Contacts of the helix formed by residues 119 - 140 (chain C) in PDB entry 2VWI
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 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C VAL 4.0 3.2 + - - +
118C LEU* 1.3 76.7 - - - +
120C GLU* 1.3 60.5 + - - +
121C SER* 3.2 11.0 + - - +
122C THR* 3.1 20.0 + - - +
123C ILE* 2.8 27.0 + - - +
259C LYS* 3.3 23.4 + - - +
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Residues in contact with GLU 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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118C LEU 3.8 0.4 + - - -
119C ASP* 1.3 73.9 - - - +
121C SER* 1.3 56.2 + - - +
123C ILE* 3.8 9.4 - - + +
124C ALA* 2.9 29.2 + - - +
259C LYS* 4.6 8.8 - - - +
260C TYR* 2.8 49.5 - - + +
262C LYS* 4.6 10.7 - - - +
264C PHE* 3.7 13.3 - - + +
290C PHE* 3.7 22.0 - - + -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASP* 4.2 9.9 + - - +
120C GLU* 1.3 75.8 - - - +
122C THR* 1.3 58.8 + - - +
124C ALA* 3.9 6.1 - - - +
125C THR* 2.7 37.6 + - - -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.0 14.6 - - + -
119C ASP* 3.1 31.5 + - - +
121C SER* 1.3 79.1 + - - +
123C ILE* 1.3 63.3 + - - +
125C THR* 3.5 5.4 + - - -
126C ILE* 3.2 48.6 + - + +
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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
----------------------------------------------------------
118C LEU* 3.4 33.2 - - + +
119C ASP 2.8 15.6 + - - +
120C GLU* 3.8 6.3 - - - +
122C THR* 1.3 74.5 - - - +
124C ALA* 1.3 59.3 + - - +
126C ILE* 3.5 0.7 + - - +
127C LEU* 3.0 53.9 + - + +
217C ALA 4.8 0.7 - - - +
220C LEU* 3.9 20.4 - - + -
221C ALA* 3.9 23.6 - - + +
260C TYR* 3.8 18.8 - - + -
264C PHE* 3.7 23.8 - - + -
290C PHE* 3.8 3.8 - - + -
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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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120C GLU 2.9 18.8 + - - +
121C SER* 3.9 8.1 - - - +
123C ILE* 1.3 75.9 - - - +
125C THR* 1.3 63.0 + - - +
128C ARG* 3.1 27.7 + - - +
290C PHE* 3.7 38.7 - - + +
291C PHE* 3.7 12.4 - - - +
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C SER 2.7 23.1 + - - -
122C THR* 3.7 7.4 - - - -
123C ILE 3.3 0.4 - - - -
124C ALA* 1.3 78.7 - - - +
126C ILE* 1.3 65.9 + - + +
128C ARG* 3.8 14.9 + - - +
129C GLU* 3.4 30.9 + - + +
160C VAL* 5.7 3.6 - - + -
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Residues in contact with ILE 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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100C VAL* 4.0 20.2 - - + -
103C ILE* 5.9 3.4 - - + -
118C LEU* 3.8 26.5 - - + -
122C THR* 3.2 28.5 + - + +
123C ILE 4.1 2.5 - - - +
125C THR* 1.3 78.5 - - + +
127C LEU* 1.3 59.1 + - - +
129C GLU* 3.3 5.5 + - - +
130C VAL* 3.0 28.8 + - + +
152C ILE* 3.9 29.4 - - + -
154C LEU* 5.0 6.5 - - + -
160C VAL* 3.7 18.5 - - + +
220C LEU* 4.4 13.0 - - + -
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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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123C ILE* 3.0 40.9 + - + +
126C ILE* 1.3 76.3 - - - +
128C ARG* 1.3 59.0 + - - +
130C VAL* 4.2 7.9 - - + -
131C LEU* 2.8 30.5 + - - +
152C ILE* 5.0 1.3 - - + -
213C PHE* 3.3 38.3 - - + -
216C THR* 4.4 16.8 - - + -
217C ALA* 3.8 26.0 - - + +
220C LEU* 4.0 17.7 - - + -
264C PHE* 4.8 0.7 - - + -
267C MET* 5.2 1.6 - - - -
290C PHE* 4.5 9.6 - - + -
291C PHE* 3.6 11.0 - - + -
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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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124C ALA 3.1 20.4 + - - +
125C THR* 3.8 15.1 + - - +
126C ILE 3.3 0.2 - - - -
127C LEU* 1.3 76.2 - - - +
129C GLU* 1.3 82.6 + - - +
131C LEU* 3.3 4.9 + - - +
132C GLU* 2.9 45.4 + - - +
286C LEU* 3.9 15.7 - - + +
291C PHE* 3.7 32.8 + - + -
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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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74C ASN* 3.1 42.3 + - - +
125C THR* 3.4 17.3 - - + +
126C ILE 3.3 3.0 + - - +
128C ARG* 1.3 110.8 + - - +
130C VAL* 1.3 65.5 + - - +
132C GLU* 3.4 9.2 + - - +
133C GLY 3.1 17.3 + - - -
160C VAL* 3.5 35.7 + - + +
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Residues in contact with VAL 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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126C ILE 3.0 20.3 + - - +
127C LEU* 3.6 9.2 - - + +
128C ARG 3.3 0.2 - - - -
129C GLU* 1.3 75.5 - - - +
131C LEU* 1.3 57.4 + - - +
133C GLY 3.1 2.1 + - - -
134C LEU* 2.9 29.6 + - + +
147C VAL* 4.5 12.1 - - + -
152C ILE* 3.8 43.7 - - + -
