Contacts of the helix formed by residues 117 - 135 (chain C) in PDB entry 4AY1
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C PRO 5.0 0.3 + - - -
115C VAL 3.3 1.8 + - - -
116C ASP* 1.3 80.7 - - - +
118C SER* 1.3 60.5 + - - +
119C THR* 3.5 10.7 + - - -
120C SER* 2.6 33.9 + - - -
121C ARG* 3.0 36.8 + - - +
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Residues in contact with SER 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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117C SER* 1.3 73.6 - - - +
119C THR* 1.3 70.6 + - - +
121C ARG* 3.7 24.5 - - - +
122C LEU* 2.9 25.3 + - - +
161C GLU* 5.5 2.4 - - - +
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER* 3.5 10.2 + - - -
118C SER* 1.3 84.1 + - - +
120C SER* 1.3 63.6 + - - +
122C LEU* 3.3 8.8 + - - +
123C GLU* 3.1 22.3 + - - +
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASN* 3.4 32.7 - - - +
113C PRO* 3.6 5.7 + - - -
114C MET* 2.8 27.3 + - - +
117C SER* 2.6 27.6 + - - -
119C THR* 1.3 78.9 + - - +
121C ARG* 1.3 63.9 + - - +
123C GLU* 3.4 5.9 + - - +
124C PHE* 3.1 23.2 + - - +
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C MET* 3.3 24.0 - - - +
115C VAL* 2.7 41.1 + - - +
116C ASP 4.3 1.2 - - - -
117C SER* 3.0 29.2 + - - +
118C SER* 3.7 23.9 - - - +
120C SER* 1.3 73.7 - - - +
122C LEU* 1.3 61.2 + - - +
124C PHE* 3.3 2.3 + - - +
125C ILE* 2.9 38.8 + - + +
154C HIS* 4.8 6.7 + - - -
157C VAL* 3.8 18.6 - - - +
158C LEU* 4.5 18.6 - - + +
161C GLU* 2.9 44.0 + - - +
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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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118C SER 2.9 18.0 + - - +
119C THR* 3.6 7.4 - - - +
121C ARG* 1.3 76.8 - - - +
123C GLU* 1.3 61.9 + - - +
125C ILE* 4.6 9.2 - - + +
126C ASN* 3.0 51.4 + - - +
161C GLU* 5.3 0.6 + - - -
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Residues in contact with GLU 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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68C ASN* 3.8 7.9 + - - +
69C ASN* 2.9 33.3 + - + -
70C LYS* 3.4 31.8 + - + -
119C THR 3.1 13.6 + - - +
120C SER* 3.6 10.0 - - - +
121C ARG 3.2 0.2 - - - -
122C LEU* 1.3 77.9 - - - +
124C PHE* 1.3 62.1 + - - +
126C ASN* 4.0 5.1 - - - +
127C SER* 3.0 24.9 + - - -
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Residues in contact with PHE 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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66C ILE* 3.8 16.6 - - + -
69C ASN 3.0 30.2 + - - +
71C VAL 4.2 10.1 - - - -
101C ILE* 3.6 23.1 - - + -
111C PHE* 5.9 1.6 - + - -
114C MET* 3.5 44.9 - - + -
120C SER 3.1 5.5 + - - -
121C ARG 3.5 6.1 - - - +
123C GLU* 1.3 77.4 - - - +
125C ILE* 1.3 62.4 + - + +
127C SER* 2.7 19.4 + - - -
128C ILE* 2.8 51.0 + - + +
140C LEU* 4.8 3.4 - - + -
142C VAL* 6.1 1.3 - - + -
158C LEU* 4.2 19.5 - - + -
162C LEU* 4.6 12.1 - - + -
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Residues in contact with ILE 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 ARG* 2.9 21.5 + - + +
122C LEU* 4.0 9.9 - - + +
124C PHE* 1.3 79.6 - - + +
126C ASN* 1.3 68.3 + - - +
128C ILE* 3.2 8.2 + - - +
129C ILE* 3.1 27.9 + - + +
158C LEU* 4.6 7.4 - - + +
161C GLU* 3.5 45.8 - - + +
162C LEU* 3.8 25.4 - - + +
165C ALA* 3.4 30.3 - - + -
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Residues in contact with ASN 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* 3.0 48.8 + - - +
123C GLU* 4.0 4.8 - - - +
125C ILE* 1.3 79.5 - - - +
127C SER* 1.3 61.5 + - - +
129C ILE* 3.4 9.1 + - - +
130C LEU* 3.4 29.0 + - + +
165C ALA* 6.0 0.5 - - - +
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Residues in contact with SER 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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70C LYS* 3.7 24.0 - - - -
