Contacts of the helix formed by residues 115 - 131 (chain C) in PDB entry 2VM8
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 SER 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C PRO* 4.7 1.6 - - - -
114C THR* 1.3 78.6 + - - +
116C LEU* 1.3 62.6 + - - +
117C LEU* 3.5 5.0 + - - +
118C ALA* 3.0 28.0 + - - +
119C ALA* 3.1 23.3 + - - +
151C GLU* 3.0 20.0 - - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 4.6 2.1 - - - +
110C PRO* 3.7 25.4 - - + -
114C THR 5.6 0.9 - - - +
115C SER* 1.3 71.6 - - - +
117C LEU* 1.3 54.1 + - - +
119C ALA* 3.7 1.2 - - - +
120C PHE* 2.8 36.5 + - - +
139C VAL* 4.0 5.9 - - + +
140C ASP 4.4 0.2 - - - +
141C ILE* 3.7 27.4 - - + -
142C SER 5.8 0.2 - - - +
148C ILE* 3.8 28.0 - - + -
151C GLU* 2.8 37.8 + - + +
152C MET* 3.9 17.3 - - + +
155C LEU* 3.7 20.8 - - + +
164C PHE* 4.7 0.2 - - + -
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Residues in contact with LEU 117 (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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115C SER* 3.2 5.3 - - - +
116C LEU* 1.3 76.5 - - - +
118C ALA* 1.3 61.4 + - - +
120C PHE* 3.6 5.8 - - - +
121C ASP* 2.9 37.2 + - - +
151C GLU* 3.7 48.0 - - + +
154C ALA* 4.7 11.2 - - + -
155C LEU* 4.2 17.0 - - + -
159C HIS* 4.0 22.7 - - + +
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Residues in contact with ALA 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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114C THR* 5.7 2.7 - - - -
115C SER* 3.0 26.4 + - - +
117C LEU* 1.3 76.5 - - - +
119C ALA* 1.3 58.5 + - - +
121C ASP* 2.9 28.9 + - - +
122C GLN* 3.1 8.2 + - - +
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 3.5 21.1 - - + -
110C PRO* 3.9 23.6 - - + -
114C THR* 5.2 2.6 - - - +
115C SER 3.1 13.6 + - - +
116C LEU 3.7 1.8 - - - +
118C ALA* 1.3 75.6 - - - +
120C PHE* 1.3 67.4 + - - +
122C GLN* 2.8 20.0 + - - +
123C TRP* 3.0 20.7 + - + -
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Residues in contact with PHE 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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108C VAL* 3.7 17.4 - - + +
116C LEU 2.8 23.6 + - - +
117C LEU* 3.6 4.3 - - - +
119C ALA* 1.3 72.8 - - - +
121C ASP* 1.3 69.6 + - - +
123C TRP* 3.5 1.7 + - - +
124C ARG* 2.9 62.0 + - + +
137C LEU* 4.1 14.8 - - + -
139C VAL* 4.0 19.7 - - + -
155C LEU* 4.0 14.8 - - + -
159C HIS* 3.5 34.5 - + + -
161C VAL* 3.7 15.3 - - + -
468C TYR* 3.6 20.2 - + - -
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Residues in contact with ASP 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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117C LEU* 2.9 17.3 + - - +
118C ALA* 2.9 15.8 + - - +
120C PHE* 1.3 91.3 - - - +
122C GLN* 1.3 55.6 + - - +
124C ARG* 3.6 6.5 - - - +
125C GLU* 3.1 28.3 + - - +
159C HIS* 5.2 8.8 + - - -
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Residues in contact with GLN 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 ALA 3.1 8.6 + - - +
119C ALA* 2.8 15.2 + - - +
121C ASP* 1.3 74.5 - - - +
123C TRP* 1.3 56.1 + - + +
125C GLU* 3.0 22.4 + - - +
126C TRP* 2.8 75.6 + - + +
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Residues in contact with TRP 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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76C PHE 4.6 2.9 + - - -
78C MET* 5.0 6.1 - - + -
79C PRO* 3.8 33.7 - - + -
89C PHE* 3.7 21.1 - + - -
106C ASP* 3.4 10.3 + - - -
