Contacts of the helix formed by residues 117 - 130 (chain C) in PDB entry 5BXD
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C TYR* 4.1 15.7 - - + -
54C SER* 3.6 24.5 - - - +
56C ILE* 4.1 5.2 - - + -
87C ILE* 3.9 30.1 - - + -
90C PHE* 4.1 16.8 - - + -
91C LEU* 3.9 26.9 - - + -
112C ALA 3.0 9.8 + - - +
115C PHE* 4.0 12.8 - - + +
116C GLN* 1.3 72.9 - - - +
118C GLN* 1.3 65.2 + - - +
119C PRO* 3.4 4.3 - - + -
120C MET* 3.0 29.7 + - + +
121C LEU* 3.1 17.0 + - - +
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Residues in contact with GLN 118 (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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113C LYS* 5.2 4.0 + - - -
116C GLN 3.4 7.5 + - - +
117C LEU* 1.3 72.5 - - - +
119C PRO* 1.3 70.7 - - + +
121C LEU* 3.3 25.9 + - - +
122C LEU* 3.2 27.9 + - + +
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Residues in contact with PRO 119 (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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51C TYR* 3.9 29.6 - - + +
90C PHE* 3.7 17.3 - - + -
117C LEU* 3.5 6.3 - - + -
118C GLN* 1.3 94.9 - - + +
120C MET* 1.3 59.1 + - - +
122C LEU* 3.6 9.0 + - + +
123C GLU* 3.2 27.7 + - - +
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Residues in contact with MET 120 (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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86C TYR 3.7 20.2 - - - +
87C ILE* 3.8 29.4 - - + -
90C PHE* 3.3 47.1 - - + -
96C LEU* 4.0 22.9 - - + -
108C LEU* 3.9 20.6 - - + -
112C ALA* 3.9 10.3 - - + -
117C LEU* 3.0 19.5 + - + +
119C PRO* 1.3 76.9 - - - +
121C LEU* 1.3 62.1 + - - +
123C GLU* 3.2 3.7 + - - +
124C MET* 2.9 39.5 + - + +
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Residues in contact with LEU 121 (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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109C TYR* 3.8 36.9 - - + +
112C ALA* 3.7 12.1 - - + +
113C LYS* 3.7 52.7 - - + +
116C GLN* 5.4 1.8 - - - -
117C LEU 3.1 21.3 + - - +
118C GLN* 3.3 33.0 + - - +
120C MET* 1.3 75.9 - - - +
122C LEU* 1.3 61.5 + - - +
124C MET* 3.2 7.3 + - - +
125C GLU* 3.1 31.8 + - - +
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Residues in contact with LEU 122 (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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118C GLN* 3.2 16.1 + - - +
119C PRO* 3.7 11.9 - - + +
121C LEU* 1.3 78.4 - - - +
123C GLU* 1.3 62.5 + - - +
125C GLU* 3.4 18.7 + - + +
126C ARG* 3.2 67.1 + - + +
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Residues in contact with GLU 123 (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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90C PHE* 4.6 10.3 - - + -
94C SER 5.2 4.0 - - - +
95C LYS* 5.4 0.8 - - - -
96C LEU* 3.7 27.6 + - + +
119C PRO* 3.2 14.4 + - + +
120C MET* 3.2 10.4 + - - +
122C LEU* 1.3 78.1 - - - +
124C MET* 1.3 58.0 + - - +
126C ARG* 2.8 41.4 + - - +
127C TRP* 2.9 27.9 + - - +
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Residues in contact with MET 124 (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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96C LEU* 3.7 25.6 - - + -
98C ILE* 6.1 0.9 - - + -
102C PHE* 5.5 0.4 - - + -
105C TYR* 3.1 52.6 + - + +
108C LEU* 3.8 26.7 - - + -
109C TYR* 3.6 44.6 - - + +
112C ALA* 4.3 14.1 - - - -
120C MET* 2.9 21.2 + - + +
121C LEU* 3.2 7.6 + - - +
123C GLU* 1.3 74.8 - - - +
125C GLU* 1.3 63.9 + - - +
127C TRP* 3.3 2.4 + - - +
128C LYS 3.1 16.5 + - - -
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Residues in contact with GLU 125 (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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105C TYR* 3.7 10.8 - - - +
109C TYR* 2.8 28.8 + - + +
121C LEU* 3.1 20.4 + - - +
122C LEU* 3.8 21.6 - - + +
124C MET* 1.3 76.1 - - - +
126C ARG* 1.3 58.0 + - + +
128C LYS* 3.4 7.2 + - - +
129C GLN* 3.1 24.7 + - - +
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Residues in contact with ARG 126 (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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122C LEU* 3.2 48.3 + - + +
123C GLU* 2.8 37.7 + - - +
124C MET 3.2 0.6 - - - -
125C GLU* 1.3 74.9 - - + +
127C TRP* 1.3 65.3 + - - +
128C LYS 3.0 2.0 - - - -
129C GLN* 3.1 47.2 + - - +
130C ASP* 3.1 11.5 - - - +
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Residues in contact with TRP 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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96C LEU* 3.7 14.4 - - + -
98C ILE* 3.4 40.2 + - + +
99C PRO 4.8 4.6 + - - -
100C ASP* 5.2 7.2 - - - -
102C PHE* 4.4 24.0 - + + -
105C TYR* 3.8 34.1 - + + -
123C GLU 2.9 13.6 + - - +
124C MET 3.3 7.4 + - - +
126C ARG* 1.3 75.1 - - - +
128C LYS* 1.3 74.9 + - + +
130C ASP* 3.6 22.7 + - - +
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Residues in contact with LYS 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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100B ASP* 5.9 0.6 + - - -
105C TYR* 3.4 61.8 - - + +
106C THR* 6.1 0.7 - - - -
124C MET 3.1 6.7 + - - +
125C GLU* 3.5 12.1 - - - +
126C ARG 3.0 0.4 - - - -
127C TRP* 1.3 87.6 - - + +
129C GLN* 1.3 62.0 + - - +
130C ASP 3.1 6.8 + - - +
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Residues in contact with GLN 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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125C GLU 3.1 10.5 + - - +
126C ARG* 3.1 44.4 + - - +
128C LYS* 1.3 76.9 - - - +
130C ASP* 1.3 75.7 + - - +
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Residues in contact with ASP 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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126C ARG* 3.1 18.2 + - - +
127C TRP* 3.6 15.4 - - - +
128C LYS 3.1 5.3 - - - +
129C GLN* 1.3 102.0 + - - +
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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