Contacts of the helix formed by residues 127 - 138 (chain B) in PDB entry 1C3B
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 SER 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.5 0.7 - - - +
126B LYS* 1.3 81.4 - - - +
128B SER* 1.3 73.7 + - - +
129B SER* 2.8 26.2 + - - -
130B ASP* 2.9 22.0 + - - +
131B LEU* 3.3 18.0 + - - +
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Residues in contact with SER 128 (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 TRP* 5.0 2.8 - - - -
127B SER* 1.3 76.2 + - - +
129B SER* 1.3 56.7 + - - +
131B LEU* 3.3 12.0 + - - +
132B LEU* 3.0 27.4 + - - +
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Residues in contact with SER 129 (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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127B SER* 2.8 15.8 + - - -
128B SER* 1.3 77.5 - - - +
130B ASP* 1.3 66.9 + - - -
132B LEU* 3.3 8.8 + - - +
133B ARG* 3.0 28.5 + - - +
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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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124B GLU 3.7 7.0 - - - +
125B VAL* 3.3 14.6 - - + +
126B LYS* 3.0 28.3 + - - +
127B SER* 2.9 28.7 + - - +
129B SER* 1.3 79.9 - - - +
131B LEU* 1.3 57.9 + - - +
133B ARG* 3.4 28.7 + - - +
134B PHE* 2.9 30.5 + - - +
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Residues in contact with LEU 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 TRP* 4.3 10.8 - - + -
121B VAL* 4.2 15.5 - - + -
125B VAL* 3.3 17.3 - - + +
127B SER 3.3 7.7 + - - +
128B SER* 3.3 15.0 + - - +
129B SER 3.2 0.2 - - - -
130B ASP* 1.3 77.7 - - - +
132B LEU* 1.3 65.6 + - - +
134B PHE* 3.3 3.8 + - + +
135B TYR* 3.1 57.0 + - + -
157B LEU* 5.6 2.0 - - + -
215B ALA* 4.3 11.0 - - + -
216B LEU* 4.2 24.7 - - + +
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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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93B TRP* 3.7 30.5 - - + +
95B GLU* 3.8 43.7 - - + +
96B LEU* 4.1 7.0 - - + -
128B SER 3.0 14.6 + - - +
129B SER* 3.3 7.8 + - - +
131B LEU* 1.3 76.0 - - - +
133B ARG* 1.3 52.8 + - - +
135B TYR* 3.2 2.3 + - - +
136B GLN* 2.7 58.4 + - + +
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Residues in contact with ARG 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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129B SER* 3.0 19.1 + - - +
130B ASP* 3.4 31.6 + - - +
132B LEU* 1.3 77.4 - - - +
134B PHE* 1.3 63.3 + - - +
136B GLN* 3.7 6.6 - - + +
137B ASN* 3.0 46.7 + - - +
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Residues in contact with PHE 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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117B LEU* 5.0 1.6 - - + -
118B PRO* 3.4 35.2 - - + -
121B VAL* 4.6 13.0 - - + -
122B PRO* 3.4 34.1 - - + -
125B VAL* 4.0 15.3 - - + -
130B ASP 2.9 18.7 + - - +
131B LEU* 3.5 4.3 - - + +
132B LEU 3.2 0.2 - - - -
133B ARG* 1.3 78.3 - - - +
135B TYR* 1.3 100.5 + + - +
137B ASN* 3.4 3.6 + - - +
138B TRP* 3.1 26.2 + + + +
153B SER* 4.5 7.4 - - - -
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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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93B TRP* 3.6 17.3 - + + -
96B LEU* 3.6 20.2 - - + -
100B GLN* 3.9 0.2 + - - -
101B TRP* 2.8 46.0 + + + -
117B LEU* 3.7 20.0 - - + -
121B VAL* 4.3 0.7 - - - +
131B LEU* 3.1 48.4 + - + +
132B LEU 3.8 0.7 - - - +
134B PHE* 1.3 92.4 - + - +
136B GLN* 1.3 58.3 + - - +
138B TRP* 3.3 12.3 + - - +
153B SER* 2.6 33.1 + - - -
157B LEU* 3.7 24.8 - - + +
216B LEU* 3.1 21.4 - - + +
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Residues in contact with GLN 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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95B GLU 3.6 12.6 + - - -
96B LEU* 3.7 8.2 - - + +
97B THR* 3.1 18.4 + - - +
98B ALA* 2.8 51.4 + - - +
100B GLN* 3.0 18.7 + - - -
101B TRP* 4.5 0.2 - - - -
132B LEU* 2.7 43.4 + - + +
133B ARG* 3.7 7.9 - - - +
135B TYR* 1.3 74.2 - - - +
137B ASN* 1.3 63.7 + - - +
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Residues in contact with ASN 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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100B GLN* 4.4 0.4 - - - -
133B ARG* 3.0 38.7 + - - +
134B PHE* 4.0 4.2 - - - +
136B GLN* 1.3 82.4 + - - +
138B TRP* 1.3 65.0 + - - +
139B GLN* 3.3 13.1 + - - +
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Residues in contact with TRP 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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100B GLN* 2.7 38.5 + - + +
101B TRP* 3.8 22.9 - + - -
104B ILE* 3.7 22.7 - - + -
114B ALA* 3.5 20.2 - - + -
115B GLY 3.4 20.9 - - - -
116B GLY 3.4 16.6 + - - -
117B LEU* 3.6 32.9 - - + +
118B PRO* 4.1 17.3 - - + -
134B PHE* 3.1 18.9 + + + +
135B TYR* 3.3 15.0 + - + +
137B ASN* 1.3 76.4 - - - +
139B GLN* 1.3 69.8 + - - +
140B PRO* 3.5 32.3 - - + -
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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