Contacts of the helix formed by residues 108 - 120 (chain A) in PDB entry 5ABT
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A THR* 2.8 27.0 + - - +
107A LYS* 1.3 88.5 + - - +
109A PRO* 1.3 66.2 - - - +
110A ASP 3.3 2.7 - - - -
111A VAL* 3.1 25.8 + - - +
112A VAL* 3.1 17.3 + - - +
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Residues in contact with PRO 109 (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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105A ALA 4.1 4.7 - - - +
106A MET 3.8 12.1 - - - +
107A LYS 3.6 7.9 - - - +
108A SER* 1.3 88.9 - - - +
110A ASP* 1.3 62.5 + - - +
112A VAL 3.3 0.7 + - - -
113A LYS* 2.8 38.8 + - - +
156A LEU* 5.6 2.7 - - + -
159A THR* 4.0 21.5 - - + -
160A TYR* 3.1 19.0 + - - +
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Residues in contact with ASP 110 (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 SER 3.3 0.6 - - - -
109A PRO* 1.3 81.2 - - - +
111A VAL* 1.3 63.7 + - + +
113A LYS* 3.6 19.4 + - - +
114A GLY* 3.4 15.2 + - - -
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Residues in contact with VAL 111 (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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83A ARG 5.4 1.3 - - - +
84A THR* 6.1 0.4 - - - -
104A THR* 4.8 2.9 - - + -
108A SER* 3.1 25.9 + - - +
110A ASP* 1.3 79.2 - - + +
112A VAL* 1.3 58.9 + - + +
114A GLY* 3.0 17.0 + - - -
115A TRP* 3.3 40.3 + - + +
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Residues in contact with VAL 112 (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 ILE* 5.3 4.7 - - + -
104A THR* 3.5 39.9 - - + +
105A ALA* 3.7 15.0 - - + +
108A SER 3.1 4.4 + - - +
111A VAL* 1.3 73.8 - - - +
113A LYS* 1.3 66.0 + - - +
115A TRP* 2.9 40.6 + - + +
116A PHE* 3.0 25.8 + - + -
124A LEU* 5.5 0.7 - - + -
160A TYR* 3.5 29.2 - - + +
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Residues in contact with LYS 113 (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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109A PRO* 2.8 25.5 + - - +
110A ASP* 3.7 18.6 + - - +
111A VAL 3.3 0.2 - - - -
112A VAL* 1.3 76.4 - - - +
114A GLY* 1.3 60.0 + - - +
116A PHE* 3.3 12.2 + - - +
117A GLU* 3.1 20.4 + - - +
159A THR* 3.3 37.0 + - - +
160A TYR* 4.0 10.7 - - + -
162A PRO* 6.0 3.5 - - - +
163A VAL* 3.9 28.5 - - + +
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Residues in contact with GLY 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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85A GLU* 5.8 2.5 - - - -
110A ASP 3.4 7.0 + - - -
111A VAL 3.0 10.6 + - - -
113A LYS* 1.3 74.9 - - - +
115A TRP* 1.3 63.1 + - - +
117A GLU* 3.2 9.2 + - - +
118A ARG* 3.0 27.9 + - - +
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Residues in contact with TRP 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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82A VAL* 4.3 4.3 - - + -
83A ARG 3.4 27.4 - - - -
84A THR* 3.4 21.3 - - - -
85A GLU* 3.4 35.3 + - + +
88A VAL* 3.9 12.3 - - + -
101A ILE* 3.5 46.7 - - + -
104A THR* 3.9 14.4 - - + -
111A VAL* 3.3 35.0 - - + +
112A VAL* 2.9 24.1 + - + +
114A GLY* 1.3 75.7 - - - +
116A PHE* 1.3 61.0 + - - +
118A ARG* 4.4 0.7 - - - +
119A PHE* 2.8 52.2 + + + +
124A LEU* 3.9 8.1 - - + -
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Residues in contact with PHE 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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112A VAL* 3.0 36.2 + - + -
113A LYS 3.5 8.1 - - - +
115A TRP* 1.3 76.0 - - - +
117A GLU* 1.3 58.1 + - - +
120A GLY* 2.9 29.0 + - - +
121A ALA* 3.9 31.8 + - + -
124A LEU* 3.8 30.5 - - + -
126A LEU* 5.3 6.7 - - + -
160A TYR* 3.7 22.0 - + + -
163A VAL* 3.8 35.5 - - + +
165A LEU* 3.9 41.3 - - + -
166A LYS 5.0 0.2 - - - -
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Residues in contact with GLU 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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113A LYS 3.1 13.0 + - - +
114A GLY* 3.4 11.4 - - - +
115A TRP 3.2 0.4 - - - -
116A PHE* 1.3 79.5 - - - +
118A ARG* 1.3 63.4 + - - +
120A GLY* 4.5 1.0 + - - -
163A VAL* 5.8 0.2 - - - +
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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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85A GLU* 2.7 52.1 + - - +
86A GLU* 5.2 4.0 + - - +
89A ALA* 3.5 22.6 - - - +
114A GLY 3.0 15.2 + - - +
115A TRP* 3.2 2.7 + - - +
117A GLU* 1.3 81.6 - - - +
119A PHE* 1.3 91.4 + - + +
120A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 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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85A GLU* 3.3 35.9 - - + -
88A VAL* 3.6 23.6 - - + -
89A ALA* 3.7 24.5 - - + -
92A LEU* 3.5 16.4 - - + -
115A TRP* 2.8 39.4 + - + +
118A ARG* 1.3 108.2 - - + +
120A GLY* 1.3 67.4 + - - +
122A GLN* 6.0 0.2 - - - +
123A ALA* 3.8 21.6 + - + +
124A LEU* 4.6 6.3 - - + -
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Residues in contact with GLY 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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116A PHE* 2.9 22.8 + - - -
117A GLU 4.5 1.0 + - - -
118A ARG 3.5 1.6 - - - -
119A PHE* 1.3 83.7 - - - +
121A ALA* 1.3 63.7 + - - -
122A GLN* 3.2 3.6 - - - -
123A ALA* 3.2 13.2 + - - +
124A LEU* 3.8 9.5 - - - +
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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