Contacts of the helix formed by residues 116 - 133 (chain A) in PDB entry 1ESG
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY* 1.3 67.6 - - - -
117A ILE* 1.3 65.8 + - + +
118A SER* 3.3 13.4 - - - +
119A SER* 2.7 46.0 + - - +
120A ALA 3.1 1.0 + - - -
155A ARG* 3.3 28.3 - - + +
157A THR* 2.9 12.3 + - - -
116B ASN* 5.9 1.2 + - - -
118B SER* 5.2 1.4 - - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 1.3 75.2 - - + +
118A SER* 1.3 67.8 + - - +
120A ALA* 3.0 10.7 + - + +
121A HIS* 3.1 32.0 + - + +
155A ARG 4.1 4.0 + - - -
157A THR* 3.4 21.7 + - + +
161A GLU* 3.7 48.7 + - + +
162A LEU* 4.1 30.3 - - + +
122B ARG* 3.6 27.4 - - - +
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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
----------------------------------------------------------
116A ASN* 3.2 11.9 - - - +
117A ILE* 1.3 79.3 - - - +
119A SER* 1.3 62.2 + - - +
121A HIS* 3.2 4.7 + - - +
122A ARG 3.1 17.0 + - - -
116B ASN* 5.2 0.9 - - - -
118B SER* 3.5 34.1 - - - +
119B SER* 3.8 12.8 - - - -
122B ARG* 3.4 33.8 + - - +
2D G 5.4 2.8 + - - -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 4.1 4.4 + - - +
115A GLY* 3.3 12.8 + - - -
116A ASN* 2.7 40.8 + - - +
118A SER* 1.3 75.9 - - - +
120A ALA* 1.3 58.3 + - - +
122A ARG* 3.2 13.9 + - - +
123A SER* 2.9 28.1 + - - -
118B SER* 3.8 17.2 - - - -
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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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113A GLU* 3.6 22.0 - - + +
116A ASN 3.1 0.8 + - - -
117A ILE* 3.0 13.3 + - + +
119A SER* 1.3 78.8 + - - +
121A HIS* 1.3 62.3 + - - +
123A SER* 3.3 1.7 + - - -
124A MET* 2.9 30.2 + - - +
141A ILE* 4.7 0.2 - - - +
157A THR* 3.3 37.7 - - + +
162A LEU* 4.3 13.2 - - + +
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Residues in contact with HIS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.1 39.5 + - + +
118A SER 3.2 7.8 + - - +
120A ALA* 1.3 76.6 - - - +
122A ARG* 1.3 63.1 + - - +
124A MET* 3.4 5.4 + - - +
125A ASN* 3.0 29.6 + - - -
162A LEU* 4.0 14.8 - - + +
165A TYR* 3.5 50.0 - + - -
121B HIS* 4.2 2.2 - - - -
122B ARG* 3.6 43.4 - - + +
125B ASN* 3.1 27.8 + - + +
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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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89A LYS 5.9 3.1 - - - +
90A GLY* 5.2 15.6 + - - -
118A SER 3.1 8.8 + - - +
119A SER* 3.5 16.5 + - - +
120A ALA 3.2 0.2 - - - -
121A HIS* 1.3 77.4 - - - +
123A SER* 1.3 56.3 + - - +
125A ASN* 3.3 2.9 + - - +
126A LYS* 2.9 41.0 + - + +
117B ILE* 3.6 24.3 - - - +
118B SER* 3.4 27.1 + - - +
121B HIS* 3.6 40.1 + - + +
165B TYR* 5.8 0.9 - - - +
2C G 3.9 24.4 + - - -
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Residues in contact with SER 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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111A GLU* 2.5 34.6 + - - +
113A GLU* 2.6 39.8 + - - -
119A SER 2.9 11.7 + - - -
120A ALA 3.5 2.2 - - - -
122A ARG* 1.3 74.8 - - - +
124A MET* 1.3 65.1 + - - +
126A LYS* 3.2 9.9 + - - +
127A LEU* 3.1 24.1 + - - +
141A ILE* 4.2 2.4 - - - +
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Residues in contact with MET 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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120A ALA 2.9 17.1 + - - +
121A HIS* 3.8 5.4 - - - +
123A SER* 1.3 75.6 - - - +
125A ASN* 1.3 66.6 + - - +
127A LEU* 3.3 4.7 + - - +
128A LEU* 2.9 30.8 + - + +
141A ILE* 3.7 17.1 - - + +
162A LEU* 4.6 11.7 - - + -
165A TYR* 4.1 28.0 - - + +
168A LEU* 4.4 10.3 - - + -
169A THR* 3.8 22.2 - - + -
174A PHE* 3.9 18.2 - - + -
176A PHE* 3.8 14.8 - - - -
125B ASN* 3.4 27.8 - - - +
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Residues in contact with ASN 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 HIS 3.0 17.5 + - - +
122A ARG 3.7 1.1 - - - +
124A MET* 1.3 79.5 - - - +
126A LYS* 1.3 60.8 + - - +
128A LEU* 3.7 13.9 - - - +
129A LEU* 2.9 25.1 + - - +
121B HIS* 3.1 34.1 + - + +
124B MET* 3.5 8.3 - - - +
125B ASN* 3.3 37.8 + - - +
