Contacts of the helix formed by residues 117 - 132 (chain A) in PDB entry 2E9D
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 ASN 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLU* 4.0 16.4 + - - +
115A ARG* 3.9 2.4 + - - +
116A PHE* 1.3 81.5 - - - +
118A SER* 1.3 60.4 + - - +
119A ARG* 2.9 26.2 + - + +
120A LEU* 2.8 43.0 + - - +
121A GLN* 2.9 17.0 + - - +
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Residues in contact with SER 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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117A ASN* 1.3 71.6 - - - +
119A ARG* 1.3 67.7 + - - +
121A GLN* 3.8 14.4 - - - +
122A GLU* 3.5 19.2 + - - +
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Residues in contact with ARG 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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117A ASN* 2.9 13.3 + - + +
118A SER* 1.3 77.6 + - - +
120A LEU* 1.3 68.0 + - + +
121A GLN 3.1 0.7 + - - -
122A GLU* 3.1 10.5 + - - +
123A ARG* 2.9 64.4 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 4.1 22.9 - - + +
90A VAL* 3.2 45.6 - - + +
116A PHE* 4.0 20.9 - - + -
117A ASN* 2.8 44.6 + - - +
119A ARG* 1.3 85.1 - - + +
121A GLN* 1.3 51.7 + - - +
123A ARG* 3.1 30.5 - - - +
124A ILE* 2.8 40.0 + - + +
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Residues in contact with GLN 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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113A THR* 3.2 25.7 + - - +
114A SER* 4.1 11.2 + - - -
116A PHE* 2.3 34.1 + - + +
117A ASN 2.9 17.0 + - - +
118A SER* 3.8 12.4 - - - +
119A ARG 3.1 0.6 - - - -
120A LEU* 1.3 74.4 - - - +
122A GLU* 1.3 65.4 + - - +
124A ILE* 3.2 14.8 - - + +
125A ARG* 3.2 20.6 + - - +
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Residues in contact with GLU 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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118A SER 3.5 9.0 + - - +
119A ARG* 3.1 11.4 + - - +
121A GLN* 1.3 74.0 - - - +
123A ARG* 1.3 53.6 - - + +
124A ILE 2.6 15.8 + - - -
125A ARG* 2.9 12.7 + - - +
126A LYS* 2.7 57.4 + - + +
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Residues in contact with ARG 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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87A GLU 5.3 1.0 + - - -
90A VAL* 4.3 7.3 - - + +
91A TRP* 3.3 35.6 - - - +
93A LEU 5.2 0.3 - - - +
94A ASP* 2.7 42.9 + - - +
119A ARG* 2.9 63.7 - - + +
120A LEU* 3.1 41.5 - - - +
122A GLU* 1.3 78.7 - - + +
124A ILE* 1.3 50.2 + - - +
126A LYS* 4.2 9.6 - - - +
127A SER* 2.4 26.7 + - - -
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Residues in contact with ILE 124 (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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90A VAL* 5.0 11.9 - - + -
93A LEU* 5.8 5.8 - - + -
109A ILE* 4.0 26.2 - - + +
113A THR* 4.2 31.4 - - + +
116A PHE* 5.7 3.8 - - + -
120A LEU* 2.8 27.6 + - + +
121A GLN* 3.2 18.6 - - + +
122A GLU 2.6 5.5 + - - -
123A ARG* 1.3 74.7 - - - +
125A ARG* 1.3 54.4 + - + +
126A LYS 3.1 1.6 - - - -
127A SER* 2.9 9.2 - - - -
128A GLU* 2.8 56.0 + - - +
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Residues in contact with ARG 125 (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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121A GLN 3.2 9.5 + - - +
122A GLU* 2.9 11.8 + - - +
124A ILE* 1.3 77.4 - - - +
126A LYS* 1.3 62.0 + - - +
128A GLU* 3.6 14.4 - - + +
129A ALA* 2.6 53.1 + - + +
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Residues in contact with LYS 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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122A GLU* 2.7 47.4 + - + +
123A ARG* 4.2 8.7 - - - +
125A ARG* 1.3 86.5 - - - +
127A SER* 1.3 54.6 + - - +
129A ALA* 3.1 5.4 - - + +
130A LEU* 2.8 39.4 + - + +
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Residues in contact with SER 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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93A LEU* 4.8 3.4 + - - +
97A VAL* 4.1 31.4 - - - +
107A LEU* 4.3 18.6 - - - -
109A ILE* 5.9 0.9 - - - -
123A ARG 2.4 28.1 + - - -
124A ILE* 2.9 12.9 - - - -
126A LYS* 1.3 74.0 - - - +
128A GLU* 1.3 64.1 + - - -
129A ALA 3.2 0.2 + - - -
130A LEU* 3.3 5.5 + - - +
131A THR* 3.1 29.4 + - - +
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Residues in contact with GLU 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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107A LEU* 3.1 28.4 - - + +
108A ARG* 3.8 28.9 + - - +
109A ILE* 3.2 29.5 + - + +
124A ILE* 2.8 43.9 + - + +
125A ARG* 3.6 14.7 - - + +
127A SER* 1.3 72.9 - - - +
129A ALA* 1.3 57.8 + - - +
131A THR* 3.9 0.6 + - - -
132A ALA* 2.8 33.8 + - - +
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Residues in contact with ALA 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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125A ARG* 2.6 41.0 + - - +
126A LYS* 3.1 9.0 - - + +
128A GLU* 1.3 72.9 - - - +
130A LEU* 1.3 67.1 + - - +
132A ALA* 2.9 21.5 - - - +
133A GLY 4.5 0.5 + - - -
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Residues in contact with LEU 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 VAL* 4.4 18.2 - - + -
98A LYS* 5.9 3.6 - - + -
101A HIS* 3.8 44.3 - - + +
126A LYS 2.8 20.6 + - - +
127A SER* 3.5 5.4 - - - +
129A ALA* 1.3 75.6 - - - +
131A THR* 1.3 63.6 + - + +
133A GLY 4.3 2.8 + - - -
134A ASN* 5.0 0.2 - - - +
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Residues in contact with THR 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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97A VAL* 4.6 9.6 - - + +
100A LEU* 4.6 2.9 - - + -
101A HIS* 3.9 29.4 - - + +
105A VAL 2.8 27.6 - - - +
106A ARG* 3.7 4.1 - - - -
107A LEU* 2.6 33.1 + - + +
127A SER 3.1 15.7 + - - +
128A GLU 3.9 1.6 + - - -
130A LEU* 1.3 76.7 - - + +
132A ALA* 1.3 54.2 + - - +
133A GLY 2.6 19.4 + - - -
134A ASN* 2.8 25.0 + - - +
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Residues in contact with ALA 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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106A ARG* 2.7 35.7 + - - +
108A ARG* 6.2 1.3 - - - +
128A GLU 2.8 23.5 + - - +
129A ALA* 2.9 17.4 + - - +
131A THR* 1.3 74.0 + - - +
133A GLY* 1.3 53.9 + - - +
134A ASN 4.7 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