160C VAL* 4.0 4.0 - - + -
162C ILE* 3.4 30.0 - - + +
213C PHE* 3.7 23.3 - - + -
216C THR* 6.3 0.2 - - + -
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Residues in contact with LEU 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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127C LEU 2.8 20.6 + - - +
128C ARG 3.7 4.9 - - - +
129C GLU 3.3 0.2 - - - -
130C VAL* 1.3 73.7 - - - +
132C GLU* 1.3 57.3 + - - +
134C LEU* 3.4 10.9 + - + +
135C GLU* 2.8 28.4 + - - +
210C ILE* 5.0 2.9 - - + -
213C PHE* 3.9 18.4 - - + -
282C ALA* 3.8 22.9 - - + +
285C LEU* 3.6 36.3 - - + +
286C LEU* 3.6 39.0 - - + +
291C PHE* 3.9 16.4 - - + -
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Residues in contact with GLU 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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72C HIS* 3.6 18.2 + - - +
74C ASN* 3.6 20.4 - - - +
128C ARG* 2.9 35.2 + - - +
129C GLU* 4.4 11.1 - - - +
130C VAL 3.3 0.2 - - - -
131C LEU* 1.3 73.8 - - - +
133C GLY* 1.3 62.8 + - - +
135C GLU* 3.5 12.7 + - - +
136C TYR* 3.2 17.7 + - - +
286C LEU* 3.7 25.8 - - + +
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Residues in contact with GLY 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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72C HIS* 4.1 5.4 - - - -
74C ASN* 3.7 21.3 - - - +
75C ILE* 3.6 18.4 - - - +
129C GLU 3.1 10.1 + - - -
130C VAL 3.1 4.9 + - - -
132C GLU* 1.3 76.6 - - - +
134C LEU* 1.3 60.3 + - - +
136C TYR* 3.5 5.0 + - - +
137C LEU* 3.3 24.9 + - - +
162C ILE* 4.2 1.3 - - - -
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Residues in contact with LEU 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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130C VAL* 2.9 17.7 + - + +
131C LEU* 3.7 15.3 - - + +
133C GLY* 1.3 75.4 - - - +
135C GLU* 1.3 59.2 + - - +
137C LEU* 3.2 5.9 + - + +
138C HIS* 2.9 49.3 + - + +
144C HIS* 3.8 30.3 - - + -
147C VAL* 3.8 21.1 - - + -
162C ILE* 4.0 9.9 - - + -
209C ASP* 3.8 24.7 - - + +
210C ILE* 5.5 1.6 - - + -
213C PHE* 4.1 25.8 - - + -
282C ALA* 4.6 2.9 - - + -
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Residues in contact with GLU 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 LEU 2.8 18.3 + - - +
132C GLU* 3.5 13.1 - - - +
133C GLY 3.3 0.2 - - - -
134C LEU* 1.3 76.6 - - - +
136C TYR* 1.3 61.8 + - - +
138C HIS* 3.5 3.1 + - - +
139C LYS* 3.0 57.5 + - + +
282C ALA* 3.8 14.3 - - + +
283C ALA* 3.4 32.3 - - + +
286C LEU* 3.4 25.8 - - + +
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C GLN 3.5 6.4 + - - -
70C CYS* 3.4 18.5 - - + -
71C HIS* 3.0 46.6 + - - +
72C HIS* 3.5 38.8 - + + +
75C ILE* 4.6 1.8 - - + -
132C GLU 3.2 7.2 + - - +
133C GLY 3.6 8.3 - - - +
134C LEU 3.3 0.2 - - - -
135C GLU* 1.3 79.5 - - - +
137C LEU* 1.3 72.7 + - + +
139C LYS* 3.3 14.4 + - + +
140C ASN* 3.1 46.1 + - - +
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Residues in contact with LEU 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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70C CYS* 3.9 20.4 - - + -
75C ILE* 3.9 24.0 - - + -
133C GLY 3.3 10.9 + - - +
134C LEU* 3.2 13.9 + - + +
136C TYR* 1.3 85.7 - - + +
138C HIS* 1.3 64.7 + - + +
140C ASN* 3.1 10.6 + - - -
141C GLY 3.3 0.2 + - - -
142C GLN* 2.8 37.7 + - + +
143C ILE 5.0 0.2 - - - +
144C HIS* 3.9 25.6 - - + +
165C PHE* 3.7 47.6 - - + -
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Residues in contact with HIS 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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134C LEU* 2.9 35.6 + - + +
135C GLU* 4.0 4.0 - - - +
137C LEU* 1.3 79.4 - - + +
139C LYS* 1.3 62.1 + - + +
141C GLY* 3.1 13.4 + - - -
142C GLN 3.2 21.1 - - - -
206C PHE* 3.6 47.1 - + + +
209C ASP* 2.9 34.0 + - + +
210C ILE* 4.3 11.9 - - + -
282C ALA* 3.9 14.8 + - + +
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Residues in contact with LYS 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 GLU* 3.0 49.3 + - + +
136C TYR* 3.3 11.4 + - + +
138C HIS* 1.3 75.3 - - - +
140C ASN* 1.3 64.1 + - - +
141C GLY 3.2 2.9 + - - -
283C ALA* 5.9 3.1 - - - -
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Residues in contact with ASN 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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1293A AU 4.3 1.6 - - - -
69C GLN 5.3 0.2 - - - +
70C CYS* 4.0 18.4 - - - -
136C TYR* 3.1 48.0 + - - +
137C LEU 3.1 9.3 + - - +
139C LYS* 1.3 80.4 + - - +
141C GLY* 1.3 60.2 + - - +
142C GLN* 3.3 13.7 + - + +
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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