Contacts of the helix formed by residues 123 - 140 (chain C) in PDB entry 2VGB
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C GLY* 1.3 72.7 - - - -
124C HIS* 1.3 66.4 + - - +
125C GLU* 2.9 22.1 + - - +
126C TYR* 3.1 27.7 + - - +
127C HIS* 3.0 20.4 + - - -
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Residues in contact with HIS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 4.0 13.7 - + - -
123C SER* 1.3 72.4 - - - +
125C GLU* 1.3 77.9 + - - +
127C HIS* 3.1 4.1 + - - -
128C ALA* 2.9 20.8 + - - +
267C GLN* 3.7 13.2 + - - -
270C ARG* 3.9 15.8 + - - +
271C ASP* 2.9 34.3 + - - -
274C PHE* 3.3 48.2 - + + +
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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
----------------------------------------------------------
123C SER* 2.9 23.1 + - - +
124C HIS* 1.3 84.6 + - - +
126C TYR* 1.3 62.0 + - - +
128C ALA* 3.2 9.2 + - - +
129C GLU* 3.1 32.2 + - - +
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Residues in contact with TYR 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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94C ILE* 4.7 4.2 + - + -
95C GLY* 4.0 17.0 - - - -
96C PRO* 4.1 6.8 - - - +
99C ARG* 2.9 74.2 + - - +
121C HIS 4.9 1.8 - - - -
122C GLY* 4.1 12.8 - - - -
123C SER* 3.1 26.1 + - - +
125C GLU* 1.3 78.6 - - - +
127C HIS* 1.3 84.3 + + - +
129C GLU* 3.4 5.6 + - - -
130C SER* 3.4 14.5 + - - -
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Residues in contact with HIS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.0 14.7 - - + +
118C ASN 3.5 24.0 + - - -
119C PHE* 3.4 50.4 - + + -
121C HIS 2.8 28.7 + - - -
122C GLY 3.6 7.5 + - - -
123C SER 3.0 22.8 + - - -
124C HIS 3.1 4.5 + - - +
126C TYR* 1.3 89.1 - + - +
128C ALA* 1.3 60.3 + - - +
129C GLU 3.3 0.2 - - - -
130C SER* 3.2 8.5 + - - -
131C ILE* 2.9 32.6 + - - +
274C PHE* 4.2 5.8 - - + -
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Residues in contact with ALA 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 HIS 2.9 13.4 + - - +
125C GLU* 3.5 12.1 - - - +
127C HIS* 1.3 79.1 - - - +
129C GLU* 1.3 56.4 + - + +
131C ILE* 3.3 7.1 + - - +
132C ALA* 2.9 30.8 + - - +
274C PHE* 3.8 14.7 - - + -
278C HIS* 4.2 16.6 + - + +
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Residues in contact with GLU 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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99C ARG* 2.8 38.8 + - - +
125C GLU* 3.1 23.2 + - - +
126C TYR* 3.6 5.6 - - - +
127C HIS 3.3 0.2 - - - -
128C ALA* 1.3 76.9 - - + +
130C SER* 1.3 57.2 + - - +
132C ALA* 3.5 6.3 + - - +
133C ASN* 2.9 40.3 + - - +
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 3.8 16.8 - - - +
99C ARG* 3.2 28.1 + - - +
104C LEU* 5.5 0.2 - - - +
117C LEU* 4.0 20.8 - - - +
126C TYR* 3.4 13.5 + - - -
127C HIS* 3.2 13.5 + - - -
128C ALA 3.2 0.4 - - - -
129C GLU* 1.3 74.7 - - - +
131C ILE* 1.3 66.4 + - - +
133C ASN* 3.1 5.6 + - - +
134C VAL* 2.9 29.9 + - - +
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Residues in contact with ILE 131 (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* 3.8 24.9 - - + -
127C HIS 2.9 22.2 + - - +
128C ALA* 3.7 4.9 - - - +
130C SER* 1.3 76.9 - - - +
132C ALA* 1.3 64.0 + - - +
134C VAL* 3.1 3.4 + - - +
135C ARG* 2.9 66.3 + - - +
153C ILE* 4.1 17.9 - - + -
274C PHE* 3.9 14.4 - - + -
278C HIS* 3.8 28.7 - - + +
280C VAL* 4.4 10.8 - - + -
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Residues in contact with ALA 132 (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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128C ALA 2.9 17.4 + - - +
129C GLU* 3.6 9.0 - - - +
131C ILE* 1.3 78.1 - - - +
133C ASN* 1.3 62.8 + - - +
135C ARG* 3.7 6.3 + - - +