107C HIS 3.1 26.1 + - - -
108C VAL* 3.9 16.4 - - + -
109C VAL* 3.5 37.2 - - + -
119C ALA* 3.0 24.0 + - + +
120C PHE 3.8 6.7 - - - +
122C GLN* 1.3 77.9 - - + +
124C ARG* 1.3 65.6 + - - +
126C TRP* 3.1 33.0 + + - +
127C ALA* 2.8 26.9 + - - +
137C LEU* 3.4 36.6 - - + -
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Residues in contact with ARG 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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120C PHE* 2.9 57.0 + - + +
121C ASP* 3.6 8.5 - - - +
123C TRP* 1.3 73.6 - - - +
125C GLU* 1.3 58.3 + - - +
128C ASP* 2.8 65.7 + - - +
135C TYR* 3.3 15.6 + - - -
137C LEU* 4.2 3.8 - - + +
159C HIS* 5.6 0.6 + - - +
468C TYR* 3.7 41.1 - - - +
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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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121C ASP 3.1 11.7 + - - +
122C GLN* 3.0 26.3 + - - +
124C ARG* 1.3 81.7 - - - +
126C TRP* 1.3 60.7 + - + +
128C ASP* 4.3 3.1 - - - +
129C SER* 3.1 25.6 + - - -
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Residues in contact with TRP 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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77C GLN* 3.4 37.3 - - - +
79C PRO* 4.3 17.3 - - + -
89C PHE* 3.8 12.3 - + + -
122C GLN* 2.8 45.1 + - + +
123C TRP* 3.5 61.2 - + - +
125C GLU* 1.3 76.4 - - + +
127C ALA* 1.3 60.4 + - - +
129C SER* 2.8 20.4 + - - -
130C LYS* 3.4 21.6 + - + +
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Residues in contact with ALA 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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89C PHE* 3.7 33.9 - - + -
123C TRP 2.8 16.4 + - - +
126C TRP* 1.3 71.7 - - - +
128C ASP* 1.3 61.6 + - - +
129C SER 3.2 0.4 - - - -
131C SER* 2.8 35.4 + - - -
135C TYR* 3.2 37.4 - - + -
137C LEU* 5.7 0.2 - - + -
466C GLY 4.9 0.5 - - - +
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG* 2.8 52.5 + - - +
125C GLU* 4.3 3.8 - - - +
127C ALA* 1.3 76.6 - - - +
129C SER* 1.3 57.1 + - - +
130C LYS 3.6 0.2 - - - -
135C TYR* 2.3 37.4 + - - -
464C GLY* 3.4 21.9 - - - +
466C GLY 4.7 5.2 - - - +
467C ARG* 5.5 0.2 - - - -
468C TYR* 4.2 4.5 + - - +
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Residues in contact with SER 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 13.8 + - - -
126C TRP* 2.8 23.0 + - - -
128C ASP* 1.3 79.7 - - - +
130C LYS* 1.3 64.8 + - - +
463C GLU* 3.6 16.5 - - - +
464C GLY* 3.6 11.5 - - - -
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Residues in contact with LYS 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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77C GLN* 3.0 36.3 + - - +
88C ASP* 3.1 27.4 + - - +
89C PHE* 3.7 4.0 - - + +
90C PHE* 3.3 35.2 - - + +
126C TRP* 3.4 16.5 + - + +
129C SER* 1.3 90.2 + - - +
131C SER* 1.3 63.6 + - - +
132C CYS 3.4 0.7 + - - -
463C GLU* 3.6 19.2 - - - +
464C GLY 3.3 10.1 + - - -
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 3.8 5.6 - - - +
93C THR* 3.6 21.2 - - - +
127C ALA* 2.8 31.5 + - - -
130C LYS* 1.3 72.2 - - - +
132C CYS* 1.3 58.1 + - - +
133C CYS* 2.5 29.9 + - - -
135C TYR* 4.1 13.6 - - - +
464C GLY* 2.9 18.0 + - - +
465C SER 3.0 11.8 + - - -
466C GLY* 3.0 9.2 + - - -
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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
------------------------------------------------------------
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