Contacts of the helix formed by residues 136 - 152 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 4.4 8.5 - - + -
133B GLN* 2.6 28.0 + - + +
135B ASP* 1.3 112.4 + - - +
137B ARG* 1.3 61.3 + - - -
138B ASP 3.4 2.9 - - - -
139B LEU* 3.3 29.9 + - - +
140B ILE* 3.1 33.8 + - + +
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Residues in contact with ARG 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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129B MET* 2.6 44.4 + - + +
130B ASP* 3.0 34.6 + - - +
132B VAL* 2.8 26.6 + - + +
133B GLN 3.6 3.1 - - - +
134B GLU* 3.5 38.7 + - - +
135B ASP 3.6 0.2 - - - -
136B GLN* 1.3 73.9 - - - +
138B ASP* 1.3 65.6 + - - +
140B ILE* 3.4 0.9 + - - -
141B PHE* 3.0 25.7 + - - +
161B ARG* 3.5 31.5 - - - +
166B ASP* 5.8 2.0 + - - -
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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
----------------------------------------------------------
134B GLU 5.1 0.8 + - - -
135B ASP 5.4 1.7 + - - +
136B GLN 3.4 0.6 - - - -
137B ARG* 1.3 78.4 - - - +
139B LEU* 1.3 56.9 + - - +
141B PHE* 3.4 7.1 + - - +
142B LYS* 2.9 55.5 + - - +
161B ARG* 3.7 25.6 + - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP 5.8 0.4 - - - +
136B GLN* 3.3 34.3 + - - +
138B ASP* 1.3 79.5 - - - +
140B ILE* 1.3 64.3 + - + +
142B LYS* 4.1 8.7 - - + +
143B GLU* 3.2 46.7 + - + +
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Residues in contact with ILE 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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94B VAL* 4.0 15.5 - - + -
129B MET* 4.8 3.4 - - + -
132B VAL* 3.9 21.5 - - + -
136B GLN* 3.1 25.9 + - + +
137B ARG 3.9 3.4 - - - +
139B LEU* 1.3 77.2 - - + +
141B PHE* 1.3 67.2 - - - +
142B LYS 3.2 0.2 + - - -
143B GLU* 3.3 19.3 + - - +
144B ARG* 2.9 61.7 + - - +
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Residues in contact with PHE 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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126B VAL* 4.4 16.6 - - + -
129B MET* 4.9 3.0 - - - +
137B ARG 3.0 18.4 + - - +
138B ASP* 3.7 6.3 - - - +
140B ILE* 1.3 75.1 - - - +
142B LYS* 1.3 61.4 + - + +
144B ARG* 2.9 8.8 + - - +
145B GLU* 2.7 44.4 + - + +
159B CYS* 3.5 36.6 - - + -
160B PHE* 3.3 11.4 - - - -
161B ARG* 3.3 56.1 - - + -
249C ILE* 4.3 26.5 - - + -
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Residues in contact with LYS 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* 2.9 39.0 + - - +
139B LEU* 4.1 11.2 - - + +
140B ILE 3.2 0.2 - - - -
141B PHE* 1.3 81.1 - - + +
143B GLU* 1.3 55.8 + - - +
145B GLU* 3.3 5.8 + - - +
146B GLU* 3.0 34.4 + - - +
242C THR* 4.9 9.7 - - - +
245C ASN* 3.1 37.1 + - - +
246C LEU* 3.7 28.1 - - - +
249C ILE* 4.0 10.8 - - + -
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Residues in contact with GLU 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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139B LEU* 3.2 44.2 + - + +
140B ILE* 3.5 21.1 - - - +
142B LYS* 1.3 76.7 - - - +
144B ARG* 1.3 64.4 + - + +
146B GLU* 3.5 6.9 + - - +
147B ASP* 3.0 36.4 + - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP 5.0 0.4 + - - -
94B VAL* 2.8 45.0 + - - +
96B SER 4.6 0.8 + - - -
99B LEU* 3.4 34.8 - - + +
126B VAL* 4.5 20.2 - - + +
140B ILE* 2.9 45.5 + - - +
141B PHE* 3.5 4.0 - - - +
143B GLU* 1.3 81.0 + - + +
145B GLU* 1.3 58.2 - - - +
147B ASP* 3.5 12.2 + - + +
148B LEU* 3.1 35.7 + - + +
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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
----------------------------------------------------------
126B VAL* 5.8 0.4 - - - -
141B PHE* 2.7 28.5 + - + +
142B LYS* 3.5 6.1 - - - +
