Contacts of the helix formed by residues 118 - 140 (chain C) in PDB entry 2DSA
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 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ALA 3.6 3.4 + - - -
117C SER* 1.3 76.7 - - - +
119C ASP* 1.3 64.8 + - - +
120C GLU* 3.1 12.8 - - - +
121C TRP* 3.1 32.0 + - - +
122C LYS* 3.2 11.7 + - - +
118D SER* 4.3 12.8 + - - -
120D GLU* 3.5 25.6 + - - +
121D TRP* 4.7 6.9 + - - +
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Residues in contact with ASP 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 3.8 2.1 + - - +
118C SER* 1.3 73.0 - - - +
120C GLU* 1.3 62.8 + - - +
121C TRP 3.5 0.2 - - - -
122C LYS* 3.9 19.1 + - - +
123C ASN* 2.6 47.3 + - - +
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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
----------------------------------------------------------
118C SER* 3.1 13.6 - - - +
119C ASP* 1.3 82.5 - - - +
121C TRP* 1.3 64.8 + - - +
123C ASN* 3.3 7.0 + - - +
124C ALA* 3.1 24.4 + - - +
118D SER* 4.9 16.8 - - - +
121D TRP* 4.5 7.5 - - + -
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Residues in contact with TRP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C PRO* 3.3 38.2 - - + +
114C ASN* 4.9 6.7 - - - -
117C SER* 3.6 27.6 - - - -
118C SER* 3.1 21.2 + - - +
120C GLU* 1.3 78.0 - - - +
122C LYS* 1.3 57.8 + - - +
124C ALA* 3.3 2.1 + - - +
125C VAL* 3.1 31.6 + - + +
121D TRP* 3.4 62.8 - + + +
124D ALA* 4.1 24.2 - - + -
125D VAL* 4.1 19.3 - - + -
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Residues in contact with LYS 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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111C PRO* 3.9 19.1 - - + +
112C LEU* 3.7 34.1 + - + +
114C ASN 2.7 30.0 + - - -
115C PRO* 4.3 6.1 + - - +
117C SER* 3.6 24.4 + - - +
118C SER 3.2 9.9 + - - +
119C ASP* 4.0 18.5 + - - +
121C TRP* 1.3 76.8 - - - +
123C ASN* 1.3 57.6 + - - +
125C VAL* 3.6 3.2 + - - +
126C ARG* 2.9 40.0 + - - +
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Residues in contact with ASN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASP* 2.6 37.3 + - - +
120C GLU* 3.3 8.1 + - - +
122C LYS* 1.3 73.7 - - - +
124C ALA* 1.3 65.2 + - - +
126C ARG* 3.5 14.0 + - - +
127C GLN* 3.2 25.6 + - - +
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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
----------------------------------------------------------
120C GLU 3.1 17.5 + - - +
121C TRP 3.6 4.0 - - - +
123C ASN* 1.3 76.1 - - - +
125C VAL* 1.3 58.5 + - - +
127C GLN* 3.1 10.6 + - - +
128C SER* 3.0 30.4 + - - -
121D TRP* 3.9 23.1 - - + -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LYS 5.1 0.2 - - - +
108C SER* 2.8 45.0 - - - +
111C PRO* 3.9 20.4 - - + -
112C LEU* 3.7 24.9 - - + -
121C TRP* 3.1 22.4 + - + +
122C LYS* 3.8 5.2 - - - +
124C ALA* 1.3 77.0 - - + +
126C ARG* 1.3 59.3 + - - +
128C SER* 3.4 7.7 + - - +
129C LEU* 3.0 30.7 + - + +
121D TRP* 5.7 2.2 - - + -
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Residues in contact with ARG 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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112C LEU* 3.6 32.1 - - + +
122C LYS* 2.9 26.4 + - - +
123C ASN* 3.7 14.4 - - - +
124C ALA 3.3 0.2 - - - -
125C VAL* 1.3 76.3 - - - +
127C GLN* 1.3 58.7 + - - +
129C LEU* 3.7 8.0 + - - +
130C ASN* 3.1 24.9 + - - +
168C VAL* 2.6 34.9 + - - +
169C ASN* 3.9 17.4 + - - +
170C ILE* 3.7 20.2 - - + +
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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
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123C ASN 3.2 13.8 + - - +
124C ALA* 3.1 13.4 + - - +
126C ARG* 1.3 77.0 - - - +
128C SER* 1.3 63.8 + - - +
129C LEU 3.2 0.2 - - - -
130C ASN* 3.3 16.5 + - - +
131C THR* 3.3 25.3 + - - +
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Residues in contact with SER 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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104C GLU 5.7 1.8 - - - -
108C SER* 4.4 13.5 - - - -
124C ALA 3.0 16.7 + - - -
125C VAL* 3.8 8.2 - - - +
127C GLN* 1.3 73.1 - - - +
129C LEU* 1.3 58.1 + - - +
131C THR* 3.2 8.2 + - - -
132C ARG* 2.9 39.5 + - - +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU 4.3 1.6 - - - +
105C LEU* 3.8 34.3 - - + +
108C SER* 3.8 16.8 - - - +
109C PHE* 3.8 30.7 - - + -
112C LEU* 4.1 13.2 - - + -
125C VAL 3.0 20.0 + - - +
126C ARG* 3.8 6.5 - - - +
128C SER* 1.3 74.8 - - - +
130C ASN* 1.3 58.1 + - - +
132C ARG* 4.3 2.2 - - - -
133C LEU* 2.7 48.5 + - + +
170C ILE* 3.7 29.2 - - + -
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Residues in contact with ASN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG 3.1 15.5 + - - +
127C GLN* 3.3 21.9 + - - +
