Contacts of the helix formed by residues 123 - 143 (chain C) in PDB entry 1SIW
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 THR 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 5.6 7.9 - - - +
121C THR 4.9 4.0 - - - +
122C THR* 1.3 89.2 + - - +
124C GLY* 1.3 66.0 + - - +
125C ALA* 3.7 8.2 + - - +
126C ASP* 2.5 43.6 + - - +
127C ILE* 3.5 6.3 + - - +
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Residues in contact with GLY 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 THR* 1.3 73.4 - - - +
125C ALA* 1.3 62.3 + - - +
127C ILE* 3.0 12.4 + - - +
128C LEU* 2.9 24.1 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C THR* 3.3 8.2 + - - +
124C GLY* 1.3 75.8 - - - +
126C ASP* 1.3 58.7 + - - +
128C LEU* 3.9 10.3 - - + +
129C ILE* 2.9 33.8 + - - +
200C PHE 4.3 17.9 - - - +
201C SER* 4.7 10.9 - - - -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 5.3 5.3 - - - +
112C ARG* 4.0 13.9 + - - +
122C THR* 3.3 19.2 + - - +
123C THR* 2.5 39.2 + - - +
124C GLY 3.1 0.8 - - - -
125C ALA* 1.3 78.8 - - - +
127C ILE* 1.3 61.9 + - - +
129C ILE* 3.5 7.4 - - - +
130C LEU* 3.3 24.6 + - - +
202C ARG* 3.5 41.9 + - - +
806C HEM 4.8 1.2 - - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.6 4.6 - - + +
112C ARG* 4.1 23.1 - - + +
113C LEU* 3.9 30.7 - - + -
119C ARG* 4.1 14.8 - - - +
122C THR* 3.9 19.5 - - + +
123C THR 3.5 8.9 + - - +
124C GLY* 3.0 10.6 + - - +
126C ASP* 1.3 75.0 - - - +
128C LEU* 1.3 66.4 + - - +
130C LEU* 4.1 1.6 - - - +
131C SER* 2.9 39.3 + - - +
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Residues in contact with LEU 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 GLY 2.9 15.1 + - - +
125C ALA* 3.9 8.3 - - - +
127C ILE* 1.3 78.4 - - - +
129C ILE* 1.3 65.0 + - - +
131C SER* 3.3 5.8 + - - -
132C LEU* 3.0 51.7 + - + +
197C LEU* 4.3 20.4 - - + -
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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
----------------------------------------------------------
125C ALA 2.9 20.9 + - - +
126C ASP* 3.5 11.9 - - - +
128C LEU* 1.3 78.3 - - - +
130C LEU* 1.3 67.3 + - + +
132C LEU* 3.4 7.4 + - - +
133C LEU* 3.2 33.0 + - + +
194C LEU* 4.4 9.4 - - + -
197C LEU* 5.7 8.1 - - + -
201C SER* 3.8 16.4 - - - +
202C ARG* 4.2 21.5 - - + -
203C LEU* 3.3 46.7 - - + -
806C HEM 4.7 2.7 - - + -
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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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55C PHE* 4.4 17.3 - - + -
105C GLY 4.3 9.9 - - - +
108C LEU* 3.8 10.5 - - + +
109C LEU* 3.5 47.3 - - + +
112C ARG* 4.5 5.4 - - - -
126C ASP 3.3 15.3 + - - +
127C ILE 4.1 1.8 - - - +
129C ILE* 1.3 81.2 - - + +
131C SER* 1.3 66.6 + - - +
133C LEU* 3.2 5.0 + - + +
134C VAL* 3.0 24.9 + - + +
806C HEM 3.4 44.2 - - + +
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.7 28.4 - - - +
113C LEU* 5.7 0.7 - - - +
127C ILE* 2.9 27.8 + - - +
128C LEU* 3.6 7.0 - - - -
130C LEU* 1.3 76.5 - - - +
132C LEU* 1.3 61.1 + - - +
134C VAL* 3.3 3.7 + - - +
135C ILE* 3.0 35.6 + - - +
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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 LEU* 3.0 39.2 + - + +
129C ILE* 3.8 2.2 - - - +
130C LEU 3.2 0.2 - - - -
131C SER* 1.3 80.7 - - - +
133C LEU* 1.3 56.4 + - - +
135C ILE* 3.6 10.6 - - + +
136C GLN* 2.8 30.0 + - - +
190C LEU* 4.0 24.0 - - + +
193C THR* 5.1 4.9 - - + -
194C LEU* 3.8 22.8 - - + +
197C LEU* 3.9 28.7 - - + -
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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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55C PHE* 4.0 21.5 - - + -
59C ILE* 4.7 1.8 - - + -
101C CYS* 5.6 0.4 - - - -
129C ILE* 3.2 38.5 + - + +
130C LEU* 3.2 6.7 + - - +
132C LEU* 1.3 73.5 - - - +
134C VAL* 1.3 62.3 + - - +
136C GLN* 4.2 2.9 - - - -
137C CYS* 2.9 31.0 + - - +
194C LEU* 3.7 23.6 - - + -
203C LEU* 4.3 1.8 - - + -
806C HEM 3.7 50.7 - - + -
807C HEM 3.3 25.0 - - + +
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Residues in contact with VAL 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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55C PHE* 5.7 0.9 - - + -
102C LEU* 3.7 20.6 - - + +
