Contacts of the helix formed by residues 126 - 146 (chain C) in PDB entry 5MYV
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 ALA 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LYS* 3.5 2.0 - - - +
125C SER* 1.3 82.6 + - - +
127C GLN* 1.3 67.8 + - - +
128C HIS* 4.6 4.0 - - + +
129C TYR* 3.0 38.1 + - + +
130C THR 3.1 9.2 + - - -
169C ASN 5.5 2.7 - - - -
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 4.5 11.6 - - - -
218A LYS* 4.4 16.5 - - - +
125C SER 3.5 2.9 + - - +
126C ALA* 1.3 72.4 - - - +
128C HIS* 1.3 57.5 + - - +
130C THR* 3.3 16.4 + - - +
131C GLU* 3.0 58.4 + - + +
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ALA* 3.3 3.3 - - + +
127C GLN* 1.3 77.4 - - - +
129C TYR* 1.3 75.6 + + + +
131C GLU* 3.7 6.9 + - + +
132C THR* 3.1 34.1 + - - -
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.3 52.4 - + + -
123C VAL* 4.0 12.6 - - + +
124C LYS* 3.7 41.7 - - + +
126C ALA* 3.0 32.4 + - + +
128C HIS* 1.3 88.1 - + + +
130C THR* 1.3 60.4 + - - +
132C THR* 3.3 8.0 + - - -
133C ALA* 2.9 29.3 + - - +
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C VAL* 5.2 0.6 - - - +
124C LYS 3.8 7.0 + - - -
125C SER 3.7 8.8 + - - -
126C ALA 3.1 8.1 + - - -
127C GLN* 3.9 19.7 - - - +
129C TYR* 1.3 76.5 - - - +
131C GLU* 1.3 58.1 + - + +
133C ALA* 3.2 7.8 + - - +
134C LEU* 2.9 41.8 + - + +
164C LYS* 6.3 0.2 - - - -
171C ILE* 3.7 35.2 + - + +
173C VAL* 4.0 18.6 + - + +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 3.8 12.1 - - - +
218A LYS* 5.2 5.2 - - - +
220A LYS* 3.2 30.2 + - - +
127C GLN* 3.0 46.5 + - + +
128C HIS* 4.1 6.7 - - - +
130C THR* 1.3 77.3 - - - +
132C THR* 1.3 62.0 + - - +
134C LEU* 3.4 17.1 + - - +
135C ASP* 3.2 29.1 + - - +
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 6.4 2.2 - - + -
128C HIS* 3.1 29.2 + - - -
129C TYR* 3.5 11.4 - - - +
130C THR 3.3 0.2 - - - -
131C GLU* 1.3 78.5 - - - +
133C ALA* 1.3 64.5 + - - +
135C ASP* 3.1 11.1 + - - +
136C GLU* 3.0 21.9 + - - +
543C GLY* 3.9 24.9 - - - +
544C ASN* 6.2 0.2 - - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C VAL* 3.9 22.0 - - + -
129C TYR 2.9 17.0 + - - +
130C THR 3.2 4.9 + - - +
132C THR* 1.3 76.8 - - - +
134C LEU* 1.3 62.4 + - - +
136C GLU* 3.2 10.0 + - - +
137C ILE* 3.1 27.5 + - - +
173C VAL* 3.9 25.8 - - + -
175C MET* 3.9 9.3 - - + +
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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 THR* 2.9 33.3 + - + +
131C GLU* 3.8 18.4 - - - +
132C THR 3.3 0.2 - - - -
133C ALA* 1.3 75.9 - - - +
135C ASP* 1.3 63.5 + - - +
137C ILE* 3.4 16.3 + - + +
138C LYS* 3.2 25.4 + - - +
164C LYS* 4.3 22.7 - - - +
173C VAL* 4.3 16.8 - - + -
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Residues in contact with ASP 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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220A LYS* 5.6 6.3 - - - -
131C GLU* 3.2 17.0 + - - +
132C THR* 3.1 13.9 + - + +
134C LEU* 1.3 75.0 - - - +
136C GLU* 1.3 63.7 + - - +
138C LYS* 3.2 20.9 + - - +
139C LEU* 3.0 27.7 + - + +
547C TRP* 4.7 2.3 - - + -
550C LYS* 5.5 3.1 + - - -
552C PHE* 3.7 38.3 - - + -
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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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121C LYS* 3.1 32.8 + - - +
123C VAL* 5.5 0.3 - - - +
132C THR* 3.0 14.0 + - - +
133C ALA* 3.2 13.1 + - - +
135C ASP* 1.3 74.1 - - - +
137C ILE* 1.3 59.2 + - - +
139C LEU* 3.2 11.8 + - - +
140C LEU* 2.9 49.9 + - + +
175C MET* 3.5 20.9 - - + +
177C PHE* 5.0 2.6 - - - -
541C ASP* 5.2 1.4 - - - -
542C LEU* 4.1 20.7 + - + +
543C GLY* 3.9 24.8 + - - +
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Residues in contact with ILE 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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133C ALA 3.1 14.8 + - - +
134C LEU* 3.5 18.2 - - + +
135C ASP 3.3 0.4 - - - -
136C GLU* 1.3 75.2 - - - +
138C LYS* 1.3 59.0 + - + +
140C LEU* 3.3 6.3 + - - +
141C LYS* 2.8 58.9 + - + +
