Contacts of the helix formed by residues 118 - 128 (chain C) in PDB entry 3B4V
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 ASP 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C PRO 3.6 13.0 - - - +
104C ALA* 3.4 11.4 - - - +
105C ARG* 3.0 28.7 + - - +
106C LEU 3.3 9.2 - - - +
108C VAL* 4.0 6.3 - - - -
116C TYR* 3.2 5.2 + - - +
117C ARG* 1.3 79.4 - - - +
119C GLU* 1.3 65.4 + - - +
120C CYS* 2.9 19.2 + - + +
121C GLU* 2.9 38.4 + - - +
122C LEU 3.3 6.4 + - - -
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Residues in contact with GLU 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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102C LEU* 4.0 23.8 - - + +
103C PRO* 4.3 11.9 + - + +
106C LEU 4.3 0.6 + - - -
108C VAL* 3.8 18.5 - - + +
118C ASP* 1.3 73.1 - - - +
120C CYS* 1.3 56.6 + - - +
122C LEU* 3.3 4.3 + - + +
123C ARG* 2.7 79.8 + - - +
135C VAL* 4.0 12.6 - - + +
138C ARG* 3.0 35.2 + - - +
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Residues in contact with CYS 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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97C PRO* 4.1 0.8 - - - +
99C CYS* 2.0 55.9 - - + -
102C LEU* 3.9 12.2 - - + +
103C PRO 6.5 0.2 - - - -
104C ALA* 5.9 1.6 - - + -
118C ASP* 2.9 19.2 + - - +
119C GLU* 1.3 80.6 - - - +
121C GLU* 1.3 61.8 + - - +
123C ARG* 3.4 5.3 + - - +
124C ALA* 3.3 19.9 + - - +
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Residues in contact with GLU 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 TYR* 4.4 13.6 - - + -
117C ARG* 3.6 52.6 + - + +
118C ASP* 2.9 23.1 + - - +
120C CYS* 1.3 74.0 - - - +
122C LEU* 1.3 61.5 + - - +
124C ALA* 3.1 9.1 + - - +
125C ALA* 2.8 28.2 + - - +
128C ARG* 4.6 11.1 + - - -
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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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108C VAL* 4.3 5.6 - - + -
110C GLY* 4.1 16.4 - - - -
116C TYR* 4.2 25.4 - - + -
118C ASP 3.3 4.4 + - - +
119C GLU* 3.4 15.5 - - - +
121C GLU* 1.3 76.2 - - - +
123C ARG* 1.3 93.1 + - - +
125C ALA* 3.0 4.9 + - - +
126C ARG* 2.9 24.3 + - + +
133C LEU* 3.8 17.8 - - + +
134C SER* 3.7 29.6 - - - +
135C VAL* 4.0 22.2 - - + +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PRO* 3.8 22.8 - - + +
98C ASP 5.6 3.4 - - - +
99C CYS* 5.0 0.2 - - - -
102C LEU* 3.8 27.8 - - + +
119C GLU* 2.7 62.7 + - - +
120C CYS* 3.5 7.6 - - - +
121C GLU 3.4 0.2 - - - -
122C LEU* 1.3 85.2 - - - +
124C ALA* 1.3 57.1 + - - +
126C ARG* 3.0 47.6 + - - +
127C CYS* 3.2 25.8 + - - +
134C SER* 5.6 0.8 - - - +
135C VAL* 4.5 6.9 - - - +
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Residues in contact with ALA 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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95C CYS* 4.1 6.1 - - + +
97C PRO* 3.8 21.8 - - + -
120C CYS 3.3 9.3 + - - +
121C GLU* 3.1 13.4 + - - +
122C LEU 3.0 0.8 - - - -
123C ARG* 1.3 78.4 - - - +
125C ALA* 1.3 63.2 - - - +
127C CYS* 3.3 6.3 - - - +
128C ARG* 3.2 48.3 + - - +
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Residues in contact with ALA 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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116C TYR* 3.8 20.4 - - + +
121C GLU 2.8 13.2 + - - +
122C LEU 3.0 6.7 + - - +
124C ALA* 1.3 74.0 - - - +
126C ARG* 1.3 64.9 + - - +
128C ARG* 3.1 34.3 + - - +
130C HIS* 3.6 14.1 + - + +
133C LEU* 3.7 17.3 - - + -
6H PRO* 5.7 3.6 - - + -
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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* 2.9 18.1 + - + +
123C ARG* 3.0 53.6 + - - +
125C ALA* 1.3 75.2 - - - +
127C CYS* 1.3 64.3 + - - +
129C GLY 3.4 0.5 + - - -
130C HIS* 2.9 46.0 + - - +
131C PRO* 3.3 22.5 - - + +
133C LEU* 3.1 31.4 + - + +
134C SER* 4.3 9.5 - - - +
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Residues in contact with CYS 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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80C PRO 5.3 1.6 - - - -
81C GLY 4.3 7.2 - - - -
82C LYS* 3.8 28.2 + - - -
95C CYS* 2.0 52.6 - - + -
96C ALA 5.0 0.2 - - - -
97C PRO* 5.3 4.0 - - + -
123C ARG 3.2 12.2 + - - +
124C ALA* 3.3 9.2 - - - +
126C ARG* 1.3 78.0 - - - +
128C ARG* 1.3 55.1 + - - +
129C GLY 3.0 7.0 + - - -
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Residues in contact with ARG 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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82C LYS* 5.7 0.4 - - - +
95C CYS* 3.8 19.8 + - - +
121C GLU* 4.6 9.5 + - - -
124C ALA* 3.2 32.4 + - - +
125C ALA* 3.1 37.5 + - - +
126C ARG 3.0 2.0 + - - -
127C CYS* 1.3 71.9 - - - +
129C GLY* 1.3 62.9 + - - +
130C HIS* 3.1 16.6 + - - +
6H PRO* 5.7 6.9 - - - +
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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