71C VAL* 3.4 24.6 + - - +
123C GLU 3.0 17.7 + - - -
124C PHE 2.7 16.9 + - - -
126C ASN* 1.3 73.6 - - - +
128C ILE* 1.3 54.0 + - - +
130C LEU* 3.5 6.9 + - - +
131C PHE* 2.8 36.4 + - - +
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Residues in contact with ILE 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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71C VAL* 3.6 29.4 - - + -
101C ILE* 4.1 5.6 - - + -
124C PHE* 2.8 56.4 + - + +
125C ILE* 3.3 10.3 - - - +
127C SER* 1.3 73.7 + - - +
129C ILE* 1.3 59.0 + - - +
131C PHE* 3.2 0.9 + - - +
132C LEU* 2.9 46.6 + - + +
140C LEU* 4.1 17.7 - - + -
162C LEU* 4.3 2.5 - - + -
166C PHE* 3.7 32.5 - - + -
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Residues in contact with ILE 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 ILE* 3.1 17.0 + - + +
126C ASN* 3.9 9.0 - - - +
127C SER 3.4 0.2 - - - -
128C ILE* 1.3 76.5 - - - +
130C LEU* 1.3 70.5 + - + +
132C LEU* 3.5 1.4 + - - +
133C ARG* 3.1 34.5 + - + +
165C ALA* 3.8 41.3 - - + +
166C PHE* 3.7 21.1 - - + -
169C ASP* 3.6 30.7 - - + +
178C LEU* 4.2 11.8 - - + +
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Residues in contact with LEU 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 ASN* 3.4 19.3 + - + +
127C SER* 3.9 5.4 - - - +
128C ILE 3.3 0.2 - - - -
129C ILE* 1.3 83.3 - - + +
131C PHE* 1.3 61.6 + - - +
133C ARG* 3.9 5.8 - - + +
134C ASN* 2.8 50.6 + - - +
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Residues in contact with PHE 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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71C VAL* 3.4 33.2 - - + -
72C ILE* 4.7 5.4 - - - -
73C ILE* 3.8 21.3 - - + -
82C TYR* 3.7 22.2 - - - -
99C LEU* 3.6 32.8 - - + -
127C SER 2.8 20.0 + - - +
128C ILE 3.6 2.0 - - - +
130C LEU* 1.3 76.1 - - - +
132C LEU* 1.3 68.8 + - + +
134C ASN* 4.4 3.1 - - - +
135C HIS* 3.0 56.3 + + - +
137C PHE* 4.1 8.1 - + - -
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Residues in contact with LEU 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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99C LEU* 3.9 27.1 - - + -
128C ILE* 2.9 40.1 + - + +
129C ILE 3.9 3.1 - - - +
131C PHE* 1.3 80.8 - - + +
133C ARG* 1.3 63.3 + - - +
135C HIS 3.4 0.2 + - - -
136C ASN 3.2 3.3 + - - -
137C PHE* 3.0 53.4 + - + +
139C GLY* 3.8 33.0 - - - +
140C LEU* 4.0 10.1 - - + +
166C PHE* 4.1 8.3 - - + -
178C LEU* 4.1 18.8 - - + -
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Residues in contact with ARG 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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129C ILE* 3.1 25.4 + - + +
130C LEU* 3.9 7.4 - - + +
132C LEU* 1.3 74.0 - - - +
134C ASN* 1.3 65.7 + - - +
135C HIS 3.1 1.9 + - - -
136C ASN* 3.3 10.8 + - - +
137C PHE 5.0 3.8 + - - -
138C ASP* 6.0 0.4 - - - +
169C ASP* 2.7 32.2 + - - +
170C PHE* 5.2 0.6 - - - +
173C SER* 4.3 5.7 + - - -
175C LYS* 4.0 45.4 - - - +
176C GLU* 2.9 30.9 + - - +
177C ARG* 4.6 0.8 - - - +
178C LEU* 3.6 31.8 - - - +
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Residues in contact with ASN 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 LEU* 2.8 44.4 + - - +
131C PHE* 3.8 1.6 - - - +
133C ARG* 1.3 75.3 - - - +
135C HIS* 1.3 79.5 + - + +
136C ASN 3.6 0.2 - - - -
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Residues in contact with HIS 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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82C TYR* 3.3 53.9 + + + +
85C ILE* 4.0 12.8 - - - +
86C ASN* 4.9 0.6 - - - +
131C PHE* 3.0 54.2 + + - +
133C ARG 3.1 0.6 - - - -
134C ASN* 1.3 92.6 - - + +
136C ASN* 1.3 72.4 + - - +
137C PHE* 3.3 23.5 + - + -
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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