Contacts of the helix formed by residues 113 - 125 (chain A) in PDB entry 3KYB
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.9 2.9 - - - -
111A THR 3.6 1.4 + - - -
112A CYS* 1.3 75.2 - - - +
114A PRO* 1.3 77.4 - - - +
115A ASP* 3.8 4.8 + - - +
116A GLU* 3.0 35.0 + - - +
117A ALA* 3.0 19.8 + - - +
262B ASP 5.4 0.2 - - - -
263B TYR* 3.6 15.3 - - - -
264B GLN* 5.1 2.0 - - - +
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Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.7 6.0 - - + -
113A SER* 1.3 86.2 - - - +
115A ASP* 1.3 59.1 + - - +
117A ALA* 3.1 5.4 + - + +
118A ARG* 2.9 43.8 + - - +
179A PHE* 3.1 30.5 - - + +
262B ASP* 3.6 24.5 - - + +
263B TYR 3.6 7.2 - - - +
264B GLN 3.5 33.4 - - - +
265B GLY* 3.6 8.1 - - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 3.3 4.9 + - - +
114A PRO* 1.3 80.1 - - - +
116A GLU* 1.3 62.6 + - + +
118A ARG* 3.1 32.8 + - - +
119A ALA* 3.2 21.3 + - - +
259B TYR* 2.4 38.8 + - - +
260B GLN 4.8 3.3 - - - +
261B GLY* 5.3 1.4 - - - -
262B ASP 4.7 5.7 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 4.0 3.8 - - - +
112A CYS* 3.4 22.3 - - + -
113A SER* 3.0 35.4 + - - +
115A ASP* 1.3 77.7 - - + +
117A ALA* 1.3 56.5 + - - +
119A ALA* 3.4 7.2 + - - +
120A LEU* 3.0 27.2 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.4 33.2 - - + -
104A ILE* 4.2 13.0 - - + -
112A CYS* 3.7 11.4 - - + +
113A SER 3.0 8.8 + - - +
114A PRO 3.5 4.3 - - - +
116A GLU* 1.3 74.2 - - - +
118A ARG* 1.3 67.2 + - - +
120A LEU* 3.1 3.9 + - - +
121A ILE* 2.9 28.4 + - - +
179A PHE* 3.8 14.6 - - + -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 2.9 28.9 + - - +
115A ASP* 3.1 34.9 + - - +
116A GLU 3.4 0.2 - - - -
117A ALA* 1.3 75.3 - - - +
119A ALA* 1.3 56.4 + - - +
121A ILE* 3.9 0.7 - - - +
122A ALA* 2.8 33.0 + - - +
179A PHE* 3.7 47.3 + - + +
262B ASP* 4.7 15.2 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP 3.2 11.2 + - - +
116A GLU* 3.8 9.9 - - - +
118A ARG* 1.3 78.3 - - - +
120A LEU* 1.3 62.1 + - - +
122A ALA* 4.1 5.3 - - - +
123A GLU* 3.2 23.7 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 4.1 17.5 - - + -
108A PHE* 3.8 34.3 - - + -
110A LYS* 4.3 21.3 - - + -
112A CYS* 4.5 13.5 - - - -
116A GLU 3.0 17.0 + - - +
117A ALA 3.1 3.1 + - - +
119A ALA* 1.3 79.6 - - - +
121A ILE* 1.3 61.3 + - + +
123A GLU* 3.5 9.3 + - + +
124A LYS* 2.9 49.0 + - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 4.0 15.9 - - + -
108A PHE* 4.0 17.9 - - + -
117A ALA 2.9 19.2 + - - +
120A LEU* 1.3 80.4 - - + +
122A ALA* 1.3 68.2 + - - +
123A GLU 3.1 1.6 - - - -
124A LYS* 2.8 16.2 + - + -
125A GLY* 2.9 11.6 + - - -
142A PHE 3.2 27.1 - - - +
143A ILE* 4.3 9.2 - - - +
147A LEU* 3.6 28.9 - - + -
177A VAL* 4.9 4.9 - - + -
179A PHE* 3.6 30.5 - - + -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ARG 2.8 22.7 + - - +
119A ALA* 4.1 5.8 - - - +
121A ILE* 1.3 72.2 - - - +
123A GLU* 1.3 62.5 + - - +
125A GLY* 3.5 16.2 + - - +
127A SER* 5.6 3.6 + - - -
141A ARG* 6.4 0.2 - - - +
179A PHE* 5.8 0.2 - - - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 3.2 16.2 + - - +
120A LEU* 3.6 13.5 - - + +
121A ILE 3.1 0.8 - - - -
122A ALA* 1.3 82.1 - - - +
124A LYS* 1.3 75.6 + - + +
125A GLY 3.8 3.8 - - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.8 28.5 - - + -
120A LEU* 2.9 42.8 - - + +
121A ILE* 2.8 17.6 + - + +
123A GLU* 1.3 86.9 + - + +
125A GLY* 1.3 61.5 + - - +
126A ASP* 5.4 0.3 - - - +
140A LEU 4.4 1.0 - - - +
143A ILE 4.2 4.7 - - - +
144A GLY* 3.6 24.5 - - - -
145A LYS 4.6 2.8 + - - +
146A GLU* 3.2 27.4 + - - +
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE 2.9 14.2 + - - -
122A ALA* 3.5 13.0 + - - +
123A GLU 3.4 4.6 - - - +
124A LYS* 1.3 80.1 - - - +
126A ASP* 1.3 61.8 + - - -
127A SER* 3.6 3.9 + - - -
140A LEU 3.4 6.7 - - - -
141A ARG* 3.4 18.2 - - - -
142A PHE 4.8 2.0 - - - -
144A GLY* 4.4 6.6 - - - +
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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