Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 3Q19
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PRO* 3.3 2.7 - - + +
105A TYR* 1.3 77.4 - - - +
107A PRO* 1.3 70.9 - - - +
108A TYR* 3.3 13.8 + - - +
109A GLU* 2.9 42.7 + - + +
110A ARG* 2.9 31.0 + - - +
81B GLN* 5.5 0.3 + - - -
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Residues in contact with PRO 107 (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 TYR 3.4 8.5 - - - +
106A ASP* 1.3 92.3 - - - +
108A TYR* 1.3 56.1 + - - +
110A ARG* 3.4 8.1 + - + +
111A ALA* 2.9 29.3 + - - +
92B TYR* 3.7 11.0 - - + +
95B ASP* 4.0 22.7 - - + +
96B ALA* 3.9 39.3 - - + +
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Residues in contact with TYR 108 (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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106A ASP* 3.3 11.3 + - - +
107A PRO* 1.3 75.9 - - - +
109A GLU* 1.3 82.2 + - - +
111A ALA* 3.2 2.0 + - + +
112A ARG* 2.9 58.5 + - + +
115A MET* 5.6 0.7 - - - -
81B GLN* 3.3 55.8 - - + +
82B LEU 4.0 21.3 + - - -
83B ILE* 3.9 22.0 - - + -
92B TYR* 3.6 17.1 - - + +
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Residues in contact with GLU 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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104A PRO* 3.8 25.6 - - + -
106A ASP* 2.9 28.2 + - + +
108A TYR* 1.3 93.7 - - - +
110A ARG* 1.3 61.3 + - - +
112A ARG* 3.3 19.5 + - - +
113A GLN* 3.1 27.0 + - - +
167A GLY* 5.1 7.7 - - - +
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Residues in contact with ARG 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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91A GLU* 2.8 37.0 + - - +
94A ASP* 4.9 1.2 + - - -
95A ASP* 3.3 35.2 + - - -
101A LYS* 5.8 2.2 - - - +
103A PHE* 3.7 34.0 - - + +
104A PRO* 3.9 27.0 + - + +
105A TYR 5.8 1.1 - - - -
106A ASP 2.9 16.7 + - - +
107A PRO* 3.6 7.9 - - + +
109A GLU* 1.3 74.9 - - - +
111A ALA* 1.3 64.9 + - - +
113A GLN* 3.2 14.0 + - - +
114A LYS* 3.2 24.1 + - - +
95B ASP* 4.4 18.8 + - - +
110B ARG* 4.9 7.1 - - - +
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Residues in contact with ALA 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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107A PRO 2.9 18.9 + - - +
108A TYR* 3.6 4.7 - - - +
110A ARG* 1.3 76.2 - - - +
112A ARG* 1.3 56.1 + - - +
114A LYS* 3.2 9.7 + - - +
115A MET* 3.0 33.4 + - - +
83B ILE* 4.3 11.4 - - + -
88B ILE* 3.8 21.6 - - + +
92B TYR* 4.1 23.1 - - + +
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Residues in contact with ARG 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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108A TYR* 2.9 45.3 + - + +
109A GLU* 3.5 23.3 - - - +
110A ARG 3.2 0.2 - - - -
111A ALA* 1.3 77.1 - - - +
113A GLN* 1.3 57.0 + - + +
115A MET* 3.1 16.6 + - + +
116A LEU* 2.9 49.0 + - + +
157A ILE* 4.3 13.9 - - - +
160A TYR* 4.9 12.5 - - - -
161A GLN* 2.3 43.9 + - - +
166A PHE 4.1 3.4 + - - -
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Residues in contact with GLN 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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103A PHE* 3.7 12.5 - - + -
104A PRO* 3.5 27.0 - - + +
109A GLU* 3.1 15.2 + - - +
110A ARG 3.2 7.2 + - - +
112A ARG* 1.3 76.1 - - + +
114A LYS* 1.3 58.9 + - - +
116A LEU* 3.3 9.6 + - + -
117A LEU* 3.0 24.6 + - - +
167A GLY* 3.8 16.0 + - - -
172A SER* 2.8 23.5 + - - -
173A MET* 3.7 12.5 + - - +