159C LEU* 4.0 8.5 - - + -
162C ASP* 3.9 27.6 - - + +
173C VAL* 4.3 10.3 - - + -
175C MET* 3.3 38.6 - - + -
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Residues in contact with LYS 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 3.2 12.0 + - - +
135C ASP* 3.2 23.4 + - - +
137C ILE* 1.3 80.9 - - + +
139C LEU* 1.3 55.8 + - - +
141C LYS* 3.4 9.1 + - + +
142C CYS* 3.1 26.5 + - - +
547C TRP* 4.2 18.1 - - + -
550C LYS* 6.3 1.1 - - - +
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ASP* 3.0 22.3 + - + +
136C GLU* 3.2 10.7 + - - +
138C LYS* 1.3 76.2 - - - +
140C LEU* 1.3 57.7 + - - +
142C CYS* 3.1 6.0 + - - +
143C VAL* 3.0 30.1 + - - +
221C ILE* 3.9 21.5 - - + +
542C LEU* 3.7 27.6 - - + +
543C GLY 5.7 1.1 - - - -
545C ALA* 3.5 26.0 - - + +
546C CYS 4.2 12.6 - - - +
547C TRP* 3.7 39.5 - - + -
552C PHE* 4.6 6.3 - - + -
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Residues in contact with LEU 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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136C GLU* 2.9 39.0 + - + +
137C ILE* 3.9 3.4 - - - +
139C LEU* 1.3 76.7 - - - +
141C LYS* 1.3 58.5 + - - +
143C VAL* 3.4 8.4 + - + +
144C ARG* 3.1 25.6 + - - +
157C VAL* 3.8 24.4 - - + +
158C GLN* 6.0 0.2 - - - -
159C LEU* 4.0 27.5 + - + +
175C MET* 4.2 8.1 - - - -
177C PHE* 3.9 33.9 - - + -
542C LEU* 3.9 28.5 - - + -
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Residues in contact with LYS 141 (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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137C ILE* 2.8 40.1 + - + +
138C LYS* 3.7 9.6 - - + +
140C LEU* 1.3 75.7 - - - +
142C CYS* 1.3 63.0 + - - +
144C ARG* 3.3 34.1 + - - +
145C GLU* 3.1 41.5 + - - +
159C LEU* 4.6 3.1 - - + -
162C ASP* 3.7 21.9 + - - -
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Residues in contact with CYS 142 (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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138C LYS 3.1 14.0 + - - +
139C LEU* 3.1 10.0 + - - +
141C LYS* 1.3 77.5 - - - +
143C VAL* 1.3 56.6 + - - +
145C GLU* 4.9 1.8 - - - -
146C SER* 2.9 50.5 + - - +
219C CYS* 3.8 21.1 - - - -
221C ILE* 4.0 3.8 - - + -
547C TRP* 3.7 27.6 - - + +
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Residues in contact with VAL 143 (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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139C LEU 3.0 18.1 + - - +
140C LEU* 3.6 10.8 - - + +
141C LYS 3.3 0.4 - - - -
142C CYS* 1.3 76.2 - - - +
144C ARG* 1.3 56.9 + - - +
153C LYS* 4.5 1.9 - - - +
156C VAL* 3.8 18.6 - - + -
157C VAL 4.3 5.4 - - - +
158C GLN* 3.6 25.5 + - - +
214C TYR* 2.7 35.3 + - + -
215C LEU* 3.7 25.4 - - + -
219C CYS* 3.9 6.7 - - - -
221C ILE* 3.9 9.4 - - + -
542C LEU* 4.0 16.2 - - + -
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Residues in contact with ARG 144 (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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140C LEU 3.1 13.1 + - - +
141C LYS* 3.5 43.2 - - - +
142C CYS 3.3 0.2 - - - -
143C VAL* 1.3 79.5 - - - +
145C GLU* 1.3 74.6 + - + +
146C SER 3.8 0.2 - - - -
148C PRO* 4.8 6.6 - - - +
153C LYS* 3.9 20.4 + - - +
158C GLN* 3.7 20.9 - - - +
159C LEU* 3.0 45.4 + - - +
160C ILE 4.2 10.7 + - - -
161C ASP* 5.3 0.6 - - - +
162C ASP* 5.2 2.8 + - - -
214C TYR* 4.5 0.9 + - - -
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LYS* 3.1 30.2 + - - +
142C CYS* 4.4 2.4 - - - +
144C ARG* 1.3 105.9 + - + +
146C SER* 1.3 64.9 + - - +
147C ASP 3.4 3.0 + - - -
148C PRO* 3.7 15.7 - - - +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C CYS* 2.9 39.1 + - - -
145C GLU* 1.3 75.8 - - - +
147C ASP* 1.3 63.7 + - - +
148C PRO* 4.3 0.9 - - - +
214C TYR* 3.7 10.1 + - - -
218C LYS* 3.5 21.9 + - - +
219C CYS* 3.5 14.9 - - - -
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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
------------------------------------------------------------
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