Contacts of the helix formed by residues 116 - 127 (chain B) in PDB entry 4A04
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 MET 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B GLU* 1.4 82.4 + - + +
117B LYS* 1.4 63.9 + - - +
118B ALA* 3.3 3.1 - - - -
119B LEU* 3.1 34.0 + - + +
120B TRP* 3.1 18.8 + - + +
141B PRO* 5.5 4.9 - - + -
142B THR 5.7 2.5 - - - +
144B GLN* 4.0 19.3 - - + +
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Residues in contact with LYS 117 (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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114B LEU* 3.8 28.9 - - + +
115B GLU 3.2 3.6 - - - -
116B MET* 1.4 75.4 - - - +
118B ALA* 1.4 57.4 + - - +
120B TRP* 3.2 3.5 + - - +
121B ASP* 2.9 51.0 + - - +
267B GLU* 2.8 31.2 + - - +
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Residues in contact with ALA 118 (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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116B MET 3.3 0.6 - - - -
117B LYS* 1.4 77.7 - - - +
119B LEU* 1.3 56.6 + - - +
121B ASP* 3.5 6.7 + - - +
122B GLU* 3.1 29.5 + - - +
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Residues in contact with LEU 119 (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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116B MET* 3.1 28.6 + - + +
118B ALA* 1.3 74.1 - - - +
120B TRP* 1.4 64.1 + - - +
122B GLU* 3.4 21.9 + - - +
123B PHE* 3.2 51.2 + - + -
140B PHE* 4.2 9.9 - - + -
141B PRO* 4.2 20.6 - - + -
284B LEU* 4.8 3.8 - - + -
288B SER* 3.9 29.8 - - - +
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Residues in contact with TRP 120 (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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114B LEU* 3.7 26.1 - - + +
115B GLU 3.7 10.0 + - - -
116B MET* 3.1 25.2 + - + +
117B LYS 3.5 7.4 - - - +
119B LEU* 1.4 75.6 - - - +
121B ASP* 1.3 56.1 + - - +
123B PHE* 3.3 5.5 + - + +
124B ASN* 2.9 29.3 + - - +
128B THR* 4.6 9.4 - - + -
130B MET* 3.7 16.6 - - + -
139B MET* 3.6 22.9 - - + -
141B PRO* 3.3 49.8 - - + +
142B THR 3.9 16.2 + - - -
143B PHE* 4.2 5.5 - + - +
144B GLN 5.1 0.2 - - - +
267B GLU* 3.6 34.1 - - + +
268B THR* 3.7 33.9 - - + -
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Residues in contact with ASP 121 (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 LYS* 2.9 49.7 + - - +
118B ALA* 3.9 6.9 + - - +
120B TRP* 1.3 71.7 - - - +
122B GLU* 1.3 64.4 + - - +
124B ASN* 3.8 7.9 - - - +
125B GLN* 3.1 26.0 + - - +
267B GLU* 3.4 24.3 - - - +
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Residues in contact with GLU 122 (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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118B ALA 3.1 17.6 + - - +
119B LEU* 3.6 21.5 - - - +
120B TRP 3.3 0.2 - - - -
121B ASP* 1.3 77.0 - - - +
123B PHE* 1.4 61.3 + - - +
125B GLN* 3.7 12.4 + - - +
126B LEU* 3.7 19.2 + - + +
284B LEU* 3.3 34.7 - - + +
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Residues in contact with PHE 123 (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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119B LEU* 3.2 42.1 + - + -
120B TRP* 3.3 8.7 + - + +
122B GLU* 1.4 76.5 - - - +
124B ASN* 1.4 58.4 + - - +
126B LEU* 3.1 8.5 + - - +
127B GLY 2.9 22.5 + - - -
128B THR* 3.2 28.2 + - + +
140B PHE* 4.2 4.7 - + - -
141B PRO* 3.7 24.9 - - + -
281B ILE* 3.9 21.8 - - + +
284B LEU* 3.9 27.6 - - + -
285B LYS* 3.8 49.4 - - + -
288B SER* 4.1 6.1 - - - -
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Residues in contact with ASN 124 (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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120B TRP 2.9 17.0 + - - +
121B ASP* 3.8 10.6 - - - +
123B PHE* 1.4 76.5 - - - +
125B GLN* 1.3 60.3 + - - +
127B GLY* 3.2 12.0 + - - +
128B THR* 3.2 8.5 + - - +
266B GLU 4.4 2.1 - - - +
267B GLU* 3.6 26.8 + - - +
269B ARG* 4.0 32.5 + - - +
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Residues in contact with GLN 125 (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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121B ASP 3.1 18.1 + - - +
122B GLU* 3.8 10.2 - - - +
123B PHE 3.3 0.4 - - - -
124B ASN* 1.3 76.7 - - - +
126B LEU* 1.3 60.1 + - + +
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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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122B GLU* 3.7 17.7 + - + +
123B PHE 3.1 6.6 + - - +
125B GLN* 1.3 78.1 - - + +
127B GLY* 1.3 60.4 + - - +
179B TRP* 5.4 5.0 + - - -
278B ASN* 3.3 22.2 + - - +
280B ARG* 3.8 66.2 - - + +
281B ILE* 3.7 19.1 - - + -
284B LEU* 3.9 23.1 - - + -
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Residues in contact with GLY 127 (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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123B PHE 2.9 5.6 + - - -
124B ASN* 3.2 12.5 + - - -
126B LEU* 1.3 79.3 - - - +
128B THR* 1.3 66.5 + - - +
129B GLU* 3.5 10.0 + - - +
179B TRP* 4.6 10.7 + - - -
271B THR* 5.8 0.4 - - - -
281B ILE* 3.4 15.6 - - - +
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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