Contacts of the helix formed by residues 136 - 151 (chain A) in PDB entry 6S6A
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.7 13.5 - - + -
133A GLN* 3.0 32.2 + - + +
135A ASP* 1.3 98.2 + - - +
137A ARG* 1.3 58.3 + - - +
138A ASP 3.4 1.6 - - - -
139A LEU* 3.2 24.8 + - - +
140A ILE* 2.9 39.0 + - + +
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Residues in contact with ARG 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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129A MET* 2.8 47.5 + - + +
130A ASP* 3.4 22.3 + - - +
132A VAL* 3.0 23.3 + - + -
133A GLN* 3.3 11.4 + - - +
134A GLU* 3.3 42.4 + - - +
136A GLN* 1.3 76.5 - - - +
138A ASP* 1.3 58.2 + - - +
140A ILE* 3.3 0.7 + - - -
141A PHE* 2.9 31.5 + - - +
161A ARG* 3.8 32.2 - - - +
166A ASP* 5.4 5.7 + - - -
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Residues in contact with ASP 138 (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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134A GLU 4.8 2.5 + - - +
135A ASP 5.0 2.5 + - - +
136A GLN 3.4 0.2 - - - -
137A ARG* 1.3 77.6 - - - +
139A LEU* 1.3 64.1 + - - +
141A PHE* 3.4 4.1 + - - -
142A LYS* 3.0 43.7 + - + +
161A ARG* 3.1 30.7 + - - +
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Residues in contact with LEU 139 (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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135A ASP 4.8 5.7 + - - +
136A GLN* 3.2 30.0 + - - +
138A ASP* 1.3 79.9 - - - +
140A ILE* 1.3 65.8 + - + +
142A LYS* 3.3 12.5 + - + +
143A GLU* 3.3 23.1 + - + +
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Residues in contact with ILE 140 (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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94A VAL* 4.0 25.1 - - + -
126A VAL* 5.5 0.2 - - + -
129A MET* 5.0 3.4 - - + -
132A VAL* 3.5 32.3 - - + -
136A GLN* 2.9 26.3 + - + +
137A ARG* 4.0 3.8 - - - +
139A LEU* 1.3 75.7 - - + +
141A PHE* 1.3 64.0 + - - +
142A LYS 3.3 0.2 + - - -
143A GLU* 3.5 6.8 + - - +
144A ARG* 3.1 45.6 + - + +
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Residues in contact with PHE 141 (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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126A VAL* 4.0 19.7 - - + -
129A MET* 5.0 3.1 - - - +
137A ARG 2.9 18.3 + - - +
138A ASP* 3.9 4.7 - - - +
140A ILE* 1.3 78.5 - - - +
142A LYS* 1.3 74.0 + - + +
144A ARG* 3.2 4.8 + - - +
145A GLU* 2.9 49.6 + - + +
159A CYS* 3.6 23.6 - - + -
160A PHE* 3.4 41.3 - - - -
161A ARG* 3.7 38.8 - - + -
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Residues in contact with LYS 142 (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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138A ASP* 3.0 41.3 + - + +
139A LEU* 3.9 7.9 - - + +
140A ILE 3.3 0.2 - - - -
141A PHE* 1.3 90.1 - - + +
143A GLU* 1.3 63.9 + - - +
144A ARG 3.3 0.3 + - - -
145A GLU* 3.3 25.6 + - - +
146A GLU* 3.0 26.9 + - - +
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Residues in contact with GLU 143 (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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139A LEU* 3.3 20.7 + - + +
140A ILE* 3.5 12.1 - - + +
142A LYS* 1.3 77.9 - - - +
144A ARG* 1.3 66.3 + - + +
146A GLU* 3.7 4.4 + - - +
147A ASP* 3.1 32.5 + - - +
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Residues in contact with ARG 144 (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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92A PHE* 6.0 3.2 - - - +
93A ASP 4.2 1.8 + - - -
94A VAL* 3.1 48.8 + - - +
99A LEU* 4.0 38.0 - - - +
126A VAL* 4.2 24.1 - - + +
140A ILE* 3.1 33.2 + - + +
141A PHE* 3.2 4.0 + - - +
143A GLU* 1.3 77.8 - - + +
145A GLU* 1.3 54.1 + - - +
147A ASP* 3.1 11.0 + - - +
148A LEU* 2.7 44.6 + - + +
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Residues in contact with GLU 145 (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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141A PHE* 2.9 33.9 + - + +
142A LYS* 3.5 30.5 + - - +
144A ARG* 1.3 76.0 - - - +
146A GLU* 1.3 52.0 + - - +
148A LEU* 3.0 5.0 + - - +
149A ARG* 2.9 63.9 + - - +
159A CYS* 3.9 39.9 + - + +
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Residues in contact with GLU 146 (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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142A LYS 3.0 14.6 + - - +
143A GLU* 3.8 6.3 - - - +
145A GLU* 1.3 77.9 - - - +
147A ASP* 1.3 63.9 + - - +
149A ARG* 3.2 18.6 + - - +
150A ARG* 3.1 46.6 + - - +
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Residues in contact with ASP 147 (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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103A MET* 5.5 3.1 - - + -
143A GLU* 3.1 19.0 + - - +
144A ARG* 3.1 14.0 + - - +
146A GLU* 1.3 75.2 - - - +
148A LEU* 1.3 57.7 + - + +
149A ARG 3.2 0.2 + - - -
150A ARG* 2.9 30.8 + - - +
151A LEU* 2.8 48.6 + - + +
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Residues in contact with LEU 148 (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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92A PHE* 3.5 39.0 - - + -
103A MET* 3.7 18.8 - - + -
106A TYR* 3.8 18.8 - - + -
124A CYS* 3.7 25.8 - - + -
126A VAL* 4.3 15.9 - - + -
144A ARG* 2.7 25.5 + - + +
145A GLU 3.0 5.1 + - - +
147A ASP* 1.3 74.3 - - - +
149A ARG* 1.3 55.7 + - - +
151A LEU* 3.9 3.2 - - - -
152A SER* 2.6 37.1 + - - -
157A CYS* 3.6 3.3 - - - -
159A CYS* 4.0 16.2 - - - -
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Residues in contact with ARG 149 (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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145A GLU* 2.9 44.4 + - - +
146A GLU* 4.0 17.7 + - - +
147A ASP 3.1 0.2 - - - -
148A LEU* 1.3 75.8 - - - +
150A ARG* 1.3 67.9 + - - +
152A SER* 3.5 11.5 + - - -
153A ARG 4.1 4.7 + - - +
155A LEU 4.8 2.5 - - - +
156A GLU* 5.3 11.6 + - - +
157A CYS* 3.3 42.2 - - - +
159A CYS* 4.6 2.5 - - - +
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Residues in contact with ARG 150 (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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146A GLU* 3.1 42.5 + - - +
147A ASP* 2.9 34.9 + - - +
149A ARG* 1.3 76.1 - - - +
151A LEU* 1.3 69.5 + - + +
152A SER 3.0 5.5 + - - -
153A ARG* 3.2 28.5 + - - +
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Residues in contact with LEU 151 (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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103A MET* 3.5 44.0 - - + -
106A TYR* 4.6 3.2 - - + -
107A GLN* 3.2 39.0 + - - +
110A LEU* 4.0 3.5 - - - +
147A ASP* 2.8 36.7 + - + +
148A LEU* 3.9 3.1 - - - +
150A ARG* 1.3 82.9 - - + +
152A SER* 1.3 54.5 - - - +
153A ARG* 3.2 22.4 - - - +
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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
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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