136C GLU* 3.1 28.1 + - - +
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Residues in contact with ASN 133 (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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99C ARG* 2.9 33.1 + - - +
100C SER* 4.5 1.2 - - - -
101C VAL* 3.8 26.7 + - + +
104C LEU* 4.1 4.9 - - + +
129C GLU* 2.9 24.5 + - - +
130C SER* 3.1 4.9 + - - +
132C ALA* 1.3 82.1 + - - +
134C VAL* 1.3 68.7 + - - +
136C GLU* 3.7 6.2 + - - +
137C ALA* 2.9 22.0 + - - +
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Residues in contact with VAL 134 (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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94C ILE* 4.5 12.1 - - + -
104C LEU* 4.3 20.3 - - + +
112C MET* 5.4 3.6 - - + -
115C ALA* 4.1 19.7 - - + -
117C LEU* 5.4 2.2 - - + -
130C SER* 2.9 21.7 + - - +
131C ILE* 3.4 7.6 - - - +
133C ASN* 1.3 74.1 - - - +
135C ARG* 1.3 55.0 + - + +
137C ALA* 2.8 6.2 + - - +
138C VAL* 2.7 52.3 + - + +
151C VAL* 4.1 14.4 - - + +
153C ILE* 3.9 26.2 - - + -
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Residues in contact with ARG 135 (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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131C ILE* 2.9 44.1 + - - +
132C ALA* 4.0 6.3 - - - +
134C VAL* 1.3 72.6 - - + +
136C GLU* 1.3 57.5 + - - +
138C VAL* 3.4 7.3 + - + +
139C GLU* 2.9 43.5 + - + +
153C ILE* 4.2 16.5 - - + +
278C HIS* 2.4 36.3 + - - +
279C GLY* 3.4 18.0 + - - -
280C VAL* 4.3 0.6 - - - +
281C ASP* 5.2 1.2 + - - -
504C ARG* 5.7 5.5 - - - +
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Residues in contact with GLU 136 (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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101C VAL* 3.8 29.8 - - + +
105C LYS* 6.0 0.4 - - - -
132C ALA 3.1 18.5 + - - +
133C ASN* 3.7 9.1 + - - +
134C VAL 3.1 0.2 - - - -
135C ARG* 1.3 74.3 - - - +
137C ALA* 1.3 66.4 + - - +
139C GLU* 3.2 4.2 + - - +
140C SER* 3.1 23.6 + - - -
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Residues in contact with ALA 137 (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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101C VAL* 3.9 14.3 - - + +
104C LEU* 3.4 29.2 - - + -
105C LYS* 3.9 15.9 - - + +
108C ILE* 4.0 8.1 - - + -
133C ASN 2.9 13.9 + - - +
134C VAL* 2.8 10.3 + - - +
136C GLU* 1.3 71.9 - - - +
138C VAL* 1.3 62.9 + - - +
140C SER* 2.7 23.1 + - - -
141C PHE* 3.3 9.5 - - - -
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Residues in contact with VAL 138 (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 ILE* 3.7 15.9 - - + -
134C VAL* 2.7 36.6 + - + +
135C ARG* 3.8 4.9 - - + +
137C ALA* 1.3 75.4 - - - +
139C GLU* 1.3 72.8 + - - +
140C SER 3.1 4.7 + - - -
141C PHE* 3.3 15.5 + - + +
148C TYR* 3.6 21.3 - - + +
149C ARG 3.7 21.0 - - - +
151C VAL* 3.6 32.5 - - + +
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Residues in contact with GLU 139 (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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135C ARG* 2.9 28.6 + - + +
136C GLU* 3.2 4.7 + - - +
138C VAL* 1.3 80.2 - - - +
140C SER* 1.3 58.9 + - - +
141C PHE 3.0 6.1 - - - -
142C ALA* 3.1 28.7 + - + +
143C GLY 4.8 0.2 + - - -
148C TYR* 3.0 31.4 + - - -
518C ARG* 4.8 5.7 + - - -
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Residues in contact with SER 140 (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 LYS* 3.4 31.3 - - - +
136C GLU* 3.1 10.8 + - - -
137C ALA 2.7 19.5 + - - -
138C VAL 3.0 1.4 - - - -
139C GLU* 1.3 78.3 - - - +
141C PHE* 1.3 69.7 + - - +
142C ALA 3.4 0.8 + - - -
143C GLY* 4.5 4.6 + - - -
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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