Contacts of the helix formed by residues 124 - 133 (chain A) in PDB entry 3CQ6
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.3 26.8 + - - -
122A SER 3.3 5.2 + - - -
123A TYR* 1.3 78.8 - - - +
125A MET* 1.3 62.7 + - - +
127A PRO* 3.4 14.1 - - - +
128A ILE* 3.3 21.1 - - - +
402A PO4 3.2 24.8 + - - -
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Residues in contact with MET 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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21A TYR* 3.8 33.9 - - + -
99A ASN* 3.8 12.8 - - - +
123A TYR* 3.2 41.9 - - + +
124A SER* 1.3 80.3 + - - +
126A HIS* 1.3 61.0 + - - +
127A PRO 3.5 0.2 - - - -
128A ILE* 3.5 37.5 - - + -
129A LEU* 2.7 53.9 + - + +
255C LEU* 5.2 0.4 - - + -
256C PRO* 3.6 26.0 - - + -
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Residues in contact with HIS 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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102A LEU* 3.7 24.2 - - + +
106A LEU* 4.7 0.3 - - - +
122A SER* 4.7 4.9 + - - -
123A TYR* 3.3 23.3 + + + +
125A MET* 1.3 77.8 - - - +
127A PRO* 1.3 67.5 - - + +
129A LEU* 3.9 3.1 - - + +
130A ALA* 2.9 28.2 + - - +
137A PHE* 4.3 7.6 - - + -
166A PHE* 3.6 55.4 - + + +
168A THR* 3.2 27.3 + - - -
197A ASP* 3.2 28.3 + - + +
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Residues in contact with PRO 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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120A GLN* 4.0 17.3 - - - +
123A TYR 3.4 11.2 - - - +
124A SER* 3.4 14.8 - - - +
126A HIS* 1.3 94.6 - - + +
128A ILE* 1.3 54.7 + - + +
130A ALA* 3.3 2.1 + - + +
131A LYS* 2.9 31.1 + - - +
137A PHE* 3.8 41.9 - - + +
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Residues in contact with ILE 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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21A TYR* 3.6 43.3 - - + -
124A SER* 3.3 20.6 + - - +
125A MET* 3.4 26.4 + - + +
126A HIS 3.3 0.6 - - - -
127A PRO* 1.3 79.6 - - + +
129A LEU* 1.3 58.9 + - + +
131A LYS* 3.4 6.8 + - - +
132A GLY* 3.0 23.9 + - - -
252C LEU 6.0 2.0 - - - +
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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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99A ASN* 3.8 14.6 - - - +
102A LEU* 3.7 38.1 - - + -
103A GLN* 4.3 10.8 - - + +
106A LEU* 3.4 16.2 - - + -
125A MET* 2.7 50.1 + - + +
126A HIS* 3.9 2.7 - - - +
128A ILE* 1.3 69.0 - - + +
130A ALA* 1.3 66.9 + - - +
132A GLY* 3.2 2.8 + - - +
133A THR* 2.9 28.6 + - - +
255C LEU* 3.2 35.2 - - + -
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Residues in contact with ALA 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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106A LEU* 3.5 7.7 - - + +
116A ALA* 4.6 6.7 - - + -
126A HIS 2.9 18.7 + - - +
127A PRO* 3.4 10.8 - - + +
129A LEU* 1.3 75.9 - - - +
131A LYS* 1.3 56.4 + - - +
133A THR* 2.9 14.1 + - - -
135A THR* 2.7 52.6 + - + +
137A PHE* 4.1 17.7 - - + -
166A PHE* 5.4 0.2 - - + -
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.7 34.1 + - + +
15A LEU* 5.0 9.0 - - + -
18A GLU* 2.7 36.8 + - - -
127A PRO 2.9 17.0 + - - +
128A ILE* 3.7 7.0 - - - +
130A ALA* 1.3 74.7 - - - +
132A GLY* 1.3 58.6 + - - +
134A HIS* 3.0 25.6 + - - +
135A THR 3.7 7.2 + - - -
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Residues in contact with GLY 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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15A LEU* 6.4 1.6 - - - -
128A ILE 3.0 15.5 + - - -
129A LEU* 3.2 4.9 + - - -
131A LYS* 1.3 77.1 - - - +
133A THR* 1.3 59.7 + - - +
134A HIS* 3.3 12.5 + - - -
107C GLN* 3.6 26.5 + - - +
253C VAL* 6.5 1.3 - - - -
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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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103A GLN* 3.9 29.6 - - + +
106A LEU* 3.5 29.7 - - + +
107A GLN* 4.4 11.4 - - + -
111A GLY* 3.3 15.4 - - - -
112A PRO* 3.9 2.4 - - - +
129A LEU* 2.9 18.2 + - - +
130A ALA* 2.9 10.7 + - - -
132A GLY* 1.3 77.7 - - - +
134A HIS* 1.3 73.9 + - - +
135A THR* 3.0 14.4 + - - -
107C GLN* 5.8 0.7 - - - +
134C HIS* 5.1 3.1 + - - -
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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