Contacts of the helix formed by residues 116 - 133 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASN* 5.9 1.2 + - - -
118A SER* 5.2 0.9 - - - -
115B GLY* 1.3 67.9 - - - -
117B ILE* 1.3 67.2 + - + +
118B SER* 3.2 11.8 + - - -
119B SER* 2.7 41.4 + - - -
120B ALA 3.2 1.2 + - - -
155B ARG* 3.3 28.9 - - + +
157B THR* 2.9 12.5 + - - -
3D A 5.8 0.4 + - - -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 3.6 26.9 - - - +
116B ASN* 1.3 75.8 - - + +
118B SER* 1.3 64.8 + - - +
120B ALA* 3.1 10.3 + - + +
121B HIS* 3.1 26.4 + - + +
155B ARG 4.1 4.0 + - - -
157B THR* 3.5 26.5 + - + +
161B GLU* 3.8 48.5 - - + +
162B LEU* 4.1 28.0 - - + +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 5.2 1.1 - - - -
118A SER* 3.5 34.4 - - - +
119A SER* 3.8 9.9 - - - -
122A ARG* 3.4 38.9 + - - -
116B ASN* 3.2 11.4 + - - -
117B ILE* 1.3 80.9 - - - +
119B SER* 1.3 64.4 + - - +
121B HIS* 3.1 5.2 + - - +
122B ARG 3.1 17.3 + - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.8 17.6 - - - -
113B GLU* 4.0 4.0 + - - +
115B GLY* 3.3 13.2 + - - -
116B ASN* 2.7 40.1 + - - -
118B SER* 1.3 78.0 - - - +
120B ALA* 1.3 57.1 + - - +
122B ARG* 3.3 7.4 + - - +
123B SER* 2.9 27.2 + - - -
157B THR* 4.5 0.3 + - - -
2D G 5.4 7.4 - - - -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 3.6 14.9 - - - +
116B ASN 3.2 0.2 + - - -
117B ILE* 3.1 11.8 + - + +
118B SER 3.1 0.6 - - - -
119B SER* 1.3 79.0 + - - +
121B HIS* 1.3 59.6 + - - +
123B SER* 3.3 1.2 + - - -
124B MET* 2.9 30.0 + - - +
141B ILE* 4.7 0.2 - - - +
143B MET* 3.6 14.1 - - + -
157B THR* 3.4 37.9 - - + +
162B LEU* 4.4 7.0 - - + +
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Residues in contact with HIS 121 (chain B).
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* 4.2 1.6 - - - -
122A ARG* 3.6 44.0 - - + +
125A ASN* 3.1 27.4 + - + +
117B ILE* 3.1 43.5 + - + +
118B SER 3.4 7.0 - - - +
120B ALA* 1.3 76.0 - - - +
122B ARG* 1.3 64.1 + - - +
124B MET* 3.5 5.6 + - - +
125B ASN* 3.0 29.3 + - - -
162B LEU* 4.1 11.6 - - + +
165B TYR* 3.5 50.0 - + - -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 3.6 22.2 - - - +
118A SER* 3.4 27.5 + - - +
121A HIS* 3.6 40.3 - - + +
165A TYR* 5.8 2.5 - - + +
90B GLY* 5.0 13.6 - - - -
91B GLY 5.5 4.3 - - - +
118B SER 3.1 8.6 + - - +
119B SER* 3.6 11.8 + - - +
120B ALA 3.2 0.4 - - - -
121B HIS* 1.3 77.8 - - - +
123B SER* 1.3 57.4 + - - +
125B ASN* 3.3 2.4 + - - +
126B LYS* 2.8 40.3 + - + +
1D T 5.5 2.0 - - - -
2D G 4.2 21.6 + - - -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 2.5 34.3 + - - +
113B GLU* 2.6 41.4 + - - -
119B SER 2.9 12.3 + - - -
120B ALA 3.6 1.1 - - - -
121B HIS 3.3 0.2 - - - -
122B ARG* 1.3 74.2 - - - +
124B MET* 1.3 65.8 + - - +
126B LYS* 3.1 8.8 + - - +
127B LEU* 3.0 27.1 + - - +
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Residues in contact with MET 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.5 26.7 - - - +
120B ALA 2.9 17.1 + - - +
121B HIS* 3.8 5.6 - - - +
123B SER* 1.3 76.2 + - - +
125B ASN* 1.3 63.4 + - - +
127B LEU* 3.3 3.6 + - - +
128B LEU* 2.9 30.9 + - + +
141B ILE* 3.7 16.7 - - + +
162B LEU* 4.5 11.7 - - + -
165B TYR* 4.0 30.7 - - + +
168B LEU* 4.4 9.6 - - + -
169B THR* 3.9 13.7 - - + -
174B PHE* 3.9 16.9 - - + -
176B PHE* 3.8 25.4 - - + -
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Residues in contact with ASN 125 (chain B).
