Contacts of the helix formed by residues 117 - 127 (chain C) in PDB entry 3VJR
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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12C LEU* 3.8 14.1 - - + -
24C HIS* 3.3 24.4 - + - -
71C MET* 3.7 24.7 - - + -
96C HIS* 3.9 9.2 - - + +
97C ASP* 2.6 47.1 + - - -
114C HIS* 3.0 18.1 + - - +
115C GLY 3.3 2.2 + - - -
116C GLY* 1.3 73.5 - - - +
118C ASN* 1.3 61.7 + - - +
119C GLY 3.2 19.1 + - - -
120C LEU* 3.2 19.6 + - + +
121C LYS* 3.0 28.7 + - - +
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Residues in contact with ASN 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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24C HIS* 2.8 33.0 + - - -
71C MET* 3.2 18.3 - - - +
72C ASN* 3.9 22.5 - - + +
116C GLY 3.2 8.0 + - - +
117C HIS* 1.3 71.9 - - - +
119C GLY* 1.3 64.3 + - - +
121C LYS* 3.5 15.8 - - + +
122C ASP* 3.3 22.3 + - - +
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.0 8.3 - - - -
71C MET* 3.3 31.6 - - - -
74C SER* 4.0 1.8 - - - -
117C HIS* 3.2 8.0 + - - -
118C ASN* 1.3 83.7 - - - +
120C LEU* 1.3 62.8 + - - +
122C ASP* 3.3 3.9 + - - +
123C ILE* 3.1 27.4 + - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.1 1.8 - - + +
94C VAL* 3.9 15.9 - - + -
96C HIS* 3.5 48.7 - - + +
113C GLY 4.6 0.4 - - - +
114C HIS* 3.8 37.0 - - + +
117C HIS* 3.2 17.0 + - + +
119C GLY* 1.3 72.3 - - - +
121C LYS* 1.3 66.2 + - - +
123C ILE* 3.2 5.3 + - + +
124C ILE* 2.9 32.4 + - + +
133C PHE* 3.8 28.7 - - + -
135C ARG* 4.4 11.9 - - + +
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Residues in contact with LYS 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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114C HIS* 3.6 45.7 - - + +
116C GLY* 4.6 11.7 + - - +
117C HIS 3.0 14.3 + - - +
118C ASN* 3.5 20.0 - - + +
120C LEU* 1.3 77.3 - - - +
122C ASP* 1.3 56.8 - - - +
124C ILE* 3.3 5.3 + - - +
125C SER* 3.0 26.9 + - - -
1D G 4.8 10.4 + - - +
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Residues in contact with ASP 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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72C ASN 2.8 27.7 - - - +
73C LEU* 3.1 16.2 - - - +
74C SER 4.4 0.4 - - - +
75C GLY* 2.9 26.3 + - - +
118C ASN 3.3 10.3 + - - +
119C GLY 3.7 4.9 - - - +
120C LEU 3.2 0.6 - - - -
121C LYS* 1.3 76.9 - - - +
123C ILE* 1.3 61.7 + - - +
125C SER* 3.2 5.0 + - - -
126C LYS* 2.8 65.8 + - - +
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Residues in contact with ILE 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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12C LEU* 3.6 32.3 - - + -
74C SER* 4.0 1.6 - - - -
75C GLY* 3.8 17.3 - - - +
78C VAL* 3.8 32.1 - - + -
94C VAL* 3.9 18.8 - - + -
119C GLY 3.1 17.8 + - - +
120C LEU* 3.7 8.1 - - + +
122C ASP* 1.3 76.1 - - - +
124C ILE* 1.3 63.8 + - - +
125C SER 3.2 0.2 + - - -
126C LYS* 3.2 0.7 + - - +
127C LEU* 2.9 37.9 + - + +
133C PHE* 3.6 26.9 - - + -
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Residues in contact with ILE 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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112C GLY 4.3 8.3 - - - +
113C GLY* 5.3 0.2 - - - -
114C HIS* 4.2 31.6 - - + +
120C LEU* 2.9 19.9 + - + +
121C LYS* 3.5 7.9 - - - +
123C ILE* 1.3 76.9 - - - +
125C SER* 1.3 58.3 + - - +
127C LEU 3.7 0.2 + - - -
128C GLY 3.6 2.3 + - - -
129C ASN* 2.9 42.2 + - - +
130C ASN 2.9 29.6 + - - +
131C PRO* 3.9 21.8 - - + -
133C PHE* 3.6 20.0 - - + -
135C ARG* 4.4 4.7 - - - +
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Residues in contact with SER 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 LYS 3.0 13.9 + - - -
122C ASP* 3.5 11.2 - - - -
123C ILE 3.2 0.2 - - - -
124C ILE* 1.3 78.1 - - - +
126C LYS* 1.3 72.7 + - - +
127C LEU 3.2 0.2 - - - -
128C GLY* 3.0 17.5 + - - -
129C ASN* 3.3 11.7 + - - +
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Residues in contact with LYS 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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73C LEU* 4.5 13.5 - - - +
75C GLY* 3.6 31.4 - - - +
76C LYS* 4.4 11.9 - - + +
79C ALA* 3.6 17.4 - - + +
122C ASP* 2.8 46.0 + - - +
123C ILE 3.8 0.4 - - - +
125C SER* 1.3 82.0 + - - +
127C LEU* 1.3 61.4 + - + +
128C GLY 3.2 5.1 + - - -
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Residues in contact with LEU 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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75C GLY 5.5 0.2 - - - +
78C VAL* 3.8 24.2 - - + -
79C ALA* 4.3 17.3 - - + +
82C ALA* 4.8 5.4 - - + -
89C PRO* 4.2 23.9 - - + +
92C ILE* 4.1 22.4 - - + -
123C ILE* 2.9 24.3 + - + +
124C ILE 4.1 0.4 - - - +
126C LYS* 1.3 77.5 - - + +
128C GLY* 1.3 58.9 + - - +
130C ASN* 3.8 24.0 + - + +
133C PHE* 3.8 28.9 - - + -
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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