Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 1D5C
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 THR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 4.9 0.3 + - - -
132A ARG* 3.6 12.1 - - + +
133A LYS 5.6 1.8 - - - +
134A VAL* 1.3 78.9 - - - +
136A TYR* 1.3 65.8 + - - +
137A GLU* 3.6 13.4 + - - +
138A GLU* 3.1 42.4 + - - +
139A GLY* 3.3 9.4 + - - -
152A GLU* 4.5 1.2 - - - +
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Residues in contact with TYR 136 (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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132A ARG* 3.5 8.4 - - - +
135A THR* 1.3 73.2 - - - +
137A GLU* 1.3 65.6 + - - +
139A GLY 3.2 1.9 + - - -
140A MSE 2.9 50.0 + - + -
150A PHE* 3.5 32.4 + + - -
151A HIS* 5.7 0.4 - - - -
152A GLU* 3.4 47.1 - - + +
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Residues in contact with GLU 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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135A THR* 3.6 13.1 + - - +
136A TYR* 1.3 84.2 - - - +
138A GLU* 1.3 63.6 + - + +
140A MSE 3.1 17.9 + - + +
141A GLN* 2.9 39.5 + - + +
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Residues in contact with GLU 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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96A ARG* 2.8 44.9 + - - -
99A PHE* 3.8 12.2 - - + -
133A LYS 4.1 0.2 - - - +
134A VAL* 3.5 9.7 - - + -
135A THR* 3.1 37.9 + - - +
137A GLU* 1.3 78.1 - - + +
139A GLY* 1.3 64.1 + - - +
141A GLN* 3.3 15.0 + - - +
142A LYS* 3.1 22.9 + - - +
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Residues in contact with GLY 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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91A TYR* 3.6 12.1 + - - -
99A PHE* 4.0 11.8 - - - -
121A LEU* 3.5 10.7 - - - +
134A VAL* 4.6 0.2 - - - +
135A THR 3.3 5.0 + - - -
136A TYR 3.2 3.8 + - - -
138A GLU* 1.3 78.4 - - - +
140A MSE 1.3 61.2 + - - +
142A LYS 3.3 1.7 + - - -
143A ALA 3.1 17.7 + - - -
150A PHE* 3.4 27.9 - - - -
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Residues in contact with MSE 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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136A TYR* 2.9 40.4 + - + +
137A GLU* 3.1 19.0 + - + +
139A GLY* 1.3 77.0 - - - +
141A GLN* 1.3 59.6 + - + +
143A ALA* 3.3 2.6 + - - +
144A GLN* 3.0 34.6 + - + +
150A PHE* 3.4 23.6 - - + -
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Residues in contact with GLN 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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137A GLU* 2.9 28.1 + - + +
138A GLU* 3.3 18.4 + - - +
140A MSE 1.3 76.3 - - + +
142A LYS* 1.3 67.2 + - - +
144A GLN* 3.2 16.1 + - - +
145A GLU* 2.9 23.4 + - - +
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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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99A PHE* 4.1 15.7 - - + -
102A THR* 4.1 16.4 - - - +
103A THR* 3.1 26.0 + - - +
106A ILE* 4.4 8.2 - - + +
121A LEU* 3.8 17.0 - - + -
138A GLU 3.1 12.1 + - - +
139A GLY 3.6 8.1 - - - +
140A MSE 3.3 0.2 - - - -
141A GLN* 1.3 76.1 - - - +
143A ALA* 1.3 62.7 + - - +
145A GLU* 3.0 45.0 + - - +
146A TYR* 3.5 23.5 + - + -
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Residues in contact with ALA 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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106A ILE* 6.1 0.4 - - - -
121A LEU* 3.9 8.0 - - + +
139A GLY 3.1 10.1 + - - +
140A MSE 3.6 7.6 - - + +
141A GLN 3.2 0.2 - - - -
142A LYS* 1.3 77.3 - - - +
144A GLN* 1.3 56.7 - - - +
146A TYR 3.4 1.6 + - - -
147A ASN 2.9 8.1 + - - -
148A THR* 2.8 56.0 + - - +
149A MSE 3.8 2.2 - - - +
150A PHE* 3.6 28.7 - - + -
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Residues in contact with GLN 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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140A MSE 3.0 24.1 + - + +
141A GLN* 3.2 15.7 + - - +
143A ALA* 1.3 74.4 - - - +
145A GLU* 1.3 66.8 + - - +
146A TYR 3.2 0.5 + - - -
147A ASN* 3.3 19.7 + - - +
148A THR 5.4 0.4 - - - -
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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 GLN 2.9 11.4 + - - +
142A LYS* 3.0 38.0 + - - +
144A GLN* 1.3 77.7 - - - +
146A TYR* 1.3 86.6 + - + +
147A ASN* 3.5 4.4 + - - -
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Residues in contact with TYR 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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103A THR* 3.7 18.4 - - + +
106A ILE* 3.9 28.7 - - + -
107A GLN* 3.1 31.0 + - - -
110A LEU* 4.0 18.5 - - + +
119A ILE* 5.8 1.4 - - + +
142A LYS* 3.5 30.6 + - + -
143A ALA 3.4 2.0 + - - -
144A GLN 3.2 0.2 - - - -
145A GLU* 1.3 108.0 + - + +
147A ASN* 1.3 75.8 + - - +
148A THR* 3.3 22.7 + - + +
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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