Contacts of the helix formed by residues 101 - 114 (chain C) in PDB entry 4U2M
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 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C CYS* 3.9 23.3 - - + +
46C SER* 4.3 2.7 - - - -
73C VAL* 3.7 15.3 - - + -
76C PHE* 3.8 20.0 - - + -
77C MET* 3.6 36.3 - - + -
96C ALA* 2.8 16.4 + - + +
99C LEU* 3.7 25.4 - - + +
100C GLN* 1.3 71.7 - - - +
102C GLN* 1.3 59.9 + - - +
103C ASP* 3.4 2.5 - - + -
104C ILE* 3.1 33.8 + - + +
105C ILE* 3.0 29.5 + - - +
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Residues in contact with GLN 102 (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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100C GLN 3.4 8.4 + - - +
101C MET* 1.3 71.2 - - - +
103C ASP* 1.3 60.8 + - - +
105C ILE* 3.2 28.9 + - + +
106C THR* 2.9 46.9 + - - -
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Residues in contact with ASP 103 (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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114B LEU* 4.1 2.9 - - - +
76C PHE* 4.9 9.0 - - + -
101C MET* 5.2 0.9 - - + -
102C GLN* 1.3 77.8 - - - +
104C ILE* 1.3 66.3 + - + +
106C THR* 3.7 4.9 + - - -
107C ALA* 3.1 22.7 + - - +
134C PHE* 3.9 30.5 - - + -
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Residues in contact with ILE 104 (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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73C VAL* 4.0 18.4 - - + -
76C PHE* 3.6 32.8 - - + -
82C LEU* 4.0 22.9 - - + -
92C VAL* 3.6 25.1 - - + -
96C ALA* 3.5 19.1 - - + -
101C MET* 3.1 42.2 + - + +
103C ASP* 1.3 75.4 - - + +
105C ILE* 1.3 67.0 + - - +
107C ALA* 3.2 1.6 + - - +
108C CYS* 3.0 23.7 + - - -
134C PHE* 5.8 0.2 - - + -
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Residues in contact with ILE 105 (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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93C LEU* 4.0 13.3 - - + +
96C ALA* 3.8 28.7 - - + +
97C THR* 3.9 19.7 - - + +
100C GLN* 4.7 4.3 - - - -
101C MET 3.0 24.6 + - - +
102C GLN* 3.2 34.3 + - - +
104C ILE* 1.3 77.1 - - - +
106C THR* 1.3 64.2 + - - +
108C CYS* 3.3 3.6 + - - +
109C HIS* 3.1 46.2 + - + +
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Residues in contact with THR 106 (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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113B SER* 3.7 28.7 - - - +
114B LEU* 3.9 17.3 - - + +
102C GLN* 2.9 28.2 + - - -
103C ASP* 4.0 4.9 - - - -
105C ILE* 1.3 77.0 - - - +
107C ALA* 1.3 54.8 + - - +
109C HIS* 3.2 8.8 + - + +
110C ALA* 2.8 33.1 + - - +
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Residues in contact with ALA 107 (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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114B LEU* 3.6 14.7 - - + +
82C LEU* 3.8 17.0 - - + -
84C LEU* 3.8 3.5 - - + +
103C ASP 3.1 18.2 + - - +
104C ILE 3.2 4.9 + - - +
106C THR* 1.3 75.1 - - - +
108C CYS* 1.3 57.7 + - - +
110C ALA* 3.3 5.9 + - - +
111C LEU* 2.9 28.6 + - - +
132C ILE* 3.6 29.0 - - + +
134C PHE* 4.5 3.8 - - + -
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Residues in contact with CYS 108 (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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84C LEU* 4.1 10.5 - - - -
89C VAL* 3.8 22.6 - - + +
92C VAL* 3.7 30.3 - - - -
93C LEU* 3.7 32.1 - - + -
104C ILE* 3.0 20.5 + - - -
105C ILE 3.6 7.9 - - - +
107C ALA* 1.3 76.6 - - - +
109C HIS* 1.3 62.2 + - - +
111C LEU* 3.2 3.1 + - - +
112C LYS* 3.0 28.3 + - - +
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Residues in contact with HIS 109 (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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93C LEU* 3.8 25.5 - - + +
105C ILE* 3.1 39.5 + - + +
106C THR* 3.7 9.9 - - + +
108C CYS* 1.3 75.8 - - - +
110C ALA* 1.3 58.3 + - - +
112C LYS* 3.2 12.8 + - + +
113C SER* 2.8 30.8 + - - -
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Residues in contact with ALA 110 (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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110B ALA* 3.8 35.9 - - + +
113B SER* 3.8 10.8 - - - +
114B LEU* 4.8 6.1 - - + -
106C THR 2.8 21.4 + - - +
107C ALA* 3.4 9.4 - - - +
109C HIS* 1.3 74.8 - - - +
111C LEU* 1.3 63.6 + - - +
113C SER* 2.7 26.4 + - - -
114C LEU* 3.5 3.2 + - - +
132C ILE* 6.2 0.9 - - + -
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Residues in contact with LEU 111 (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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84C LEU* 3.8 30.3 - - + -
85C SER 4.2 8.7 - - - +
86C PRO* 4.6 1.8 - - + -
89C VAL* 4.2 20.4 - - + -
107C ALA 2.9 13.5 + - - +
108C CYS 3.2 8.0 + - - +
110C ALA* 1.3 76.6 - - - +
112C LYS* 1.3 60.0 + - - +
114C LEU* 2.9 45.1 + - + +
115C ALA* 4.2 1.0 + - - +
128C ALA* 3.7 30.5 - - + +
130C SER* 3.9 23.8 - - - -
132C ILE* 6.2 0.4 - - + -
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Residues in contact with LYS 112 (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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89C VAL* 4.2 24.2 - - + -
90C ASP* 2.8 31.6 + - - -
93C LEU* 4.5 12.3 - - + +
108C CYS 3.0 23.0 + - - +
109C HIS* 3.7 16.6 - - + +
111C LEU* 1.3 75.7 - - + +
113C SER* 1.3 62.7 + - - +
114C LEU 3.0 1.8 + - - -
115C ALA* 3.0 23.4 + - - +
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Residues in contact with SER 113 (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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106B THR* 3.6 16.0 - - - +
110B ALA* 3.9 13.3 + - - +
109C HIS 2.8 15.0 + - - -
110C ALA* 2.7 20.8 + - - -
112C LYS* 1.3 74.7 - - - +
114C LEU* 1.3 60.0 + - - +
115C ALA 3.3 7.8 + - - +
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Residues in contact with LEU 114 (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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103B ASP* 4.0 8.3 - - - +
106B THR* 3.6 17.2 - - + +
107B ALA* 3.5 38.1 - - + +
110B ALA* 4.7 4.5 - - + -
132B ILE* 4.5 17.7 - - + -
134B PHE* 4.6 10.0 - - + -
110C ALA 4.2 8.3 - - - +
111C LEU* 2.9 34.7 + - + +
113C SER* 1.3 82.3 + - - +
115C ALA* 1.3 58.2 + - - +
126C GLY* 5.9 0.2 - - - -
128C ALA* 4.2 19.3 - - + -
130C SER* 6.1 0.2 - - - -
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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