129C LEU* 1.3 76.5 - - - +
131C THR* 1.3 63.1 + - - +
134C GLY* 3.3 15.4 + - - -
174C PRO* 5.7 2.8 - - - +
175C TRP* 3.5 34.9 + - - -
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Residues in contact with THR 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 GLN* 3.3 12.9 + - - +
128C SER* 3.2 9.3 + - - -
129C LEU 3.1 0.2 - - - -
130C ASN* 1.3 77.8 + - - +
132C ARG* 1.3 84.9 + - - +
134C GLY* 3.3 3.8 + - - -
135C GLN* 3.2 19.1 + - - +
138C ARG* 5.0 2.6 + - - -
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Residues in contact with ARG 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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100C PHE* 3.5 24.5 - - + -
104C GLU* 3.5 44.6 + - + +
105C LEU* 3.8 13.7 - - + -
128C SER* 2.9 24.6 + - - +
129C LEU* 3.9 2.2 - - - +
131C THR* 1.3 94.4 - - - +
133C LEU* 1.3 58.6 + - - +
135C GLN* 3.0 29.0 + - - +
136C VAL* 3.2 15.1 + - - +
49D ALA* 2.9 39.2 + - - +
51D TYR* 3.9 16.5 - - - -
4224D GSH 4.6 5.5 + - - -
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Residues in contact with LEU 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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105C LEU* 3.9 23.6 - - + -
109C PHE* 5.2 10.3 - - + -
129C LEU* 2.7 39.8 + - + +
132C ARG* 1.3 70.3 - - - +
134C GLY* 1.3 58.6 + - - +
136C VAL* 3.3 6.3 + - + +
137C ALA* 2.9 29.6 + - - +
162C LEU* 3.7 27.6 - - + -
170C ILE* 4.4 10.3 - - + -
172C LEU* 4.0 13.7 - - + -
175C TRP* 3.8 32.5 - - + -
178C LEU* 3.7 14.4 - - + +
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Residues in contact with GLY 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 ASN 3.3 8.4 + - - -
131C THR 3.3 8.4 + - - -
133C LEU* 1.3 75.2 - - - +
135C GLN* 1.3 64.3 + - - +
137C ALA* 3.2 2.1 + - - +
138C ARG* 3.0 40.8 + - - +
175C TRP* 3.6 20.9 - - - +
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Residues in contact with GLN 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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97C TRP* 4.8 13.6 - - + -
100C PHE* 3.3 26.5 - - + -
131C THR 3.2 9.6 + - - +
132C ARG* 3.0 15.8 + - - +
134C GLY* 1.3 75.0 - - - +
136C VAL* 1.3 61.9 + - - +
138C ARG* 3.5 27.4 + - - +
139C GLN* 3.2 21.2 + - - +
47D ASN* 4.5 2.6 + - - -
48D PRO* 3.7 24.8 - - + +
49D ALA* 3.3 36.9 - - - +
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Residues in contact with VAL 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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97C TRP* 4.2 8.5 - - + -
100C PHE* 3.7 25.1 - - + -
105C LEU* 4.2 13.9 - - + -
132C ARG 3.2 16.0 + - - +
133C LEU* 3.8 8.5 - - + +
134C GLY 3.2 0.4 - - - -
135C GLN* 1.3 72.8 - - - +
137C ALA* 1.3 65.6 + - - +
139C GLN* 3.1 7.2 + - - +
140C LEU* 3.0 25.5 + - + +
146C LEU* 4.0 11.2 - - + -
158C LEU* 3.5 34.3 - - + -
178C LEU* 3.9 12.1 - - + -
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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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133C LEU 2.9 17.9 + - - +
134C GLY 3.2 3.8 + - - +
136C VAL* 1.3 77.4 - - - +
138C ARG* 1.3 62.5 + - + +
140C LEU* 3.3 1.1 + - - -
141C GLU* 3.1 20.8 + - - +
175C TRP* 3.6 33.7 - - + -
177C SER* 2.7 29.3 + - - +
178C LEU* 3.8 8.7 - - + +
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Residues in contact with ARG 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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131C THR 5.0 2.6 + - - -
134C GLY* 3.0 34.3 + - - +
135C GLN* 3.6 32.8 - - - +
136C VAL 3.3 0.2 - - - -
137C ALA* 1.3 75.1 - - + +
139C GLN* 1.3 63.0 + - - +
141C GLU* 3.4 31.4 + - - +
142C HIS* 4.5 5.0 + - - -
48D PRO* 4.5 19.6 + - - +
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Residues in contact with GLN 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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93C HIS* 5.1 5.4 + - - -
97C TRP* 3.5 38.0 + - + -
135C GLN* 3.2 13.6 + - - +
136C VAL* 3.1 11.8 + - - +
138C ARG* 1.3 77.6 - - - +
140C LEU* 1.3 58.6 + - - +
141C GLU 3.3 2.3 + - - -
142C HIS 4.4 0.9 + - - -
143C ALA* 4.4 15.4 + - - +
145C TYR 5.0 1.4 - - - +
146C LEU* 3.1 36.8 - - + +
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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 VAL* 3.0 13.4 + - + +
137C ALA 3.3 4.2 + - - +
138C ARG 3.2 0.2 - - - -
139C GLN* 1.3 75.8 - - - +
141C GLU* 1.3 61.2 + - - +
142C HIS 3.5 1.6 - - - -
143C ALA 3.2 15.6 - - - +
144C PRO 3.8 9.2 - - - +
145C TYR* 3.5 39.0 - - - +
146C LEU* 3.7 14.6 - - + +
158C LEU* 3.7 21.3 - - + -
177C SER* 3.7 20.6 - - - +
178C LEU* 3.9 15.9 - - + -
181C PHE* 3.7 33.2 - - + -
184C ARG* 4.5 5.5 + - - +
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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