Contacts of the helix formed by residues 116 - 127 (chain A) in PDB entry 2H5X
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 GLY 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A THR* 4.3 5.7 + - - -
114A GLY 3.7 4.4 + - - -
115A ILE* 1.3 79.2 - - - +
117A LYS* 1.3 65.7 + - - -
118A ARG* 3.0 30.0 - - - +
119A GLY* 3.9 5.4 - - - +
120A ALA* 3.0 19.9 + - - +
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Residues in contact with LYS 117 (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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106A VAL* 3.9 7.8 - - + +
110A THR* 4.5 11.4 + - - +
116A GLY* 1.3 72.9 - - - +
118A ARG* 1.3 72.0 + - + +
120A ALA* 3.7 2.8 + - - +
121A GLU* 3.0 34.7 + - - +
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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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116A GLY* 3.0 28.9 - - - +
117A LYS* 1.3 78.3 - - + +
119A GLY* 1.3 70.6 + - - +
121A GLU* 2.8 26.8 + - - +
122A ARG* 2.9 32.9 + - + +
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Residues in contact with GLY 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 ILE* 4.0 6.5 - - - -
116A GLY 3.5 10.1 + - - -
117A LYS 3.5 0.2 - - - -
118A ARG* 1.3 85.2 - - - +
120A ALA* 1.3 63.4 + - - +
122A ARG* 3.2 24.5 + - - +
123A MET* 3.1 27.0 + - - +
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Residues in contact with ALA 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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106A VAL* 3.7 25.8 - - + +
109A LEU* 3.7 23.3 - - + -
110A THR* 4.6 1.1 - - - +
115A ILE* 3.4 19.0 - - + +
116A GLY 3.0 16.6 + - - +
117A LYS 3.7 0.2 - - - +
119A GLY* 1.3 74.4 - - - +
121A GLU* 1.3 58.3 + - - +
123A MET* 3.1 5.4 + - - +
124A VAL* 2.9 35.0 + - - +
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Residues in contact with GLU 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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106A VAL* 4.3 19.1 - - + -
117A LYS* 3.0 23.4 - - - +
118A ARG* 2.8 25.9 + - - +
120A ALA* 1.3 73.3 - - - +
122A ARG* 1.3 56.0 + - + -
124A VAL* 3.5 6.5 + - - +
125A LEU* 2.9 31.7 + - - +
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Residues in contact with ARG 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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77A VAL* 4.7 7.1 - - + +
78A SER* 3.8 22.4 + - - -
79A GLY* 5.6 0.2 - - - -
118A ARG* 3.1 26.8 + - + +
119A GLY* 3.2 24.6 + - - +
121A GLU* 1.3 73.2 - - + +
123A MET* 1.3 60.9 + - - +
125A LEU* 4.3 6.1 - - - -
126A GLU* 2.8 51.6 + - - +
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Residues in contact with MET 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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74A LEU* 3.8 30.5 - - + +
77A VAL* 4.2 23.6 - - + -
80A VAL* 4.4 26.5 - - + -
84A LEU* 6.3 0.2 - - - -
85A ALA* 6.5 0.2 - - - -
88A ALA* 5.3 6.3 - - + -
97A LEU* 6.1 1.8 - - + -
101A LEU* 4.3 8.7 - - + -
109A LEU* 4.4 13.0 - - + -
115A ILE* 3.7 37.5 - - + -
119A GLY 3.1 15.1 + - - +
120A ALA* 3.4 7.4 - - - +
122A ARG* 1.3 73.2 - - - +
124A VAL* 1.3 65.8 + - - +
126A GLU 3.3 0.3 + - - -
127A LEU* 3.0 35.6 + - + +
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Residues in contact with VAL 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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101A LEU* 4.2 12.1 - - + +
104A GLY* 3.5 33.9 - - - +
106A VAL* 4.4 8.7 - - + -
109A LEU* 3.5 20.9 - - + -
120A ALA 2.9 22.3 + - - +
121A GLU* 3.8 5.8 - - - +
123A MET* 1.3 77.1 - - - +
125A LEU* 1.3 61.8 + - - +
127A LEU 5.0 0.2 - - - -
128A ARG* 2.7 63.7 + - + +
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Residues in contact with LEU 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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121A GLU 2.9 19.2 + - - +
122A ARG* 3.7 7.0 - - - +
124A VAL* 1.3 80.1 - - - +
126A GLU* 1.3 75.6 + - - +
127A LEU* 3.5 0.5 + - - -
128A ARG* 3.8 28.6 + - - +
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Residues in contact with GLU 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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76A SER 5.7 0.9 - - - +
77A VAL* 3.8 33.0 - - + +
78A SER* 5.3 5.1 + - - +
122A ARG* 2.8 44.5 + - - +
123A MET 3.8 0.4 - - - +
125A LEU* 1.3 92.6 - - - +
127A LEU* 1.3 61.0 + - + +
128A ARG 4.1 0.2 - - - -
130A LYS* 4.5 10.6 - - - +
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Residues in contact with LEU 127 (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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70A LEU* 6.5 0.2 - - + -
73A THR* 3.4 36.1 - - + +
74A LEU* 4.6 9.0 - - + -
76A SER* 4.2 4.0 - - - +
77A VAL* 3.4 28.0 - - + -
101A LEU* 3.5 36.2 - - + +
123A MET* 3.0 23.7 + - + +
124A VAL 3.8 3.8 - - - -
125A LEU 3.4 0.2 - - - -
126A GLU* 1.3 80.9 - - + +
128A ARG* 1.3 59.3 + - - +
129A ASP 3.6 0.2 - - - -
130A LYS* 4.0 24.5 - - + -
131A VAL* 3.6 18.5 - - + +
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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