Contacts of the helix formed by residues 123 - 134 (chain B) in PDB entry 4ZCU
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B VAL* 3.7 9.0 - - - +
122B ILE* 1.3 78.3 - - - +
124B GLU* 1.3 64.8 + - - +
125B GLN* 3.9 3.9 + - - +
126B GLN* 2.7 36.5 + - - +
127B ALA 3.5 13.9 + - - -
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Residues in contact with GLU 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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108B ALA* 3.0 16.0 - - - +
109B SER* 3.1 17.9 + - - -
112B VAL* 4.0 9.0 - - - +
123B SER* 1.3 75.7 - - - +
125B GLN* 1.3 59.5 + - + +
127B ALA* 3.3 7.3 + - - +
128B GLU* 2.9 43.9 + - - +
1007B SO4 2.8 32.6 + - - +
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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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123B SER* 3.5 4.2 + - - +
124B GLU* 1.3 75.7 - - - +
126B GLN* 1.3 60.7 + - - +
128B GLU* 3.4 29.6 + - + +
129B LEU* 2.8 27.8 + - + +
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Residues in contact with GLN 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 ILE* 3.2 19.5 - - + +
123B SER* 2.7 44.6 + - - +
124B GLU 3.3 0.8 - - - -
125B GLN* 1.3 76.6 - - - +
127B ALA* 1.3 58.8 + - - +
129B LEU* 3.1 8.2 + - + +
130B ILE* 3.0 31.7 + - + +
172B ILE* 3.8 37.4 - - + +
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Residues in contact with ALA 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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108B ALA* 3.3 31.4 - - + +
111B ILE* 3.8 16.7 - - + +
112B VAL* 3.9 4.9 - - + -
122B ILE* 3.9 14.0 - - + +
123B SER 3.5 1.8 + - - -
124B GLU 3.3 9.8 + - - +
125B GLN 3.3 0.2 - - - -
126B GLN* 1.3 76.9 - - - +
128B GLU* 1.3 59.0 + - - +
130B ILE* 3.2 10.4 + - - +
131B LEU* 2.9 33.4 + - - +
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Residues in contact with GLU 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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108B ALA* 3.7 15.5 - - + +
124B GLU* 2.9 34.0 + - - +
125B GLN* 3.4 39.4 + - + +
126B GLN 3.2 0.2 - - - -
127B ALA* 1.3 75.4 - - - +
129B LEU* 1.3 56.9 + - - +
131B LEU* 3.5 6.7 + - - +
132B GLN* 2.9 33.2 + - - +
140B MET* 4.3 23.3 - - + +
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Residues in contact with LEU 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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125B GLN* 2.8 16.4 + - + +
126B GLN* 3.1 11.4 + - + +
128B GLU* 1.3 74.0 - - - +
130B ILE* 1.3 59.7 + - - +
132B GLN* 3.3 19.2 + - - +
133B SER* 2.9 27.2 + - - -
170B THR* 4.7 15.7 - - + +
172B ILE* 3.7 27.8 - - + -
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Residues in contact with ILE 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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111B ILE* 4.1 18.4 - - + -
115B LEU* 5.0 0.4 - - + -
122B ILE* 4.8 5.8 - - + -
126B GLN* 3.0 16.3 + - + +
127B ALA* 3.5 14.6 - - - +
129B LEU* 1.3 75.4 - - - +
131B LEU* 1.3 59.3 + - - +
133B SER* 2.2 33.9 + - - -
134B ILE* 3.1 10.9 + - + +
166B TRP* 3.3 60.6 - - + +
170B THR* 4.2 18.8 - - + +
172B ILE* 4.9 5.4 - - + -
174B ILE* 4.1 17.3 - - + -
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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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106B ILE* 3.5 31.9 - - + +
108B ALA* 3.2 38.8 - - + +
111B ILE* 3.6 21.1 - - + -
127B ALA 2.9 15.7 + - - +
128B GLU* 3.7 4.9 - - - +
130B ILE* 1.3 76.7 - - - +
132B GLN* 1.3 62.2 + - - +
134B ILE* 3.1 16.7 + - + +
135B ASP* 3.2 17.0 + - - +
140B MET 3.1 31.2 - - - +
141B THR 4.5 0.7 - - - +
142B VAL* 3.4 22.8 - - + +
147B TRP* 6.0 1.3 - - + -
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Residues in contact with GLN 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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128B GLU* 2.9 20.9 + - - +
129B LEU* 3.7 16.8 - - - +
131B LEU* 1.3 76.3 - - - +
133B SER* 1.3 62.0 + - - +
135B ASP* 3.2 25.8 + - + +
139B THR 4.9 13.4 - - - +
140B MET* 5.2 8.1 - - - +
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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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129B LEU 2.9 12.2 + - - -
130B ILE* 2.2 34.3 + - - +
132B GLN* 1.3 77.7 - - - +
134B ILE* 1.3 61.5 + - - +
135B ASP 3.3 1.8 + - - +
150B TYR* 3.4 21.0 + - - -
166B TRP* 5.0 2.8 - - - -
169B SER* 4.7 10.1 + - - -
170B THR* 4.2 15.0 - - - +
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Residues in contact with ILE 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 ILE* 3.1 18.3 + - + +
131B LEU* 3.1 12.2 + - + +
133B SER* 1.3 81.0 - - - +
135B ASP* 1.3 60.0 + - - +
136B VAL* 5.4 1.5 - - - +
142B VAL* 3.8 21.1 - - + +
146B GLU* 4.1 17.2 - - - +
147B TRP* 4.2 10.5 - - + -
150B TYR* 3.4 48.2 - - + -
151B PHE* 4.1 14.8 - - + -
166B TRP* 3.7 36.6 - - + +
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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