Contacts of the helix formed by residues 129 - 145 (chain B) in PDB entry 1S1G
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.6 12.1 - - - -
103B LEU 2.9 19.2 + - - +
127B ILE 3.1 6.2 + - - -
128B ILE* 1.3 72.8 - - - +
130B ASP* 1.3 58.5 + - - -
131B CYS* 2.9 18.8 - - - -
132B CYS 2.9 5.1 + - - -
133B TYR* 2.8 25.5 + - - +
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Residues in contact with ASP 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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102B LYS* 5.4 1.8 - - - +
128B ILE 3.6 1.0 + - - -
129B GLY* 1.3 71.2 - - - -
131B CYS* 1.3 59.9 + - - +
132B CYS 3.2 0.6 + - - -
133B TYR* 3.8 19.0 + - - +
134B GLU* 4.6 5.5 + - - +
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Residues in contact with CYS 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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102B LYS* 3.6 31.1 - - - +
104B HIS* 3.6 9.6 - - - -
129B GLY* 2.9 9.1 - - - -
130B ASP* 1.3 80.5 - - - +
132B CYS* 1.3 59.4 + - - +
134B GLU* 5.4 1.9 + - - +
135B GLU* 5.7 1.2 + - - +
152B ZN 2.4 33.6 - - - -
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Residues in contact with CYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU 4.5 0.2 - - - +
104B HIS* 3.6 6.5 - - - -
105B TYR* 3.2 43.8 - - + +
128B ILE* 3.8 14.1 - - + -
129B GLY 2.9 2.6 + - - +
131B CYS* 1.3 83.4 - - - +
133B TYR* 1.3 64.9 + - - +
134B GLU 3.4 2.2 - - - -
135B GLU* 3.2 12.2 + - - +
136B TYR* 3.0 20.3 + - - +
152B ZN 2.4 33.0 - - - -
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Residues in contact with TYR 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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125B PRO 5.2 4.3 - - - -
126B GLU* 6.2 2.0 - - - -
128B ILE* 3.6 21.3 - - + +
129B GLY 2.8 14.6 + - - +
130B ASP* 3.8 15.7 + - - +
131B CYS 3.7 0.8 - - - -
132B CYS* 1.3 75.4 - - - +
134B GLU* 1.3 69.9 + - + +
136B TYR* 3.0 22.0 + + - +
137B LYS* 2.7 61.7 + - + +
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Residues in contact with GLU 134 (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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130B ASP 4.6 5.5 + - - +
131B CYS 5.8 2.0 - - - +
132B CYS 3.4 0.8 - - - -
133B TYR* 1.3 81.3 - - + +
135B GLU* 1.3 62.4 + - - +
137B LYS* 3.3 22.4 + - - +
138B ASP* 2.9 52.8 + - - +
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Residues in contact with GLU 135 (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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105B TYR* 4.1 9.9 - - + +
107B ARG* 3.0 41.8 - - + +
131B CYS 5.7 0.6 + - - +
132B CYS* 3.2 12.1 + - + +
133B TYR 3.2 0.6 - - - -
134B GLU* 1.3 75.4 - - - +
136B TYR* 1.3 65.6 + - - +
138B ASP* 3.4 12.2 + - - +
139B ARG* 2.8 74.9 + - - +
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Residues in contact with TYR 136 (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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105B TYR* 4.1 16.0 - + + -
111B ILE* 3.3 26.2 - - + -
114B TYR* 3.7 24.2 - + - -
115B ASP* 2.4 28.2 + - - -
125B PRO* 3.5 22.5 - - + +
128B ILE* 3.3 29.4 - - + -
132B CYS 3.0 12.4 + - - +
133B TYR* 3.0 25.4 + + - +
135B GLU* 1.3 76.5 - - - +
137B LYS* 1.3 56.0 + - - +
139B ARG* 3.7 1.2 - - - +
140B LYS* 2.8 62.7 + - + +
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Residues in contact with LYS 137 (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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133B TYR* 2.7 55.1 + - + +
134B GLU* 3.3 24.2 + - - +
136B TYR* 1.3 76.5 - - - +
138B ASP* 1.3 58.7 + - - +
140B LYS* 3.8 4.6 - - - +
141B ARG* 2.9 52.8 + - + +
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Residues in contact with ASP 138 (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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134B GLU* 2.9 38.6 + - - +
135B GLU* 3.9 14.7 - - - +
136B TYR 3.4 0.2 - - - -
137B LYS* 1.3 74.0 - - - +
139B ARG* 1.3 63.6 + - + +
141B ARG* 3.2 30.5 + - - +
142B GLU* 2.8 37.7 + - - +
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Residues in contact with ARG 139 (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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107A ARG* 3.4 37.0 - - - +
105B TYR* 2.6 30.6 + - + +
107B ARG* 2.3 46.2 + - - +
109B GLU 3.2 9.1 + - - +
111B ILE* 3.7 25.6 - - + +
135B GLU* 2.8 53.0 + - - +
138B ASP* 1.3 78.1 - - - +
140B LYS* 1.3 62.3 + - - +
142B GLU* 3.6 6.4 + - - +
143B ASN* 3.1 23.6 + - - +
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Residues in contact with LYS 140 (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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111B ILE* 4.0 11.4 - - + +
115B ASP* 3.3 20.2 + - - -
125B PRO* 5.6 3.2 - - - +
136B TYR* 2.8 55.0 + - + +
137B LYS* 3.8 6.1 - - - +
139B ARG* 1.3 74.7 - - - +
141B ARG* 1.3 60.3 + - - +
143B ASN* 3.2 13.4 + - - +
144B LEU* 2.9 51.7 + - + +
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Residues in contact with ARG 141 (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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137B LYS* 2.9 51.9 + - - +
138B ASP* 3.2 37.9 + - - +
140B LYS* 1.3 77.4 - - - +
142B GLU* 1.3 67.6 + - - +
144B LEU* 3.0 21.7 + - + +
145B GLU* 3.1 34.8 + - + +
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Residues in contact with GLU 142 (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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138B ASP* 2.8 22.6 + - - +
139B ARG* 3.8 7.4 - - - +
141B ARG* 1.3 81.2 + - - +
143B ASN* 1.3 61.9 + - - +
145B GLU* 3.4 22.7 + - - +
146B HIS* 3.3 31.1 + - + +
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Residues in contact with ASN 143 (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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131A CYS* 3.6 24.5 + - - +
111B ILE* 3.5 20.3 - - + +
112B SER* 3.6 21.1 + - - -
139B ARG 3.1 15.5 + - - +
140B LYS* 3.3 16.4 - - - +
142B GLU* 1.3 77.9 - - - +
144B LEU* 1.3 69.9 + - - +
146B HIS* 3.1 32.0 + - + +
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Residues in contact with LEU 144 (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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140B LYS* 2.9 39.9 + - + +
141B ARG* 3.0 12.8 + - + +
143B ASN* 1.3 82.4 - - - +
145B GLU* 1.3 57.5 + - + +
146B HIS 3.2 6.6 + - - +
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Residues in contact with GLU 145 (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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141B ARG* 3.1 35.9 + - + +
142B GLU* 3.8 22.1 - - - +
143B ASN 3.2 0.8 - - - -
144B LEU* 1.3 76.6 - - + +
146B HIS* 1.3 66.5 + - - +
147B HIS* 4.6 7.3 - - - -
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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