Contacts of the helix formed by residues 133 - 142 (chain D) in PDB entry 3K75
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 ASN 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D GLY 4.6 1.8 + - - -
132D LEU* 1.3 75.5 - - - +
134D HIS* 1.3 59.2 + - - +
135D HIS* 2.9 15.4 + - - +
136D GLN* 2.7 53.8 + - - +
137D ARG* 2.8 27.8 + - - +
113E LYS* 6.2 2.0 - - - +
131E LYS 3.4 18.4 - - - +
132E LEU* 4.1 10.5 - - - -
133E ASN* 3.9 11.8 - - + +
136E GLN* 4.9 5.6 - - - +
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Residues in contact with HIS 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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133D ASN* 1.3 72.4 - - - +
135D HIS* 1.3 72.0 + - - +
137D ARG* 2.7 27.6 + - + +
138D ILE* 2.8 44.5 + - + +
227D THR* 3.0 22.3 + - - -
228D LEU 4.4 4.7 - - - +
130E ASP* 3.7 23.1 + - - +
131E LYS* 4.1 39.1 + - + +
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Residues in contact with HIS 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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104D THR* 3.4 25.5 + - - -
105D GLY* 3.3 24.3 + - - -
133D ASN* 2.9 16.9 + - - +
134D HIS* 1.3 77.2 - - - +
136D GLN* 1.3 57.8 + - + +
139D GLY* 2.9 23.6 + - - -
228D LEU* 3.2 45.5 + - + +
229D SER* 4.1 13.2 - - - -
236D MET* 3.5 27.5 - - + +
113E LYS* 6.1 5.8 - - + -
117E GLU* 5.8 3.8 - - - +
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Residues in contact with GLN 136 (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 VAL* 4.2 2.4 - - - +
104D THR 3.6 8.5 - - - -
105D GLY* 3.0 33.9 + - - +
106D ILE* 3.7 19.7 - - + +
110D ALA* 3.6 26.5 - - - +
114D LEU* 5.6 0.6 - - - +
131D LYS 4.6 0.9 - - - +
132D LEU* 3.3 23.6 - - + +
133D ASN* 2.7 54.3 + - - +
135D HIS* 1.3 70.5 - - - +
137D ARG* 1.3 66.8 + - - +
139D GLY* 3.6 0.3 - - - -
140D LEU* 2.8 27.2 + - - +
133E ASN* 5.3 2.6 + - - +
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Residues in contact with ARG 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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129D GLU* 3.0 55.4 + - + +
130D ASP* 4.3 2.9 + - - +
132D LEU* 2.5 35.0 + - + +
133D ASN 2.8 10.8 + - - +
134D HIS* 2.7 25.4 + - + +
136D GLN* 1.3 72.9 - - - +
138D ILE* 1.3 59.3 + - + +
140D LEU* 3.6 10.5 - - - +
141D LYS* 3.2 20.4 + - - +
130E ASP* 3.3 33.0 + - - +
132E LEU 3.6 0.8 + - - -
137E ARG* 3.4 25.2 - - - +
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Residues in contact with ILE 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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134D HIS* 2.8 49.1 + - + +
135D HIS 4.0 1.8 - - - +
137D ARG* 1.3 77.7 - - + +
139D GLY* 1.3 66.8 + - - +
140D LEU 3.0 1.8 - - - -
141D LYS* 2.9 30.0 + - + +
142D TYR* 3.1 27.9 + - + -
226D ASP* 3.8 24.5 - - + +
227D THR 3.3 10.5 - - - +
228D LEU* 3.7 17.3 - - + -
238D VAL* 4.1 8.1 - - + -
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Residues in contact with GLY 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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103D VAL* 3.8 8.0 - - - +
104D THR* 2.7 39.8 + - - +
135D HIS 2.9 12.3 + - - -
136D GLN 3.2 3.5 + - - -
138D ILE* 1.3 76.8 - - - +
140D LEU* 1.3 58.7 + - - +
142D TYR 3.7 1.9 + - - -
143D PHE* 3.3 20.1 + - - -
146D PHE* 4.2 6.9 - - - -
228D LEU* 4.2 1.8 - - - -
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Residues in contact with LEU 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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103D VAL* 3.7 15.2 - - + +
122D LEU* 4.0 7.9 - - + -
125D LEU* 3.4 48.2 - - + +
126D ARG* 3.0 45.3 + - + +
129D GLU* 4.1 25.8 - - + +
132D LEU* 4.4 7.9 - - + -
136D GLN 2.8 16.4 + - - +
137D ARG* 3.6 11.0 - - - +
139D GLY* 1.3 74.5 - - - +
141D LYS* 1.3 74.6 + - + +
142D TYR 3.2 0.2 - - - -
143D PHE* 3.1 10.2 + - - +
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Residues in contact with LYS 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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126D ARG* 4.2 7.5 + - - +
137D ARG 3.2 12.1 + - - +
138D ILE* 3.1 24.0 - - + +
140D LEU* 1.3 86.4 - - + +
142D TYR* 1.3 97.0 + - + +
143D PHE 3.6 0.2 + - - -
144D GLU 5.2 0.3 + - - -
226D ASP* 3.5 14.6 + - - -
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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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138D ILE* 3.1 17.2 + - + -
139D GLY 3.8 2.5 - - - -
141D LYS* 1.3 110.1 + - + +
143D PHE* 1.3 66.2 + - - +
144D GLU 3.1 3.1 - - - -
145D ASP* 2.9 22.2 + - + +
146D PHE* 3.0 34.2 + + + -
225D THR* 3.6 4.0 + - - -
226D ASP* 2.2 36.3 + - - -
238D VAL* 3.8 28.7 - - + -
252D HIS* 3.6 43.2 - + + -
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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