Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 2ENV
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 GLN 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 2.9 34.0 - - - -
100A ARG* 4.9 6.7 - - - +
108A TYR* 3.0 43.9 + - + -
123A ASN* 4.6 8.0 + - - +
124A LYS 5.8 0.7 - - - +
125A CYS* 1.3 78.3 - - - +
127A TYR* 1.3 71.9 + - - +
129A ARG* 2.9 23.3 + - - +
130A PHE* 3.0 10.2 + - - +
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Residues in contact with TYR 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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108A TYR* 3.7 32.1 - - + -
109A GLU 3.0 26.2 - - - +
110A LYS* 3.5 31.3 - - + +
111A CYS* 3.3 35.2 - - + -
125A CYS* 4.0 1.9 - - - -
126A GLN* 1.3 79.4 - - - +
128A CYS* 1.3 70.6 + - - +
130A PHE* 3.0 6.4 + + + +
131A GLN* 2.8 60.1 + - + +
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Residues in contact with CYS 128 (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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111A CYS* 3.8 8.1 - - - -
114A SER* 3.6 11.4 - - - -
115A CYS* 3.0 33.4 - - + +
117A ILE* 4.2 8.5 - - + -
125A CYS* 3.6 9.7 - - + -
126A GLN 3.3 0.2 - - - -
127A TYR* 1.3 82.3 - - - +
129A ARG* 1.3 58.4 + - - +
131A GLN* 3.1 6.3 + - - +
132A LYS* 2.8 31.9 + - - +
300A ZN 2.3 36.6 - - - -
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Residues in contact with ARG 129 (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 VAL* 4.8 12.1 - - + +
93A GLY 5.3 3.0 + - - -
94A CYS* 5.6 8.5 - - - +
97A PHE* 3.1 56.2 - - + +
117A ILE* 3.4 23.1 - - + +
122A ARG* 3.0 38.1 + - - +
123A ASN* 3.1 32.5 + - - +
125A CYS 3.3 12.9 + - - +
126A GLN* 2.9 15.9 + - - +
128A CYS* 1.3 80.2 - - - +
130A PHE* 1.3 62.4 + - - +
132A LYS* 3.2 10.4 + - - +
133A CYS* 3.3 14.9 + - - -
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Residues in contact with PHE 130 (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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97A PHE* 3.4 20.0 - + + -
98A PHE* 3.8 27.1 - + - -
101A THR* 3.4 40.6 - - + -
102A ILE* 3.8 20.0 - - + -
106A LEU 5.2 2.7 - - - -
108A TYR* 4.5 11.9 - + + -
126A GLN 3.0 4.3 + - - +
127A TYR* 3.0 11.4 + + - +
129A ARG* 1.3 77.9 - - - +
131A GLN* 1.3 67.7 + - + +
133A CYS* 3.3 17.2 + - - +
134A LEU* 3.4 34.5 + - + +
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Residues in contact with GLN 131 (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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127A TYR* 2.8 56.2 + - + +
128A CYS* 3.3 11.7 - - - +
130A PHE* 1.3 76.9 - - + +
132A LYS* 1.3 68.9 + - - +
134A LEU* 2.8 38.0 + - - +
135A ALA* 2.9 13.2 + - - +
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Residues in contact with LYS 132 (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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75A ARG 3.5 15.2 + - - -
76A VAL* 2.8 32.8 + - + +
77A CYS 5.2 1.2 + - - -
116A LYS* 5.1 10.1 - - - +
117A ILE* 3.3 36.5 + - + +
128A CYS 2.8 15.0 + - - +
129A ARG 3.5 9.0 - - - +
131A GLN* 1.3 71.6 - - - +
133A CYS* 1.3 64.0 + - - +
135A ALA* 3.2 8.7 + - + +
136A LEU* 3.0 42.1 + - + +
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Residues in contact with CYS 133 (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 VAL* 3.7 23.3 - - - -
94A CYS* 5.4 4.0 - - - -
97A PHE* 5.2 4.7 - - - -
98A PHE* 3.5 24.2 - - + -
129A ARG* 3.3 15.8 + - - -
130A PHE* 3.3 12.2 + - - +
131A GLN 3.0 0.4 + - - -
132A LYS* 1.3 80.4 - - - +
134A LEU* 1.3 61.5 + - - +
136A LEU* 3.4 8.1 + - - +
137A GLY 3.3 5.5 + - - -
138A MET* 3.1 57.5 + - - +
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Residues in contact with LEU 134 (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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98A PHE* 4.5 17.5 - - + -
130A PHE* 3.6 38.8 - - + +
131A GLN* 2.8 36.8 + - - +
133A CYS* 1.3 69.9 - - - +
135A ALA* 1.3 64.5 + - - +
137A GLY* 2.9 16.1 + - - -
138A MET 4.4 11.7 - - - +
140A HIS* 5.5 7.4 - - + -
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Residues in contact with ALA 135 (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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131A GLN 2.9 11.6 + - - +
132A LYS* 3.5 13.2 - - - +
134A LEU* 1.3 77.2 - - - +
136A LEU* 1.3 64.1 + - + +
137A GLY* 3.2 1.2 + - - -
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Residues in contact with LEU 136 (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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75A ARG* 3.8 57.0 - - + +
76A VAL* 3.7 31.9 - - + -
88A VAL* 4.1 19.3 - - + +
132A LYS* 3.0 31.5 + - + +
133A CYS* 3.6 6.1 - - - +
134A LEU 3.2 0.2 - - - -
135A ALA* 1.3 75.7 - - + +
137A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 137 (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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86A TYR 3.5 8.5 - - - +
87A GLY* 5.1 1.7 - - - -
88A VAL* 5.1 4.0 + - - -
134A LEU 2.9 12.8 + - - -
135A ALA 3.1 1.1 - - - -
136A LEU* 1.3 81.5 - - - +
138A MET* 1.3 65.5 + - - +
139A SER* 3.3 4.2 + - - -
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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