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* 3.1 34.4 + - + +
124A MET* 3.4 8.5 - - - +
125A ASN* 3.3 39.1 + - - +
165A TYR* 3.5 3.9 - - + -
168A LEU* 3.7 24.0 - - + +
121B HIS 3.0 17.8 + - - +
122B ARG 3.7 1.1 - - - +
123B SER 3.2 0.2 - - - -
124B MET* 1.3 77.6 - - - +
126B LYS* 1.3 67.3 + - - +
128B LEU* 3.7 16.1 - - - +
129B LEU* 2.9 25.1 + - - +
168B LEU* 5.8 0.2 - - - +
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 3.9 21.7 - - - +
89B LYS 5.7 1.1 - - - -
90B GLY 5.5 0.4 - - - -
91B GLY* 3.2 25.4 + - - +
92B PRO* 2.9 19.6 + - + -
93B ILE* 3.7 32.3 - - + +
94B ASP* 4.5 3.6 + - - -
111B GLU* 3.0 24.5 + - - +
122B ARG* 2.8 29.0 + - + +
123B SER* 3.1 7.6 + - - +
125B ASN* 1.3 76.9 - - - +
127B LEU* 1.3 63.5 + - - +
129B LEU* 3.4 3.1 + - - +
130B GLY* 3.1 18.5 + - - -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.6 42.8 - - + -
109B GLY 4.3 8.3 - - - -
111B GLU* 4.1 15.3 - - + -
123B SER* 3.0 17.5 + - - +
124B MET 3.6 6.3 - - - +
126B LYS* 1.3 77.4 - - + +
128B LEU* 1.3 55.9 + - - +
130B GLY* 3.1 2.4 + - - -
131B LEU* 2.9 31.2 + - - +
136B ILE* 3.8 10.1 - - + +
139B ALA* 3.6 15.3 - - + -
140B ILE 4.1 8.1 - - - +
141B ILE* 3.5 32.1 - - + -
174B PHE* 3.7 15.0 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.2 16.2 - - + -
124B MET* 2.9 24.5 + - + +
125B ASN* 3.3 26.7 + - - +
127B LEU* 1.3 76.2 - - - +
129B LEU* 1.3 56.9 + - - +
131B LEU* 3.3 5.8 + - + +
132B LYS* 2.9 38.6 + - + +
168B LEU* 4.2 17.7 - - + +
169B THR* 3.9 22.4 - - + -
172B GLN* 4.4 20.0 - - + -
174B PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.7 22.0 - - + +
165A TYR* 3.6 27.8 - - + +
167A GLU* 3.6 38.6 - - + +
168A LEU* 4.1 14.5 - - + +
89B LYS* 4.1 23.6 - - - -
125B ASN 2.9 17.1 + - - +
126B LYS* 3.8 4.3 - - - +
128B LEU* 1.3 76.7 - - - +
130B GLY* 1.3 58.3 + - - +
132B LYS* 3.3 1.8 + - - +
133B HIS* 2.8 51.4 + - + +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.9 5.8 - - - -
126B LYS 3.1 14.6 + - - -
127B LEU 3.1 4.4 + - - -
129B LEU* 1.3 77.8 - - - +
131B LEU* 1.3 59.1 + - - +
133B HIS 3.4 0.9 + - - -
134B GLY 3.1 2.6 + - - -
135B GLU* 2.9 49.8 + - - +
136B ILE* 3.4 13.5 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU 2.9 15.2 + - - +
128B LEU* 3.6 9.2 - - - +
130B GLY* 1.3 77.2 - - - +
132B LYS* 1.3 62.1 + - - +
134B GLY* 3.0 14.4 + - - -
136B ILE* 3.6 28.2 - - + +
137B ASP* 3.7 23.8 - - - +
138B LEU* 3.7 4.5 - - - +
139B ALA* 3.7 15.0 - - + -
172B GLN* 3.6 30.9 + - + +
173B PRO* 3.7 29.4 - - + +
174B PHE* 3.8 15.5 - - + -
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.9 33.9 + - - +
168A LEU* 4.0 28.6 + - + -
170A GLU* 5.2 6.3 + - - +
128B LEU* 2.9 27.3 + - - +
129B LEU* 3.7 5.8 - - - +
131B LEU* 1.3 78.3 - - - +
133B HIS* 1.3 60.5 + - - +
134B GLY 3.2 1.1 + - - -
172B GLN* 4.0 29.2 - - - +
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO 5.2 1.4 + - - -
167A GLU* 2.8 37.7 + - - -
89B LYS* 4.5 15.4 - - - -
129B LEU* 2.8 39.8 + - + +
130B GLY 3.4 3.6 + - - +
132B LYS* 1.3 81.0 + - - +
134B GLY* 1.3 62.7 + - - +
135B GLU* 3.2 24.0 + - + +
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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