144B ARG* 1.3 75.3 - - - +
146B GLU* 1.3 65.8 + - - +
147B ASP 3.2 0.2 - - - -
148B LEU* 3.4 3.4 + - - +
149B ARG* 2.5 59.3 + - - +
157B CYS 5.7 0.2 - - - +
159B CYS* 3.6 35.9 + - + +
245C ASN* 3.5 17.8 + - - +
249C ILE* 3.5 27.8 - - + +
252C SER* 4.2 4.5 + - - -
253C ASN* 5.5 1.0 - - - +
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Residues in contact with GLU 146 (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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142B LYS 3.0 19.0 + - - +
143B GLU* 3.7 7.0 - - - +
145B GLU* 1.3 80.9 + - - +
147B ASP* 1.3 68.6 + - - +
149B ARG* 3.3 30.9 + - - +
150B ARG* 2.8 42.4 + - - +
245C ASN* 3.2 30.1 + - + +
248C ASN* 3.2 21.1 + - - +
274C SER* 5.3 0.4 + - - -
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Residues in contact with ASP 147 (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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103B MET* 6.0 1.8 - - + -
143B GLU* 3.0 30.8 + - - +
144B ARG* 3.7 13.9 - - + +
145B GLU 3.2 0.4 - - - -
146B GLU* 1.3 76.8 - - - +
148B LEU* 1.3 59.4 + - + +
150B ARG* 3.1 12.6 + - - +
151B LEU* 3.0 42.6 + - + +
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Residues in contact with LEU 148 (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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92B PHE* 3.3 48.5 - - + -
103B MET* 4.3 15.9 - - + -
106B TYR* 3.8 19.3 - - + -
124B CYS* 4.1 4.5 - - + -
126B VAL* 4.2 14.4 - - + -
144B ARG* 3.1 22.2 + - + +
145B GLU 3.9 4.7 - - - +
146B GLU 3.2 0.4 - - - -
147B ASP* 1.3 75.4 - - + +
149B ARG* 1.3 62.8 + - - +
151B LEU* 4.3 4.0 - - + +
152B SER* 2.5 32.3 + - - -
157B CYS* 4.2 5.6 - - - -
159B CYS* 4.0 25.6 - - - -
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Residues in contact with ARG 149 (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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145B GLU* 2.5 48.1 + - - +
146B GLU* 3.3 23.8 + - - +
147B ASP 3.3 0.2 - - - -
148B LEU* 1.3 76.3 - - - +
150B ARG* 1.3 69.4 + - + +
152B SER* 4.1 5.0 + - - -
153B ARG* 4.0 12.0 + - - +
155B LEU 4.8 2.8 - - - +
157B CYS* 4.3 20.9 + - - +
248C ASN* 3.3 32.8 - - - +
252C SER* 3.2 21.3 + - - -
274C SER* 5.0 10.1 - - - -
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Residues in contact with ARG 150 (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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146B GLU* 2.8 59.7 + - - +
147B ASP* 3.1 10.2 + - - +
148B LEU 3.1 0.2 - - - -
149B ARG* 1.3 84.5 - - + +
151B LEU* 1.3 66.3 + - + +
152B SER 3.0 6.0 + - - -
153B ARG* 3.1 51.4 + - - +
274C SER* 5.5 4.4 + - - -
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Residues in contact with LEU 151 (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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103B MET* 3.7 46.0 - - + -
106B TYR* 4.8 4.7 - - + -
107B GLN* 3.3 27.4 + - + +
110B LEU* 4.6 0.2 - - - +
147B ASP* 3.0 31.0 + - + +
148B LEU* 3.4 9.4 + - + +
150B ARG* 1.3 80.5 - - + +
152B SER* 1.3 56.3 + - - +
153B ARG 3.5 0.2 - - - -
404B 9JE 3.1 21.1 + - - -
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Residues in contact with SER 152 (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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106B TYR* 2.8 29.7 + - - -
110B LEU* 3.6 14.2 - - - +
122B ILE* 6.2 0.2 - - - -
148B LEU 2.5 23.0 + - - -
149B ARG 4.4 2.7 - - - -
150B ARG 3.0 1.4 - - - -
151B LEU* 1.3 75.4 - - - +
153B ARG* 1.3 67.3 + - - +
155B LEU* 3.1 40.0 + - - +
157B CYS* 3.7 13.3 - - - -
404B 9JE 4.5 0.8 + - - -
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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