Contacts of the helix formed by residues 117 - 129 (chain C) in PDB entry 5FDK
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 HIS 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C GLN* 3.6 26.3 + - - -
114C GLN 3.5 13.7 + - - -
115C ASN* 3.2 16.0 + - - -
116C PHE* 1.3 80.8 + - - +
118C ASP* 1.3 69.8 + - - +
119C HIS* 3.1 24.9 - + + +
120C GLN* 3.0 13.3 + - - +
121C ILE* 3.3 25.5 + - - +
156C TRP* 3.9 4.3 - - - -
2G C 5.9 0.6 + - - -
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Residues in contact with ASP 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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117C HIS* 1.3 73.6 - - - +
119C HIS* 1.3 63.2 + - + +
121C ILE* 3.2 8.8 + - - +
122C GLU* 2.8 28.3 + - - +
156C TRP* 3.0 30.2 + - - +
159C LYS* 4.9 2.6 + - - -
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Residues in contact with HIS 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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83C GLN* 2.5 39.8 + - + -
84C SER 3.9 8.1 - - - -
85C SER* 3.6 28.9 - - - -
117C HIS* 3.1 32.4 - + + +
118C ASP* 1.3 79.8 - - + +
120C GLN* 1.3 93.2 + - + +
122C GLU* 3.2 9.1 + - - +
123C HIS* 2.9 23.7 + - - +
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Residues in contact with GLN 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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84C SER 5.1 2.6 + - - +
85C SER 3.6 17.3 - - - +
86C THR 5.6 0.8 + - - -
87C THR* 4.7 13.0 - - - +
88C ASN* 4.7 6.7 - - - +
101C GLU* 3.3 29.6 + - - +
115C ASN 5.0 3.8 + - - -
116C PHE* 3.2 18.4 - - - +
117C HIS* 3.0 27.3 + - - +
118C ASP 3.2 0.4 - - - -
119C HIS* 1.3 101.5 + - + +
121C ILE* 1.3 67.4 + - + +
123C HIS* 3.0 14.9 + - - +
124C MET* 3.0 21.0 + - - +
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Residues in contact with ILE 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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116C PHE* 3.7 24.5 - - + -
117C HIS 3.3 15.5 + - - +
118C ASP 3.2 10.2 + - - +
120C GLN* 1.3 79.8 - - + +
122C GLU* 1.3 67.0 + - - +
124C MET* 3.4 12.0 - - - +
125C LYS* 2.9 23.7 + - + +
152C LEU* 4.1 22.7 - - + -
153C PHE* 4.0 18.3 - - + -
156C TRP* 4.0 42.4 - - + +
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Residues in contact with GLU 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 ASP 2.8 15.6 + - - +
119C HIS* 3.2 12.3 + - - +
121C ILE* 1.3 76.3 - - - +
123C HIS* 1.3 65.3 + - - +
125C LYS* 2.9 21.2 + - - +
126C GLN* 2.9 33.2 + - + +
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Residues in contact with HIS 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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47A LEU* 6.4 0.4 - - + -
53A VAL* 3.6 31.1 - - + +
55A HIS* 4.6 9.7 + + - -
85C SER* 4.5 9.4 - - - +
86C THR* 4.1 21.4 - - - -
87C THR* 3.9 18.7 + - - +
97C TYR* 4.6 6.3 + - - -
99C ASP* 3.2 27.6 - - - -
119C HIS 2.9 13.2 + - - +
120C GLN* 3.0 10.7 + - - +
122C GLU* 1.3 78.0 - - - +
124C MET* 1.3 61.7 + - - +
126C GLN* 2.9 28.6 + - + +
127C VAL* 3.0 25.9 + - + +
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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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87C THR* 4.7 13.5 - - - -
99C ASP* 5.5 0.7 - - - +
100C PHE* 6.2 0.9 - - - -
101C GLU* 5.6 4.3 - - - -
120C GLN* 3.0 20.9 + - - +
121C ILE* 3.4 19.3 - - - +
123C HIS* 1.3 76.8 + - - +
125C LYS* 1.3 63.4 + - - +
127C VAL* 3.7 13.1 - - + +
128C LYS* 3.5 13.9 + - - +
134C CYS* 3.4 33.6 - - - +
135C PHE 4.2 1.6 - - - +
136C VAL* 3.7 28.9 - - + -
149C ALA* 4.6 6.3 - - + -
152C LEU* 3.7 19.3 - - + -
153C PHE* 3.4 24.2 - - + -
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Residues in contact with LYS 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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121C ILE* 2.9 15.3 + - + +
122C GLU* 3.0 24.0 - - - +
123C HIS 2.9 0.8 - - - -
124C MET* 1.3 77.4 - - - +
126C GLN* 1.3 64.7 + - - +
127C VAL 3.1 0.3 + - - -
128C LYS* 3.3 4.3 + - - +
129C ALA* 2.9 22.8 + - - +
153C PHE* 4.0 14.1 - - + -
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Residues in contact with GLN 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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47A LEU* 3.1 41.1 + - + +
48A THR* 5.4 2.2 - - - +
50A GLN* 4.0 23.6 + - - +
53A VAL* 3.9 20.7 - - + +
122C GLU* 2.9 36.0 + - + +
123C HIS* 2.9 12.9 + - - +
125C LYS* 1.3 75.2 - - - +
127C VAL* 1.3 57.0 + - - +
129C ALA* 2.9 27.9 + - - +
130C GLN* 3.0 12.6 + - - +
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Residues in contact with VAL 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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53A VAL* 4.8 9.2 - - + -
92A ILE* 5.5 3.5 - - + +
97C TYR* 4.3 20.2 - - + -
99C ASP* 4.0 7.4 - - + +
123C HIS* 3.0 44.3 + - + +
124C MET* 3.7 12.3 - - + +
125C LYS 3.1 0.4 - - - -
126C GLN* 1.3 76.3 - - + +
128C LYS* 1.3 60.0 + - - +
130C GLN* 2.7 22.6 + - - +
132C GLY* 3.1 37.3 + - - -
134C CYS* 4.2 12.6 - - + -
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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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124C MET 3.5 11.9 + - - +
125C LYS 3.3 4.3 + - - +
127C VAL* 1.3 80.1 - - - +
129C ALA* 1.3 56.3 + - - +
130C GLN 3.0 3.2 + - - -
131C ASP* 3.6 8.4 + - - +
132C GLY 4.1 16.6 - - - +
134C CYS* 5.0 8.3 - - + -
149C ALA* 5.2 5.2 - - + -
150C ASP* 5.7 2.7 - - - +
153C PHE* 4.9 12.3 - - + -
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Residues in contact with ALA 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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50A GLN* 5.9 7.2 - - + +
125C LYS 2.9 15.1 + - - +
126C GLN* 2.9 21.3 + - - +
128C LYS* 1.3 76.1 - - - +
130C GLN* 1.3 61.8 + - - +
131C ASP 3.8 0.7 - - - -
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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