARG* 3.6 15.8 + - - +
132C ASP* 2.6 40.6 + - - +
133C VAL* 3.3 23.9 + - - +
166C ASP 3.4 13.1 + - - +
167C HIS* 3.9 16.8 - - - +
168C GLU 3.3 7.4 - - - -
169C LEU* 4.0 11.4 - - + -
170C VAL* 3.5 2.2 - - - -
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Residues in contact with ALA 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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129C THR* 1.3 70.6 - - - +
131C ARG* 1.3 63.8 + - - +
133C VAL* 3.5 2.5 + - - +
134C CYS* 3.0 30.0 + - - -
151C LEU* 4.3 14.0 - - + +
164C ILE* 3.6 29.8 - - + +
165C GLU 3.5 24.7 - - - +
166C ASP* 3.5 1.3 + - - +
168C GLU 3.0 8.6 + - - +
170C VAL* 3.5 9.8 - - + +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C THR* 3.9 17.8 + - - +
130C ALA* 1.3 77.4 - - - +
132C ASP* 1.3 61.6 + - - +
134C CYS* 3.2 10.3 + - - +
135C GLN* 2.9 44.2 + - + +
166C ASP* 3.1 44.1 + - + +
167C HIS* 4.1 5.5 - - - +
345C GLN* 5.4 0.2 + - - -
349C ASN* 3.4 29.7 - - - +
352C HIS 4.3 3.8 + - - -
353C PRO 3.8 19.2 + - - +
354C TYR 4.0 8.5 - - - -
355C GLN* 3.5 43.8 - - - +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ASP 5.1 0.3 - - - +
128C ILE* 3.6 26.4 - - + +
129C THR* 2.6 40.9 + - - +
130C ALA 3.3 0.2 - - - -
131C ARG* 1.3 85.0 + - - +
133C VAL* 1.3 56.5 + - - +
135C GLN* 3.3 15.0 + - - +
136C LEU* 2.9 30.6 + - - +
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Residues in contact with VAL 133 (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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110C ILE* 4.6 10.8 - - + -
112C VAL* 4.2 11.9 - - + -
122C LEU* 3.9 22.4 - - + -
124C VAL* 4.9 4.7 - - + -
128C ILE* 3.8 24.7 - - + -
129C THR 3.3 15.8 + - - +
130C ALA 3.8 5.8 - - - +
132C ASP* 1.3 71.8 - - - +
134C CYS* 1.3 67.2 + - - +
136C LEU* 3.2 9.9 + - - +
137C LEU* 3.0 33.7 + - + +
151C LEU* 4.3 14.1 - - + -
170C VAL* 3.9 11.4 - - + -
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Residues in contact with CYS 134 (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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130C ALA* 3.0 24.0 + - - +
131C ARG* 3.4 12.1 - - - +
133C VAL* 1.3 76.3 - - - +
135C GLN* 1.3 56.6 + - + +
137C LEU* 3.1 3.8 + - - +
138C ILE* 2.8 39.5 + - + +
149C TRP* 4.1 6.3 - - + +
150C THR* 3.8 13.5 - - - -
151C LEU* 3.5 34.5 - - - -
187C PHE* 3.7 20.0 - - + -
193C LYS* 5.9 0.2 - - - -
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Residues in contact with GLN 135 (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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131C ARG* 2.9 34.7 + - + +
132C ASP* 3.8 13.1 - - - +
134C CYS* 1.3 69.0 - - + +
136C LEU* 1.3 67.2 + - - +
138C ILE* 3.2 17.4 + - + +
139C LEU* 2.9 35.2 + - + +
145C ASP* 4.6 7.8 + - - +
353C PRO 3.6 22.2 + - - -
354C TYR* 3.7 31.8 + - - +
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Residues in contact with LEU 136 (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* 4.2 31.2 - - + -
123C ASP 5.9 1.3 - - - +
124C VAL* 5.0 8.7 - - + -
132C ASP 2.9 14.7 + - - +
133C VAL* 3.3 12.8 - - - +
135C GLN* 1.3 78.0 - - - +
137C LEU* 1.3 60.4 + - + +
139C LEU* 3.3 12.3 + - + +
140C LYS* 2.8 48.7 + - + +
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Residues in contact with LEU 137 (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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112C VAL* 3.6 31.4 - - + +
120C ARG* 4.1 25.8 - - + -
122C LEU* 4.3 20.9 - - + -
133C VAL* 3.0 29.1 + - + +
134C CYS 3.7 4.0 - - - +
136C LEU* 1.3 72.9 - - - +
138C ILE* 1.3 61.5 + - - +
140C LYS* 4.4 3.1 - - + +
141C ASN* 2.8 50.6 + - - +
151C LEU* 4.9 0.2 - - + -
187C PHE* 3.6 36.6 - - + -
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Residues in contact with ILE 138 (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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134C CYS* 2.8 27.8 + - + +
135C GLN* 3.6 12.8 - - + +
137C LEU* 1.3 77.4 - - - +
139C LEU* 1.3 67.8 + - + +
142C HIS* 3.2 1.4 + - - -
143C TYR* 3.0 58.3 + - + +
145C ASP* 3.9 37.7 - - + +
149C TRP* 3.7 40.6 - - + +
187C PHE* 3.9 3.8 - - + -
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Residues in contact with LEU 139 (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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135C GLN* 2.9 26.2 + - + +
136C LEU* 3.6 12.1 - - + +
138C ILE* 1.3 80.2 - - + +
140C LYS* 1.3 65.1 + - + +
142C HIS* 3.4 23.3 + - - +
143C TYR 5.6 0.2 - - - -
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Residues in contact with LYS 140 (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 ARG* 3.9 37.2 + - - +
121C ALA 5.6 1.2 + - - -
122C LEU* 4.0 29.7 - - + +
136C LEU* 2.8 39.9 + - + +
137C LEU* 4.0 5.6 - - - +
139C LEU* 1.3 75.3 - - + +
141C ASN* 1.3 61.0 + - - +
142C HIS* 3.6 12.7 + - - -
33D ASP* 2.9 42.1 + - - +
34D PRO* 3.7 14.3 + - - +
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Residues in contact with ASN 141 (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 SER* 5.8 1.8 + - - -
120C ARG* 3.7 24.4 + - - +
137C LEU* 2.8 45.7 + - - +
140C LYS* 1.3 77.1 - - - +
142C HIS* 1.3 71.1 + - - +
143C TYR* 3.2 45.9 + - + -
187C PHE* 4.5 4.0 - - - -
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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