Contacts of the helix formed by residues 124 - 134 (chain A) in PDB entry 7CE1
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS 4.9 1.0 + - - -
122A ASP 3.3 0.6 - - - -
123A SER* 1.3 80.1 + - - +
125A VAL* 1.3 66.8 + - + +
126A PRO* 3.4 1.8 - - - -
127A ILE* 3.2 5.8 + - - +
128A ARG* 3.0 52.3 + - + +
149A PRO* 3.4 35.4 - - + -
150A ARG* 3.4 38.1 - - + -
153A PHE* 4.1 23.8 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 5.0 3.1 - - + -
121A LYS 5.0 1.3 - - - +
122A ASP* 3.3 35.0 - - + +
124A MET* 1.3 74.9 - - + +
126A PRO* 1.4 77.1 - - + +
128A ARG* 3.5 20.4 + - - +
129A TYR* 3.1 21.7 + - - +
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Residues in contact with PRO 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 4.4 15.3 - - + -
115A THR* 4.5 18.2 - - - +
116A PRO 5.1 3.4 - - - +
117A HIS* 4.0 22.9 - - + +
122A ASP 3.4 10.1 - - - +
123A SER 3.7 3.4 - - - +
124A MET 3.5 2.0 - - - -
125A VAL* 1.4 102.1 - - + +
127A ILE* 1.3 71.9 + - + +
129A TYR* 3.1 13.7 - - + +
130A ILE* 2.9 33.6 + - - +
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Residues in contact with ILE 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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83A VAL* 4.2 21.8 - - + -
123A SER 3.6 21.5 - - - +
124A MET* 3.2 11.4 + - - +
126A PRO* 1.3 85.0 - - + +
128A ARG* 1.3 66.2 + - - +
130A ILE* 3.3 6.9 + - - +
131A LEU* 3.1 26.5 + - + +
139A VAL* 4.8 5.2 - - + -
141A ILE* 4.6 1.8 - - + -
150A ARG* 3.6 17.0 - - + +
153A PHE* 3.7 24.5 - - + -
154A MET* 3.6 42.4 - - + -
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Residues in contact with ARG 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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124A MET* 3.0 48.5 + - + +
125A VAL* 4.1 16.3 - - - +
127A ILE* 1.3 72.4 - - - +
129A TYR* 1.3 61.1 + - - +
131A LEU* 4.1 0.6 - - - +
132A GLU* 2.9 39.2 + - - +
153A PHE* 3.9 24.5 - - + -
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Residues in contact with TYR 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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115A THR* 5.0 14.6 - - + -
125A VAL 3.1 15.1 + - - +
126A PRO* 3.1 16.6 - - + +
128A ARG* 1.3 77.3 - - - +
130A ILE* 1.3 61.8 + - + +
132A GLU* 3.8 8.7 + - - +
133A THR* 2.9 66.6 + - + +
135A SER* 4.7 3.8 - - - -
64B GLN* 5.7 3.6 - - + -
67B ARG* 4.8 4.2 + - - -
111B HIS* 2.6 41.3 + + - -
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Residues in contact with ILE 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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81A ALA* 3.8 25.1 - - + -
83A VAL* 4.0 20.0 - - + -
115A THR* 4.2 9.6 - - + +
126A PRO 2.9 21.9 + - - +
127A ILE* 3.6 7.9 - - - +
128A ARG 3.2 0.2 - - - -
129A TYR* 1.3 82.6 - - + +
131A LEU* 1.3 59.8 + - + +
134A GLY* 2.8 29.6 + - - -
135A SER* 3.3 14.4 + - - +
136A ALA* 3.6 26.9 - - + +
139A VAL* 3.9 16.4 - - + -
159A MET* 3.8 16.7 - - + +
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Residues in contact with LEU 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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127A ILE* 3.1 35.0 + - + +
128A ARG 4.1 1.6 - - - +
130A ILE* 1.3 80.3 - - + +
132A GLU* 1.3 63.5 + - - +
134A GLY* 3.5 9.6 + - - -
139A VAL* 5.4 0.7 - - + -
153A PHE* 4.5 15.5 - - + -
154A MET* 4.1 6.7 - - + -
157A ARG* 4.3 29.4 - - + +
159A MET* 3.5 52.9 - - + -
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Residues in contact with GLU 132 (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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128A ARG* 2.9 25.8 + - + +
129A TYR* 3.8 6.3 - - - +
131A LEU* 1.3 80.2 - - - +
133A THR* 1.3 67.4 + - + +
19B ARG* 3.5 23.6 + - + +
62B GLY 4.0 18.7 + - - +
64B GLN* 4.6 12.7 - - + +
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Residues in contact with THR 133 (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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71A ARG* 4.9 3.8 + - - -
129A TYR* 2.9 51.5 + - + +
132A GLU* 1.3 80.1 - - + +
134A GLY* 1.3 63.3 + - - +
135A SER* 3.3 24.2 + - - -
19B ARG* 3.4 28.3 + - - -
64B GLN* 3.8 32.5 - - + -
66B ASN* 5.1 1.4 + - - -
67B ARG* 6.2 4.3 - - - -
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Residues in contact with GLY 134 (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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71A ARG* 4.5 1.8 + - - -
77A THR* 3.3 20.6 - - - +
130A ILE 2.8 15.3 + - - -
131A LEU* 3.9 7.2 - - - -
132A GLU 3.3 3.8 + - - -
133A THR* 1.3 77.1 - - - +
135A SER* 1.3 55.0 + - - -
136A ALA 3.3 9.1 + - - +
159A MET* 5.7 2.5 - - - -
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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