105C GLY* 3.7 37.0 - - - +
106C VAL* 4.1 11.0 - - + +
109C LEU* 4.4 17.5 - - + -
130C LEU* 3.0 21.0 + - + +
131C SER* 3.6 10.1 - - - +
133C LEU* 1.3 76.8 - - + +
135C ILE* 1.3 69.9 + - + +
137C CYS* 3.5 3.8 + - - -
138C ALA* 3.0 23.3 + - + +
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Residues in contact with ILE 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 SER* 3.0 24.2 + - - +
132C LEU* 3.6 15.0 - - + +
134C VAL* 1.3 81.3 - - + +
136C GLN* 1.3 60.9 + - - +
138C ALA* 3.0 8.6 + - + +
139C LEU* 2.8 38.8 + - + +
190C LEU* 3.7 17.7 - - + -
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Residues in contact with GLN 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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132C LEU 2.8 22.1 + - - +
133C LEU 3.8 4.3 - - - +
135C ILE* 1.3 73.2 - - - +
137C CYS* 1.3 56.7 + - - +
139C LEU* 3.4 2.9 + - - +
140C GLY 2.9 22.9 + - - -
187C HIS* 2.8 62.4 + - - +
190C LEU* 3.3 22.6 - - + +
191C GLY* 3.1 22.3 - - - -
194C LEU* 4.2 7.4 - - + -
807C HEM 3.4 37.5 - - + +
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Residues in contact with CYS 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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62C ILE* 5.6 0.2 - - - -
98C GLY* 3.3 33.4 - - - -
101C CYS* 3.6 26.0 - - - -
102C LEU* 3.7 14.4 - - + -
133C LEU 2.9 19.2 + - - +
134C VAL* 3.7 5.4 - - - +
135C ILE 3.2 0.2 - - - -
136C GLN* 1.3 74.4 - - - +
138C ALA* 1.3 66.6 + - - +
140C GLY* 3.3 1.6 + - - -
141C LEU* 3.1 23.6 + - - +
807C HEM 3.4 22.7 - - + +
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Residues in contact with ALA 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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102C LEU* 4.4 20.8 - - + +
134C VAL* 3.0 15.7 + - + +
135C ILE* 3.0 12.8 + - + +
137C CYS* 1.3 74.5 - - - +
139C LEU* 1.3 65.9 + - + +
141C LEU* 3.4 4.4 + - - +
142C LEU* 3.1 37.1 + - + +
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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
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135C ILE* 2.8 24.3 + - + +
136C GLN* 3.6 10.5 - - - +
138C ALA* 1.3 77.2 - - + +
140C GLY* 1.3 65.1 + - - +
142C LEU* 2.9 28.4 + - + +
143C THR* 3.2 15.1 + - - +
183C ILE* 3.9 10.7 - - + +
186C LEU* 4.2 26.2 - - + +
187C HIS* 3.8 26.9 - - + +
190C LEU* 3.8 26.2 - - + -
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Residues in contact with GLY 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 GLN 2.9 11.9 + - - -
137C CYS 3.7 0.9 - - - -
138C ALA 3.3 0.4 - - - -
139C LEU* 1.3 75.4 - - - +
141C LEU* 1.3 59.9 + - - +
143C THR* 2.6 29.2 + - - -
144C ILE 3.8 0.3 + - - -
187C HIS* 3.5 17.7 + - - -
807C HEM 3.1 34.2 - - - +
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Residues in contact with LEU 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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95C GLY* 3.6 23.8 - - - +
98C GLY* 3.5 22.9 - - - +
99C VAL* 4.3 12.3 - - + +
102C LEU* 4.0 21.1 - - + -
137C CYS 3.1 14.7 + - - +
138C ALA* 3.8 7.0 - - - +
139C LEU 3.2 0.2 - - - -
140C GLY* 1.3 76.2 - - - +
142C LEU* 1.3 66.4 + - + +
144C ILE* 3.1 40.8 + - + +
145C PRO* 3.5 4.0 - - - +
807C HEM 3.8 17.5 - - + +
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Residues in contact with LEU 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 ALA* 3.1 26.6 + - + +
139C LEU* 2.9 17.3 + - + +
141C LEU* 1.3 81.4 - - + +
143C THR* 1.3 56.2 + - - +
144C ILE 3.2 0.2 - - - -
145C PRO* 3.0 25.6 - - + +
146C PHE* 3.2 12.4 - - + -
183C ILE* 3.3 21.1 - - + -
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Residues in contact with THR 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 3.3 16.8 - - - +
140C GLY* 2.6 18.5 + - - +
142C LEU* 1.3 75.8 - - - +
144C ILE* 1.3 60.5 + - - +
146C PHE* 3.2 9.6 + - - +
147C SER* 2.9 29.7 + - - -
183C ILE* 3.7 29.8 - - + +
184C PHE* 3.6 27.8 - - + -
187C HIS* 4.6 9.2 - - + -
807C HEM 4.0 17.4 - - + +
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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
------------------------------------------------------------
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