165B TYR* 3.4 10.7 - - + -
168B LEU* 3.7 25.8 - - + +
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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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89A LYS 4.7 1.8 - - - +
90A GLY 3.5 13.2 + - - -
91A GLY* 3.2 23.7 + - - +
92A PRO 2.8 22.8 + - - +
93A ILE* 4.5 11.7 - - + +
94A ASP* 4.2 5.3 + - - -
111A GLU* 2.8 33.9 + - - +
122A ARG* 2.9 26.8 + - + +
123A SER* 3.3 11.9 - - - +
125A ASN* 1.3 75.4 - - - +
127A LEU* 1.3 65.2 + - + +
129A LEU* 3.3 2.8 + - - +
130A GLY* 3.0 19.1 + - - -
165B TYR* 3.7 25.5 - - - +
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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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93A ILE* 3.7 38.8 - - + -
109A GLY 4.1 9.2 - - - +
110A MET 4.5 0.4 - - - +
111A GLU* 4.4 9.4 - - + -
123A SER* 3.1 16.0 + - - +
124A MET 3.5 6.7 - - - +
126A LYS* 1.3 80.0 - - + +
128A LEU* 1.3 64.9 + - - +
130A GLY* 3.1 2.3 + - - -
131A LEU* 3.0 27.2 + - - +
136A ILE* 3.8 17.5 - - + +
139A ALA* 3.8 8.1 - - + -
140A ILE 4.0 10.3 - - - +
141A ILE* 3.5 32.3 - - + -
174A PHE* 3.8 17.0 - - + -
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Residues in contact with LEU 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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124A MET* 2.9 22.7 + - + +
125A ASN* 3.7 26.2 - - - +
127A LEU* 1.3 75.6 - - - +
129A LEU* 1.3 59.0 + - - +
131A LEU* 3.2 6.7 + - + +
132A LYS* 2.9 28.9 + - - +
168A LEU* 4.0 19.1 - - + +
169A THR* 4.1 20.9 - - + -
172A GLN* 4.2 23.0 - - + +
174A PHE* 3.9 23.1 - - + -
168B LEU* 4.2 18.2 - - + +
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Residues in contact with LEU 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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89A LYS* 4.3 19.3 - - + +
125A ASN 2.9 18.7 + - - +
126A LYS 3.7 4.0 - - - +
128A LEU* 1.3 75.6 - - - +
130A GLY* 1.3 57.7 + - - +
132A LYS* 3.3 3.1 + - + +
133A HIS* 2.9 62.1 + - + +
135A GLU* 5.3 0.2 - - - -
164B PRO* 3.7 19.3 - - + +
165B TYR* 3.6 28.9 - - + +
167B GLU* 3.6 31.6 - - + -
168B LEU* 4.1 15.6 - - + +
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Residues in contact with GLY 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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93A ILE* 4.9 6.7 - - - -
126A LYS 3.0 14.5 + - - -
127A LEU 3.1 4.2 + - - -
129A LEU* 1.3 78.3 - - - +
131A LEU* 1.3 58.9 + - - +
133A HIS 3.4 0.9 + - - -
134A GLY 3.2 2.8 + - - -
135A GLU* 2.9 48.1 + - - -
136A ILE* 3.4 14.2 + - - -
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Residues in contact with LEU 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 LEU 3.0 11.3 + - - +
128A LEU* 3.5 10.1 - - - +
130A GLY* 1.3 77.0 - - - +
132A LYS* 1.3 62.5 + - - +
134A GLY* 3.0 14.4 + - - -
136A ILE* 3.5 36.1 - - + +
137A ASP* 3.7 6.5 - - - +
138A LEU* 3.7 20.9 - - - +
139A ALA* 3.7 17.5 - - + -
172A GLN* 3.8 31.4 - - + +
173A PRO* 3.7 22.7 - - + +
174A PHE* 3.9 13.5 - - + -
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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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128A LEU 2.9 16.4 + - - +
129A LEU* 3.6 7.2 - - - +
131A LEU* 1.3 79.4 - - - +
133A HIS* 1.3 62.1 + - + +
134A GLY 3.5 0.9 + - - -
172A GLN* 4.6 10.0 + - - +
167B GLU* 2.8 50.1 + - - +
168B LEU* 4.3 15.3 - - + +
170B GLU* 3.5 20.0 + - - -
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Residues in contact with HIS 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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89A LYS* 3.6 26.1 + - - -
129A LEU* 2.9 40.0 + - + +
130A GLY 4.1 0.9 - - - +
131A LEU 3.2 0.4 - - - -
132A LYS* 1.3 78.6 - - + +
134A GLY* 1.3 61.4 + - - +
135A GLU* 3.2 23.9 + - - +
164B PRO 5.2 0.9 - - - -
167B GLU* 2.7 40.4 + - - -
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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
------------------------------------------------------------
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