Contacts of the helix formed by residues 131 - 141 (chain B) in PDB entry 6E8Y
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 LEU 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B VAL* 4.4 9.9 - - + -
129B LEU* 4.3 0.4 - - + -
130B LYS* 1.3 74.0 - - - +
132B ILE* 1.3 65.0 + - - +
133B SER* 5.0 0.2 - - - +
134B GLU* 3.1 46.3 + - + +
135B VAL* 3.3 12.3 + - - +
195B ASP* 3.7 34.5 - - + +
198B GLU* 3.4 35.0 - - + +
199B ILE* 3.8 37.2 - - + +
242B PHE* 4.9 12.2 - - + -
243B CYS* 5.7 0.7 - - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 3.3 40.8 - - + +
98B ILE* 4.2 19.3 - - + -
117B SER* 4.3 1.1 - - - +
119B ILE* 3.5 37.5 - - + +
121B GLY* 3.5 29.2 + - - +
122B VAL* 4.1 4.0 - - - +
130B LYS 3.6 0.6 + - - +
131B LEU* 1.3 72.3 - - - +
133B SER* 1.3 62.8 + - - +
135B VAL* 3.1 12.5 + - + +
136B ILE* 3.0 38.6 + - + +
198B GLU* 3.2 9.1 + - - +
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Residues in contact with SER 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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117B SER* 4.2 9.4 + - - -
131B LEU* 4.5 1.2 - - - +
132B ILE* 1.3 73.0 - - - +
134B GLU* 1.3 61.9 + - - +
136B ILE* 3.5 10.4 + - - +
137B GLY* 2.9 23.0 + - - -
144B MET* 3.4 27.3 - - - +
146B VAL* 3.7 17.4 - - - +
194B VAL* 4.5 7.6 - - - +
195B ASP* 5.5 0.7 + - - -
198B GLU* 2.5 37.8 + - - -
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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 LYS* 5.2 6.6 - - + +
131B LEU* 3.1 45.2 + - + +
132B ILE 3.1 0.4 - - - -
133B SER* 1.3 82.5 + - - +
135B VAL* 1.3 60.4 + - + +
137B GLY* 4.4 0.9 - - - +
138B GLU* 2.9 52.0 + - + +
195B ASP* 3.9 15.0 - - - +
242B PHE* 5.9 1.0 - - - -
244B SER* 5.2 1.2 + - - -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 5.6 6.7 - - + -
99B GLY* 5.3 6.3 - - - -
102B CYS* 5.7 2.2 - - - -
130B LYS* 4.5 16.6 - - + +
131B LEU 3.3 13.2 + - - +
132B ILE* 3.1 14.1 + - + +
134B GLU* 1.3 75.3 - - - +
136B ILE* 1.3 65.9 + - + +
138B GLU* 4.0 6.4 - - - +
139B ARG* 3.2 58.0 + - - +
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Residues in contact with ILE 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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91B PHE* 3.8 24.0 - - + -
98B ILE* 3.6 34.1 - - + -
102B CYS* 4.0 7.9 - - - -
117B SER* 3.9 22.7 - - - +
119B ILE* 4.3 0.7 - - + -
132B ILE* 3.0 27.3 + - + +
133B SER* 3.7 5.6 - - - +
135B VAL* 1.3 77.6 - - + +
137B GLY* 1.3 58.7 + - - +
139B ARG* 3.9 0.3 - - - +
140B LEU* 2.9 45.1 + - + +
142B ILE* 4.7 0.9 - - + -
144B MET* 3.7 29.8 - - + -
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Residues in contact with GLY 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 SER 2.9 14.5 + - - -
134B GLU* 3.9 1.1 - - - -
136B ILE* 1.3 77.3 - - - +
138B GLU* 1.3 56.6 + - - +
141B GLY* 2.8 29.8 + - - -
142B ILE* 3.5 24.1 + - - +
144B MET* 3.7 10.5 - - - -
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Residues in contact with GLU 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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106B LYS* 4.0 6.4 + - - -
134B GLU* 2.9 38.3 + - + +
135B VAL* 4.0 6.0 - - - +
137B GLY* 1.3 77.1 - - - +
139B ARG* 1.3 64.8 + - + +
141B GLY* 3.8 5.0 + - - -
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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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99B GLY* 2.9 38.5 + - - -
102B CYS* 4.1 20.2 - - + +
103B ASP* 3.2 25.1 + - - -
106B LYS* 2.8 46.3 + - + +
135B VAL* 3.2 36.7 + - + +
136B ILE 4.1 1.3 - - - +
138B GLU* 1.3 78.3 - - + +
140B LEU* 1.3 61.9 + - + +
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Residues in contact with LEU 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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91B PHE* 3.6 33.2 - - + -
102B CYS* 3.4 47.6 - - + +
105B LEU* 3.7 14.1 - - + -
106B LYS* 3.5 21.1 - - - +
107B GLY 5.4 3.9 + - - -
109B LEU* 3.8 26.1 - - + +
136B ILE* 2.9 19.9 + - + +
139B ARG* 1.3 78.4 - - - +
141B GLY* 1.3 62.3 + - - +
142B ILE* 3.6 16.0 + - + +
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Residues in contact with GLY 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 GLY 2.8 15.0 + - - -
138B GLU 3.8 4.3 + - - -
139B ARG 3.5 2.4 - - - -
140B LEU* 1.3 77.5 - - - +
142B ILE* 1.3 60.5 + - - +
143B PRO* 4.5 1.4 - - - +
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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