Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 3CUQ
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 LEU 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ILE 3.9 0.2 + - - -
120A THR* 1.3 73.2 - - - +
122A GLU* 1.3 61.5 + - - +
124A LEU* 3.7 4.4 - - + +
125A HIS* 3.1 22.9 + - - +
141A GLN* 3.8 30.7 - - + +
144A LEU* 3.9 31.0 - - + -
145A ILE* 3.5 32.5 - - + -
148A ILE* 6.1 0.2 - - + -
166A THR* 4.0 11.3 + - - +
167A TYR* 3.1 31.8 + - + +
169A ILE* 3.5 25.1 - - + +
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Residues in contact with GLU 122 (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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120A THR* 3.7 10.5 - - - +
121A LEU* 1.3 79.7 - - - +
123A GLU* 1.3 59.0 + - - +
125A HIS* 3.1 7.7 + - - +
126A GLN* 2.9 47.0 + - - +
141A GLN* 5.9 4.3 - - - +
166A THR* 4.7 6.1 + - - +
241A THR* 5.9 1.9 - - - +
243A LEU* 5.3 4.9 - - - +
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Residues in contact with GLU 123 (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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111A LEU* 4.2 14.4 - - - +
114A ARG* 5.7 2.3 - - - -
115A ASN* 4.0 10.9 + - - -
119A ILE* 3.4 27.9 - - + +
120A THR* 3.0 18.5 + - - +
122A GLU* 1.3 74.8 - - - +
124A LEU* 1.3 66.2 + - - +
126A GLN* 3.4 14.2 + - + +
127A GLN* 3.0 41.2 + - + +
238A ALA* 4.6 10.0 - - - +
242A ASP* 4.4 19.9 - - - +
243A LEU* 6.1 4.3 - - + -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 4.1 28.0 - - + -
107A VAL* 4.0 21.1 - - + -
108A CYS* 4.5 9.9 - - - -
119A ILE* 3.7 16.6 - - + +
120A THR 3.2 15.6 + - - +
121A LEU* 3.7 12.8 - - + +
123A GLU* 1.3 76.0 - - - +
125A HIS* 1.3 56.8 + - - +
127A GLN* 3.1 5.0 + - - +
128A VAL* 2.9 49.2 + - + +
144A LEU* 4.3 14.1 - - + -
148A ILE* 4.9 3.4 - - + -
169A ILE* 4.1 28.5 - - + -
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Residues in contact with HIS 125 (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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121A LEU 3.1 12.7 + - - +
122A GLU* 3.1 11.8 + - - +
124A LEU* 1.3 77.0 - - - +
126A GLN* 1.3 66.2 + - - +
128A VAL* 3.9 1.9 - - + +
129A LEU* 3.0 47.7 + - + +
139A VAL* 2.9 31.4 + - + -
140A SER* 4.0 9.7 - - - -
141A GLN* 3.7 32.7 + - + -
144A LEU* 3.6 24.9 - - + +
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Residues in contact with GLN 126 (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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122A GLU* 2.9 37.2 + - - +
123A GLU* 3.4 16.3 - - + +
125A HIS* 1.3 77.5 + - - +
127A GLN* 1.3 65.0 + - - +
129A LEU* 4.0 6.3 - - - +
130A LYS* 3.2 25.8 + - + +
243A LEU* 3.3 42.1 - - - +
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Residues in contact with GLN 127 (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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107A VAL* 3.7 23.4 - - + +
111A LEU* 4.1 21.5 - - + +
123A GLU* 3.0 31.1 + - + +
124A LEU 3.5 3.8 - - - +
126A GLN* 1.3 83.3 - - - +
128A VAL* 1.3 67.1 + - - +
129A LEU 3.1 1.1 - - - -
130A LYS* 3.4 13.3 + - - +
131A GLY* 3.2 18.4 + - - -
243A LEU* 6.1 1.0 - - - +
244A TYR 5.8 6.5 + - - +
246A GLN* 2.7 45.5 + - - +
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Residues in contact with VAL 128 (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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100A LEU* 3.8 24.7 - - + -
103A GLN* 3.5 20.2 + - + +
104A ILE* 4.3 10.8 - - + +
107A VAL* 4.0 13.7 - - + -
124A LEU* 2.9 36.8 + - + +
125A HIS* 3.9 4.3 - - + +
127A GLN* 1.3 75.1 - - - +
129A LEU* 1.3 65.2 + - + +
131A GLY 3.2 1.4 + - - -
132A ARG* 3.1 30.4 + - + +
139A VAL* 4.8 7.9 - - + -
144A LEU* 4.2 19.5 - - + -
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Residues in contact with LEU 129 (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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125A HIS* 3.0 45.8 + - + +
126A GLN* 4.0 6.5 - - - +
128A VAL* 1.3 74.5 - - + +
130A LYS* 1.3 53.9 + - - +
131A GLY 2.8 16.1 + - - -
132A ARG* 2.9 13.8 + - - +
133A GLY 3.7 1.2 + - - -
135A PHE 4.8 2.7 - - - +
136A ALA* 3.5 55.2 - - + +
137A GLN* 3.7 18.2 - - + +
138A ASP* 4.7 0.4 - - - +
139A VAL* 4.3 22.9 - - + +
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Residues in contact with LYS 130 (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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126A GLN* 3.2 18.1 + - + +
127A GLN* 3.4 17.6 + - - +
129A LEU* 1.3 76.4 - - - +
131A GLY* 1.3 56.8 + - - +
132A ARG 4.0 0.2 + - - -
133A GLY* 4.7 4.6 + - - -
136A ALA* 5.5 0.7 - - - -
243A LEU 5.6 2.0 + - - -
244A TYR* 5.4 5.5 - - - +
245A SER* 4.6 16.2 + - - +
246A GLN* 3.4 35.2 + - - +
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Residues in contact with GLY 131 (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 GLN* 4.1 10.5 + - - -
127A GLN 3.2 10.2 + - - -
128A VAL 3.7 5.2 - - - -
129A LEU 2.9 1.0 - - - -
130A LYS* 1.3 78.2 - - - +
132A ARG* 1.3 63.1 + - - +
133A GLY* 3.5 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