Contacts of the helix formed by residues 125 - 135 (chain B) in PDB entry 4C48
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 HIS 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ALA 3.9 7.0 + - - +
89B HIS 3.0 28.2 + - - -
90B PHE 3.8 4.5 + - - -
91B GLY* 3.3 28.2 + - - -
120B ALA 3.7 14.4 + - - +
123B ARG* 3.6 22.8 + - + +
124B GLY* 1.3 79.9 - - - +
126B LEU* 1.3 65.3 + - - +
127B GLU* 3.4 12.1 - - - +
128B ILE* 3.8 22.4 - - + +
129B VAL* 3.4 20.6 + - - +
161B LEU* 4.5 3.1 - - - +
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Residues in contact with LEU 126 (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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124B GLY 3.9 6.2 + - - +
125B HIS* 1.3 72.1 - - - +
127B GLU* 1.3 65.3 + - - +
129B VAL* 3.3 21.1 - - - +
130B GLU* 3.4 8.1 + - - +
158B ASN* 4.3 7.0 - - - +
160B ASP* 4.0 28.5 - - + +
161B LEU* 3.5 31.2 - - + -
164B ILE* 4.1 16.7 - - + +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY 4.6 3.8 - - - +
93B LEU* 3.1 43.0 - - + +
125B HIS* 4.6 12.3 - - + -
126B LEU* 1.3 82.1 - - - +
128B ILE* 1.3 77.9 + - + +
130B GLU* 3.3 8.6 - - - +
131B VAL* 3.1 24.8 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 4.5 1.8 - - - +
88B ALA* 4.3 11.9 - - - +
91B GLY* 3.5 38.1 - - - -
92B HIS 4.0 2.2 - - - +
93B LEU* 3.9 20.9 - - + -
96B VAL* 4.2 14.6 - - + -
120B ALA* 3.9 18.8 - - + -
125B HIS* 3.7 21.4 + - + -
126B LEU 3.3 0.4 - - - -
127B GLU* 1.3 85.9 - - + +
129B VAL* 1.3 67.7 + - - +
130B GLU 3.1 1.3 - - - -
131B VAL* 3.1 12.8 - - + +
132B LEU* 3.0 31.8 + - + +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.7 26.0 - - + +
120B ALA* 4.6 4.1 - - + +
121B ALA* 4.6 7.6 - - + +
125B HIS 3.4 9.7 + - - +
126B LEU* 3.3 15.0 - - + +
128B ILE* 1.3 79.9 - - - +
130B GLU* 1.3 65.3 + - - +
132B LEU* 3.5 6.9 + - - +
133B LEU* 3.0 30.6 + - - +
161B LEU* 3.8 26.0 - - + -
164B ILE* 4.5 17.7 - - + -
165B LEU* 3.6 25.8 - - + -
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Residues in contact with GLU 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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126B LEU 3.4 10.0 + - - +
127B GLU* 3.3 12.1 - - - +
128B ILE 3.1 0.4 - - - -
129B VAL* 1.3 84.0 - - + +
131B VAL* 1.3 59.0 + - - +
133B LEU* 3.0 11.6 + - - +
134B LYS* 2.9 52.1 + - - +
164B ILE* 5.3 10.0 - - + +
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Residues in contact with VAL 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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93B LEU 6.0 0.2 - - - +
96B VAL* 3.7 22.2 - - + -
97B GLU* 3.2 34.5 - - + +
100B LEU* 4.1 13.8 - - + +
127B GLU 3.1 11.0 + - - +
128B ILE* 3.1 30.5 - - + +
130B GLU* 1.3 78.0 - - - +
132B LEU* 1.3 64.0 + - + +
134B LYS* 3.5 12.0 + - + +
135B TYR* 3.2 36.1 + - + -
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Residues in contact with LEU 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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84B LEU* 4.3 11.0 - - + -
88B ALA* 4.6 1.3 - - + -
96B VAL* 4.1 13.0 - - + -
100B LEU* 4.0 17.9 - - + -
106B VAL* 3.8 27.1 - - + +
116B PRO* 3.5 30.5 - - + +
117B LEU* 3.6 16.2 - - + -
120B ALA* 4.0 12.6 - - + -
128B ILE* 3.0 26.9 + - + +
129B VAL* 3.8 5.2 - - - +
131B VAL* 1.3 78.4 - - + +
133B LEU* 1.3 61.5 + - - +
135B TYR 3.5 8.3 + - - -
136B GLY 3.5 0.5 + - - -
137B ALA* 3.1 30.2 + - + +
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Residues in contact with LEU 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 LEU* 3.5 28.5 - - + -
129B VAL* 3.0 27.6 + - + +
130B GLU* 3.6 11.7 - - - +
132B LEU* 1.3 75.6 - - - +
134B LYS* 1.3 64.5 + - - +
136B GLY* 3.1 13.0 + - - -
137B ALA* 4.2 7.1 - - + +
139B VAL* 3.6 26.0 - - + -
164B ILE* 4.8 14.8 - - + +
165B LEU* 3.6 19.3 - - + -
166B GLN 6.1 1.3 - - - +
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Residues in contact with LYS 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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97B GLU* 5.7 3.4 + - - -
130B GLU* 2.9 37.0 + - - +
131B VAL* 3.7 12.9 - - - +
132B LEU 3.4 0.2 - - - -
133B LEU* 1.3 78.2 - - - +
135B TYR* 1.3 71.5 + - + +
136B GLY* 3.1 3.5 + - - -
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Residues in contact with TYR 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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97B GLU* 3.2 37.3 + - - -
100B LEU* 3.5 57.2 - - + -
101B LYS* 3.4 20.1 - - - +
106B VAL* 3.9 10.5 - - + +
131B VAL* 3.2 23.0 + - + +
132B LEU 3.5 4.0 + - - +
133B LEU 3.3 0.4 - - - -
134B LYS* 1.3 92.6 - - + +
136B GLY* 1.3 62.8 + - - +
137B ALA 3.7 1.3 - - - -
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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