Contacts of the helix formed by residues 115 - 126 (chain A) in PDB entry 6MOL
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 HIS 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ALA 3.6 16.2 - - - -
79A THR 3.5 7.3 + - - -
80A MET 3.2 24.2 + - - -
81A GLY* 3.5 21.7 + - - -
110A ALA* 3.1 8.9 + - + +
113A MET* 3.6 25.4 - - + +
114A GLY* 1.3 76.0 + - - +
116A VAL* 1.3 59.4 + - - +
117A GLU* 3.3 4.9 - - - +
118A ILE* 3.3 24.4 + - + +
119A VAL* 2.9 31.1 + - - +
151A ILE* 4.3 0.2 - - - -
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Residues in contact with VAL 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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114A GLY 3.7 4.9 + - - +
115A HIS* 1.3 70.2 - - - +
117A GLU* 1.3 86.5 + - + +
119A VAL* 3.2 3.2 + - + +
120A GLU* 2.9 32.7 + - - +
150A GLU* 3.9 40.4 - - + +
151A ILE* 3.8 22.2 - - + -
154A VAL* 4.2 23.3 - - + -
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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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83A LEU* 3.7 31.0 - - + -
115A HIS* 4.5 2.8 - - - +
116A VAL* 1.3 97.4 + - + +
118A ILE* 1.3 66.1 + - + +
120A GLU* 3.5 9.6 + - - +
121A VAL* 3.2 29.3 + - + +
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Residues in contact with ILE 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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78A ALA* 4.3 9.0 - - + +
81A GLY* 4.0 16.2 - - - +
82A HIS 4.6 0.2 - - - -
83A LEU* 3.7 38.1 - - + +
86A VAL* 3.9 33.4 - - + -
110A ALA* 3.8 20.4 - - + -
115A HIS* 3.3 26.8 + - + +
117A GLU* 1.3 79.4 - - + +
119A VAL* 1.3 65.6 + - - +
121A VAL* 3.4 2.8 + - - +
122A LEU* 3.1 35.3 + - + +
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Residues in contact with VAL 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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107A LEU* 4.0 16.1 - - + +
110A ALA* 3.8 29.4 - - + +
111A ALA* 4.1 5.4 - - + +
115A HIS 2.9 21.9 + - - +
116A VAL* 3.2 8.5 + - - +
118A ILE* 1.3 78.7 - - - +
120A GLU* 1.3 61.7 + - - +
122A LEU* 3.4 1.9 + - - +
123A LEU* 3.1 42.1 + - + +
151A ILE* 4.0 21.1 - - + -
154A VAL* 4.1 13.5 - - + -
155A LEU* 4.2 9.2 - - + -
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Residues in contact with GLU 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 VAL* 2.9 26.8 + - - +
117A GLU* 4.0 9.1 - - - +
119A VAL* 1.3 77.4 - - - +
121A VAL* 1.3 58.2 - - + +
123A LEU* 3.9 4.2 - - - +
124A LYS* 3.0 29.8 + - - +
154A VAL* 3.7 37.1 - - + +
158A TYR* 4.0 13.1 + - + +
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Residues in contact with VAL 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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83A LEU* 3.8 11.2 - - + -
86A VAL* 4.5 5.4 - - + -
87A GLU* 3.8 36.1 - - + +
90A LEU* 3.7 22.0 - - + -
117A GLU 3.2 18.3 + - - +
118A ILE* 3.9 4.5 - - - +
119A VAL 3.3 0.4 - - - -
120A GLU* 1.3 75.8 - - + +
122A LEU* 1.3 61.9 + - - +
124A LYS* 3.4 4.8 + - - +
125A TYR* 2.9 37.4 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LEU* 4.2 12.8 - - + -
78A ALA* 4.6 2.0 - - + -
86A VAL* 4.6 5.8 - - + -
90A LEU* 3.7 33.0 - - + -
96A VAL* 3.8 11.4 - - + +
106A PRO* 3.6 39.7 - - + +
107A LEU* 4.0 9.2 - - + +
110A ALA* 4.6 1.8 - - + -
118A ILE* 3.1 37.0 + - + +
119A VAL 3.9 3.1 - - - +
121A VAL* 1.3 76.6 - - - +
123A LEU* 1.3 61.0 + - - +
125A TYR* 3.2 5.5 + - - +
126A GLY 3.1 7.8 + - - -
127A ALA* 3.0 30.9 + - + +
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Residues in contact with LEU 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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107A LEU* 3.9 23.3 - - + -
119A VAL* 3.1 28.2 + - + +
120A GLU 4.0 1.1 - - - +
122A LEU* 1.3 76.4 - - - +
124A LYS* 1.3 61.6 + - - +
126A GLY* 3.3 11.8 + - - -
127A ALA* 3.6 23.1 + - + +
129A VAL* 3.9 16.6 - - + -
154A VAL* 4.0 4.9 - - + -
155A LEU* 3.7 24.0 - - + -
158A TYR* 3.6 52.1 - - + -
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU 3.0 20.5 + - - +
121A VAL* 3.8 5.4 - - - +
123A LEU* 1.3 76.7 - - - +
125A TYR* 1.3 63.0 + - + +
126A GLY 3.7 0.2 + - - -
158A TYR* 4.3 12.7 + - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLU* 4.4 5.9 + - + -
90A LEU* 3.5 57.7 - - + -
91A LYS* 3.5 24.5 + - - +
96A VAL* 4.4 13.4 - - + +
121A VAL* 2.9 27.2 + - + +
122A LEU* 3.2 6.4 + - - +
124A LYS* 1.3 78.9 - - + +
126A GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 126 (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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96A VAL* 3.5 9.3 - - - +
97A ASN* 2.9 18.9 + - - -
122A LEU 3.1 1.8 + - - -
123A LEU 3.3 9.0 + - - -
124A LYS 3.3 0.6 - - - -
125A TYR* 1.3 79.3 - - - +
127A ALA* 1.3 62.8 + - - +
128A ASP 3.9 0.2 + - - -
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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