Contacts of the helix formed by residues 112 - 129 (chain B) in PDB entry 2AX1
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 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP* 3.1 27.1 + - - +
110B ASN* 3.2 8.3 - - - -
111B LEU* 1.3 80.5 - - - +
113B SER* 1.3 59.0 + - - +
114B LYS* 3.8 6.7 + - - +
115B ALA* 3.3 22.9 + - - +
116B VAL* 2.9 27.4 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU 3.7 1.0 + - - -
112B SER* 1.3 72.4 - - - +
114B LYS* 1.3 56.2 + - - +
116B VAL* 4.4 5.2 - - - -
117B ASN* 2.7 52.0 + - - -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE 3.8 13.2 - - - -
102B GLY* 2.9 34.7 + - - +
103B TYR* 4.5 5.6 - - + -
107B ASP* 6.4 0.4 - - - -
112B SER* 3.3 7.2 + - - +
113B SER* 1.3 82.5 + - - +
115B ALA* 1.3 63.6 - - - +
117B ASN* 3.8 5.4 - - - +
118B HIS* 2.8 47.7 + - + +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.6 35.4 - - + +
107B ASP* 3.9 21.5 - - + +
108B VAL* 4.0 8.7 - - + +
112B SER* 3.3 17.6 + - - +
114B LYS* 1.3 78.9 - - - +
116B VAL* 1.3 57.9 + - + +
118B HIS* 3.3 2.3 + - - +
119B ILE* 2.9 36.8 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 4.5 16.6 - - + -
86B GLU* 5.3 5.8 - - - +
89B CYS* 5.1 2.9 - - - -
111B LEU* 3.6 30.7 - - + +
112B SER 2.9 21.9 + - - +
113B SER* 3.8 4.5 - - - +
115B ALA* 1.3 74.1 - - + +
117B ASN* 1.3 69.8 + - - +
119B ILE* 3.3 8.8 + - - +
120B HIS* 3.1 45.3 + - + +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER* 2.7 39.8 + - - +
114B LYS* 3.8 6.0 - - - +
116B VAL* 1.3 77.1 - - - +
118B HIS* 1.3 66.3 + - + +
120B HIS* 3.2 10.7 + - - +
121B SER* 3.1 24.9 + - - -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.6 42.6 + + + +
103B TYR* 3.5 24.8 - + + +
114B LYS* 2.8 49.8 + - + +
115B ALA 3.7 1.1 - - - +
117B ASN* 1.3 77.2 - - + +
119B ILE* 1.3 64.7 + - - +
121B SER* 3.2 11.0 + - - -
122B VAL* 3.0 30.2 + - + +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 4.0 14.8 - - + -
89B CYS* 3.8 28.7 - - - -
103B TYR* 4.3 11.4 - - + +
108B VAL* 4.5 9.9 - - + -
115B ALA* 2.9 27.7 + - + +
116B VAL* 3.6 6.5 - - - +
117B ASN 3.3 0.4 - - - -
118B HIS* 1.3 74.5 - - - +
120B HIS* 1.3 57.8 + - - +
122B VAL* 3.3 5.9 + - - -
123B TRP* 2.9 26.5 + - - +
166B GLY* 4.7 3.6 - - - -
169B VAL* 3.8 29.4 - - + -
170B CYS* 3.6 7.0 - - - -
173B MET* 3.7 26.2 - - + -
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 3.8 26.2 - - + +
86B GLU* 5.8 1.1 - - - -
116B VAL* 3.1 40.0 + - + +
117B ASN* 3.5 11.7 + - - +
118B HIS 3.2 0.2 - - - -
119B ILE* 1.3 74.1 - - - +
121B SER* 1.3 59.4 + - - +
123B TRP* 3.3 13.8 + + + +
124B LYS* 2.8 30.4 + - - +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN 3.1 15.1 + - - -
118B HIS* 3.2 13.2 + - - -
120B HIS* 1.3 76.4 - - - +
122B VAL* 1.3 58.6 + - - +
124B LYS* 3.2 14.8 + - - +
125B ASP* 2.8 30.9 + - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 6.0 6.7 - - + -
103B TYR* 5.4 0.9 - - - +
118B HIS* 3.0 17.1 + - + +
119B ILE 3.6 6.7 - - - +
120B HIS 3.3 0.2 - - - -
121B SER* 1.3 76.3 - - - +
123B TRP* 1.3 57.6 + - - +
125B ASP* 3.3 7.4 + - - +
126B LEU* 2.9 37.3 + - + +
164B ASP* 6.1 0.2 - - - +
166B GLY* 4.0 22.4 - - - +
167B VAL* 4.1 22.7 - - + +
170B CYS* 3.6 19.5 - - + -
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.8 33.0 - - + +
119B ILE 2.9 16.6 + - - +
120B HIS* 3.6 14.8 - + + +
121B SER 3.3 0.2 - - - -
122B VAL* 1.3 76.4 - - - +
124B LYS* 1.3 63.6 + - - +
126B LEU* 3.3 10.3 + - + +
127B LEU* 3.1 44.1 + - + +
170B CYS* 3.5 35.8 - - + -
173B MET* 3.7 28.3 - - + -
174B ALA* 3.7 18.4 - - + -
248B GLU* 3.3 32.6 + - + -
252B ALA* 3.6 21.8 - - + -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B HIS 2.8 17.0 + - - +
121B SER* 3.4 11.7 - - - +
123B TRP* 1.3 79.1 - - - +
125B ASP* 1.3 65.7 + - - +
127B LEU* 3.2 11.1 + - - +
128B GLU* 2.8 66.3 + - + +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER 2.8 16.1 + - - +
122B VAL* 3.6 7.9 - - - +
124B LYS* 1.3 81.8 - - - +
126B LEU* 1.3 57.4 + - - +
128B GLU* 4.7 6.6 - - - +
129B ASP* 2.8 39.7 + - - +
259B ARG* 2.7 38.9 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 2.9 25.5 + - + +
123B TRP* 3.5 17.3 - - + +
124B LYS 3.2 0.2 - - - -
125B ASP* 1.3 78.9 - - - +
127B LEU* 1.3 64.3 + - + +
129B ASP 3.1 7.3 - - - +
130B THR* 4.1 1.2 - - - +
134B ILE* 3.8 28.9 - - + -
167B VAL* 5.9 1.1 - - + -
170B CYS* 3.7 31.2 - - + -
251B GLN* 4.7 0.2 - - - +
252B ALA* 5.1 4.0 - - + -
255B SER* 2.8 42.7 + - - +
256B LEU* 4.0 28.0 - - + +
259B ARG* 3.6 8.7 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 3.1 38.5 + - + +
124B LYS* 3.2 9.6 + - - +
126B LEU* 1.3 77.9 - - - +
128B GLU* 1.3 61.5 + - + +
248B GLU* 3.3 57.7 - - + +
251B GLN* 2.8 38.9 + - + +
252B ALA* 4.0 18.8 - - + +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 2.8 55.7 + - + +
125B ASP* 4.1 4.4 - - - +
127B LEU* 1.3 84.5 - - + +
129B ASP* 1.3 60.5 + - + +
130B THR* 4.0 4.0 + - - +
251B GLN* 5.1 0.9 + - - -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 2.8 26.4 + - - +
126B LEU 3.1 2.3 - - - +
128B GLU* 1.3 74.2 - - + +
130B THR* 1.3 61.6 + - - +
131B VAL* 2.7 35.5 + - - +
132B THR* 2.5 35.9 + - - -
255B SER* 2.9 8.3 + - - -
259B ARG* 2.7 32.7 + - - +
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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