Contacts of the strand formed by residues 126 - 136 (chain C) in PDB entry 2CFX
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 ALA 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C ALA* 4.2 6.7 - - + -
72C THR 3.1 19.5 - - - +
73C VAL* 4.1 0.9 - - - +
74C LYS* 4.1 3.5 - - - +
81C PHE* 3.8 27.4 - - + -
122C THR* 3.1 9.4 + - - +
123C SER* 3.5 25.7 + - - -
124C PRO 3.5 1.6 - - - -
125C TYR* 1.3 81.8 - - - +
127C GLN* 1.3 64.4 + - - +
128C THR* 3.8 5.5 + - + +
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 5.7 2.6 + - - -
70C GLU 3.6 0.5 - - - +
71C ALA* 3.3 5.0 - - - -
72C THR* 2.8 62.5 + - + +
74C LYS* 3.8 27.1 - - + +
123C SER* 5.5 2.2 - - - -
126C ALA* 1.3 70.2 - - - +
128C THR* 1.3 60.5 + - - +
129C VAL* 5.9 0.2 - - - -
72E THR* 5.4 6.1 + - - -
127E GLN* 5.7 3.0 + - - -
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Residues in contact with THR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C VAL* 3.8 24.2 - - + -
70C GLU 3.2 4.9 - - - +
71C ALA* 4.7 6.7 - - + -
118C PHE* 5.5 0.4 - - + -
119C ILE* 3.5 34.6 - - + +
122C THR* 3.6 27.8 - - + +
123C SER* 4.5 4.7 + - - +
126C ALA 3.8 7.2 + - - +
127C GLN* 1.3 80.6 - - - +
129C VAL* 1.3 68.2 + - - +
130C THR* 4.7 1.0 + - - -
99E GLY 3.8 7.6 - - - +
100E ALA* 4.5 5.7 - - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE 3.8 0.7 - - - +
69C VAL* 3.3 5.4 - - - +
70C GLU* 2.8 53.4 + - + +
72C THR* 6.3 3.1 - - + -
127C GLN 5.9 0.2 - - - -
128C THR* 1.3 78.9 - - - +
130C THR* 1.3 63.3 + - - +
131C HIS* 3.5 29.1 - - + +
99E GLY* 3.5 19.5 - - - -
100E ALA* 3.9 23.3 - - + +
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C CYS* 3.7 33.7 - - + -
68C ILE 3.6 2.7 - - - +
69C VAL* 4.4 6.2 - - + +
115C VAL* 4.1 12.6 - - + -
119C ILE* 3.2 28.9 - - - +
128C THR* 4.2 2.3 + - - -
129C VAL* 1.3 75.3 + - - +
131C HIS* 1.3 65.5 + - - +
132C VAL* 4.0 0.7 - - + +
98E ALA* 3.5 37.3 - - + +
99E GLY* 3.6 9.3 + - - -
134F PHE* 4.2 8.9 - - + -
98H ALA* 4.8 1.2 - - - +
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Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C CYS* 3.2 2.4 - - - -
68C ILE* 2.7 52.4 + - + +
70C GLU* 2.9 28.8 + - + -
129C VAL* 3.5 25.3 - - + +
130C THR* 1.3 75.2 + - - +
132C VAL* 1.3 64.3 + - - +
133C ILE* 3.4 1.2 + - - +
99E GLY* 5.7 1.0 - - - -
70H GLU* 6.2 0.4 - - - -
97H ILE* 3.9 21.9 - - + +
98H ALA 3.1 25.7 + - - +
99H GLY* 4.1 11.5 - - - -
100H ALA* 5.3 3.4 - - + -
101H ALA 6.2 0.4 - - - -
104H MET* 3.8 23.0 - - + +
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Residues in contact with VAL 132 (chain C).
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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65C VAL* 4.8 2.2 - - + -
66C SER 3.8 11.0 - - - +
67C CYS* 4.1 14.8 - - - -
112C LEU* 4.6 13.9 - - + -
130C THR* 4.1 1.3 + - + -
131C HIS* 1.3 71.8 - - - +
133C ILE* 1.3 66.6 + - - +
134C PHE* 3.6 3.0 + - + -
98E ALA* 4.3 13.9 - - + -
112F LEU* 3.8 35.7 - - + -
132F VAL* 3.7 36.3 - - + -
134F PHE* 5.1 0.7 - - + -
97H ILE* 3.3 4.3 - - - -
98H ALA* 2.9 31.5 + - + +
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 2.8 45.4 + - - +
67C CYS* 3.9 11.4 - - - -
68C ILE* 3.7 26.2 - - + -
106C LYS* 3.9 14.8 - - - -
132C VAL* 1.3 81.8 - - - +
134C PHE* 1.3 63.1 + - - +
135C SER* 3.6 24.0 - - - +
112F LEU* 4.3 8.7 - - - +
95H TYR* 3.8 22.9 - - + -
96H ARG 3.4 5.4 - - - +
97H ILE* 4.0 15.3 - - + -
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Residues in contact with PHE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 3.6 2.4 + - + -
133C ILE* 1.3 77.9 - - - +
135C SER* 1.3 61.1 + - - +
112F LEU* 3.5 51.4 - - + +
113F GLU* 5.2 4.9 + - - +
115F VAL* 3.8 17.0 - - + -
116F GLU* 3.4 28.8 - - + +
119F ILE* 3.4 32.5 - - + -
130F THR* 4.6 2.5 - - + -
132F VAL* 4.9 3.1 - - + -
96H ARG* 2.7 24.1 + - + +
97H ILE 3.5 28.7 - - - -
98H ALA* 3.6 22.2 - - + -
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ILE* 3.6 10.1 - - - +
134C PHE* 1.3 79.0 - - - +
136C GLU* 1.3 65.6 + - - +
116F GLU* 2.9 31.9 + - - -
95H TYR* 3.6 2.4 - - - -
96H ARG* 2.8 28.3 + - - +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS* 5.6 0.7 + - - -
133C ILE* 5.5 0.2 - - + -
135C SER* 1.3 82.0 - - - +
137C ILE* 1.3 72.9 + - - +
138C ASP* 3.8 5.2 + - + +
82H LYS* 5.1 4.3 + - - -
93H PHE* 4.9 9.0 - - - +
94H CYS 3.3 12.3 - - - +
95H TYR* 3.7 30.1 + - + +
96H ARG* 4.4 1.1 - - - +
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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