174A ILE* 3.0 51.9 + - + +
177A LEU* 5.8 1.3 - - + +
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Residues in contact with LYS 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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87A VAL* 6.1 3.5 - - + +
91A GLU* 2.5 38.5 + - - -
103A PHE* 4.1 25.1 - - + -
110A ARG* 3.2 24.0 + - - +
111A ALA* 3.2 14.2 + - - +
113A GLN* 1.3 74.2 - - - +
115A MET* 1.3 64.6 + - - +
117A LEU* 3.4 17.2 + - + +
118A GLU* 3.1 26.2 + - - +
88B ILE* 3.7 16.6 - - + -
91B GLU* 3.4 24.7 + - + +
110B ARG* 5.7 0.6 - - - +
114B LYS* 3.4 11.3 - - - +
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Residues in contact with MET 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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108A TYR* 5.6 1.1 - - - -
111A ALA 3.0 21.5 + - - +
112A ARG* 3.1 18.8 + - + +
114A LYS* 1.3 77.5 - - - +
116A LEU* 1.3 57.6 + - + +
118A GLU* 3.2 7.6 + - - +
119A LEU* 3.0 25.8 + - - +
82B LEU* 3.6 22.7 - - + +
83B ILE* 3.9 7.2 - - - -
84B TYR* 3.3 74.7 - - + +
88B ILE* 4.0 9.2 - - + -
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Residues in contact with LEU 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 ARG* 2.9 35.5 + - + +
113A GLN* 3.5 11.4 - - + +
115A MET* 1.3 74.4 - - + +
117A LEU* 1.3 65.9 - - - +
119A LEU* 3.2 15.2 + - + +
120A PHE* 3.1 22.2 + - - +
154A LEU* 5.0 5.8 - - + +
157A ILE* 4.1 35.7 - - + -
166A PHE* 3.7 46.0 - - + +
174A ILE* 3.9 15.9 - - + -
178A LEU* 5.0 2.5 - - + +
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Residues in contact with LEU 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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37A ARG* 3.8 29.2 - - - +
87A VAL* 3.6 36.8 - - + -
103A PHE* 6.4 0.4 - - + -
113A GLN 3.0 13.6 + - - +
114A LYS* 3.4 19.5 - - + +
115A MET 3.3 0.2 - - - -
116A LEU* 1.3 74.6 - - - +
118A GLU* 1.3 67.2 + - - +
120A PHE* 3.2 21.2 + - + +
121A SER* 3.5 7.3 + - - -
174A ILE* 3.7 9.3 - - + +
177A LEU* 4.1 25.4 - - + -
178A LEU* 4.5 6.3 - - + -
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Residues in contact with GLU 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 LYS 3.1 19.4 + - - +
115A MET* 3.2 8.7 + - - +
117A LEU* 1.3 81.9 - - - +
119A LEU* 1.3 62.0 + - - +
121A SER* 3.0 34.2 + - - -
88B ILE* 3.8 19.1 - - + +
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Residues in contact with LEU 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 MET 3.0 13.0 + - - +
116A LEU* 3.4 17.5 - - + +
118A GLU* 1.3 77.3 - - - +
120A PHE* 1.3 59.5 + - - +
121A SER* 3.2 0.9 + - - -
122A LYS* 4.8 0.7 + - - +
150A GLU* 3.9 18.5 - - - +
153A ASN* 4.2 31.7 + - + +
154A LEU* 4.1 21.9 - - + +
157A ILE* 4.1 25.1 - - + -
68B PRO* 6.3 3.1 - - + -
69B PHE* 6.6 0.4 - - + -
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Residues in contact with PHE 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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37A ARG* 4.2 11.0 - - - -
116A LEU 3.1 11.1 + - - +
117A LEU* 3.3 13.9 - - + +
118A GLU 3.1 0.4 - - - -
119A LEU* 1.3 75.6 - - - +
121A SER* 1.3 57.1 + - - +
122A LYS 3.2 2.5 - - - -
123A VAL* 2.9 61.3 + - + +
124A PRO* 3.5 18.5 - - + +
150A GLU* 5.6 0.2 - - - -
154A LEU* 3.9 17.5 - - + +
178A LEU* 3.6 50.3 - - + -
181A TRP* 3.8 26.2 - + + -
182A PHE* 3.8 15.9 - + - -
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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