Contacts of the helix formed by residues 122 - 132 (chain C) in PDB entry 3SWD
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 VAL 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ARG* 5.2 1.6 - - - +
94C ILE* 4.6 16.2 - - + -
111C LEU* 3.6 30.5 - - + -
112C PRO* 4.5 21.1 - - + -
120C ARG 4.1 7.2 - - - +
121C PRO* 1.3 76.6 - - - +
123C ASP* 1.3 64.7 + - - +
125C HIS* 2.9 35.0 + - + +
126C ILE* 3.3 23.2 + - + +
143C VAL* 6.0 0.2 - - + -
501C EPZ 3.1 9.6 - - + -
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Residues in contact with ASP 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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121C PRO* 3.7 12.2 - - + +
122C VAL* 1.3 77.0 - - - +
124C LEU* 1.3 72.9 + - - +
126C ILE* 3.5 9.4 + - - +
127C SER* 2.9 31.5 + - - -
160C LYS* 5.6 3.3 - - - +
501C EPZ 2.6 33.6 + - - +
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Residues in contact with LEU 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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123C ASP* 1.3 80.2 - - - +
125C HIS* 1.3 57.4 + - - +
127C SER* 4.1 7.1 - - - -
128C GLY* 3.0 26.3 + - - -
158C MET* 3.8 15.4 - - + +
159C ASP* 4.1 34.1 - - + +
160C LYS* 3.7 32.5 - - + +
162C SER* 3.8 26.0 - - - -
165C ALA* 3.7 16.5 - - + +
169C ILE* 4.4 0.9 - - - +
501C EPZ 2.7 29.8 + - + +
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Residues in contact with HIS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 4.2 27.5 - - + +
95C TRP* 4.2 5.2 - - - -
97C LEU* 6.0 4.3 - - + -
122C VAL* 2.9 39.4 + - + +
124C LEU* 1.3 74.5 - - - +
126C ILE* 1.3 68.1 + - + +
128C GLY* 3.2 1.0 + - - -
129C LEU* 3.1 28.7 + - + +
164C GLY* 3.1 33.2 - - - -
165C ALA* 3.4 17.9 + - + -
168C THR* 2.7 33.5 + - + +
169C ILE* 5.7 0.4 - - - -
501C EPZ 3.9 13.1 + + - -
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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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97C LEU* 5.5 2.9 - - + -
111C LEU* 5.1 7.2 - - + -
122C VAL* 3.3 26.8 + - + +
123C ASP* 3.8 7.9 - - - +
125C HIS* 1.3 76.0 - - + +
127C SER* 1.3 64.7 + - - +
129C LEU* 3.1 3.7 + - - -
130C GLU* 3.0 36.8 + - - +
136C ILE* 3.6 38.0 - - + +
143C VAL* 4.6 23.3 - - + -
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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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123C ASP 2.9 20.0 + - - -
124C LEU* 4.1 8.3 - - - -
126C ILE* 1.3 78.6 - - - +
128C GLY* 1.3 61.6 + - - +
130C GLU* 3.3 14.6 + - - +
131C GLN* 3.1 41.6 + - - +
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Residues in contact with GLY 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 LEU 3.0 12.0 + - - -
125C HIS 3.7 0.9 - - - -
127C SER* 1.3 75.2 - - - +
129C LEU* 1.3 62.9 + - - +
131C GLN* 3.3 6.6 + - - +
132C LEU* 3.2 23.9 + - - +
156C ILE* 3.7 11.7 - - - +
158C MET* 5.6 0.4 - - - -
169C ILE* 3.6 33.7 - - - -
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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
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97C LEU* 3.8 36.3 - - + +
98C GLY* 4.4 9.0 - - - +
101C VAL* 5.3 5.6 - - + -
125C HIS 3.1 15.8 + - - +
126C ILE 3.1 8.2 + - - +
128C GLY* 1.3 74.6 - - - +
130C GLU* 1.3 65.2 + - - +
132C LEU* 2.9 21.6 + - + +
133C GLY 3.4 0.2 + - - -
134C ALA* 3.2 24.0 + - + +
136C ILE* 3.9 13.5 - - + -
145C ALA* 5.0 4.9 - - + -
151C LEU* 5.0 5.8 - - + -
168C THR* 4.1 22.4 - - + +
169C ILE* 4.8 1.1 - - - +
172C ALA* 3.8 29.6 - - + -
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Residues in contact with GLU 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 32.2 + - - +
127C SER* 3.3 13.4 + - - +
129C LEU* 1.3 75.0 - - - +
131C GLN* 1.3 54.0 + - + +
133C GLY* 2.8 25.3 + - - -
134C ALA 3.5 19.7 + - - +
136C ILE* 4.0 30.5 + - + +
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Residues in contact with GLN 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 SER* 3.1 31.0 + - - +
128C GLY* 3.7 7.8 - - - +
129C LEU 3.2 0.4 - - - -
130C GLU* 1.3 75.7 - - + +
132C LEU* 1.3 58.8 + - - +
133C GLY 3.0 3.6 + - - -
152C LYS* 4.2 1.6 - - - +
154C ALA* 3.6 18.3 - - + +
155C HIS 4.1 5.0 - - - +
156C ILE* 3.5 44.4 - - + +
157C VAL 4.7 5.3 + - - -
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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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128C GLY 3.2 12.0 + - - +
129C LEU* 2.9 16.0 + - + +
131C GLN* 1.3 74.7 - - - +
133C GLY* 1.3 56.7 + - - +
134C ALA 3.5 1.8 - - - -
151C LEU* 3.3 24.0 - - + +
152C LYS* 2.8 49.0 + - - +
154C ALA* 4.0 4.9 - - + +
156C ILE* 3.9 18.8 - - + -
169C ILE* 4.1 14.4 - - + +
172C ALA* 3.9 28.7 - - + -
173C ALA* 4.1 13.7 - - - +
176C ALA* 5.4 1.1 - - + -
180C THR* 3.7 22.4 - - + +
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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