Contacts of the helix formed by residues 108 - 126 (chain C) in PDB entry 1SA0
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 TYR 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 4.4 2.9 - + - -
104C ALA* 3.2 25.9 + - + +
105C ARG 3.4 3.7 + - - -
107C HIS* 1.3 107.1 + + - +
109C THR* 1.3 73.7 + - - +
112C LYS* 3.2 27.5 + - - +
411C GLU* 5.2 1.3 - - + +
412C GLY 5.4 0.4 - - - -
413C MET* 3.5 31.2 - - + -
417C GLU* 2.5 35.2 + - - -
104E LYS* 4.2 22.5 - - + +
105E MET* 4.3 16.8 - - + -
108E ASN* 3.0 44.2 - - + +
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Residues in contact with THR 109 (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 ALA 3.8 0.2 + - - -
105C ARG* 3.3 19.7 + - + +
108C TYR* 1.3 84.3 - - - +
110C ILE* 1.3 66.7 + - + +
112C LYS* 4.1 8.7 - - - +
113C GLU* 4.4 8.5 + - - +
411C GLU* 3.0 40.4 + - - +
108E ASN* 4.4 0.9 + - - -
112E ARG* 3.5 36.0 + - - +
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Residues in contact with ILE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 3.3 31.1 - - + +
95C GLY 5.9 0.4 - - - +
97C GLU* 3.6 39.9 - - + +
98C ASP 4.1 18.4 - - - +
99C ALA* 4.3 2.9 - - - -
105C ARG* 3.0 43.1 + - + +
106C GLY* 4.2 1.6 - - - -
109C THR* 1.3 80.5 - - + +
111C GLY* 1.3 65.3 + - - +
113C GLU* 3.8 15.6 + - + +
114C ILE* 4.1 5.0 + - - +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 4.7 2.5 - - - -
105C ARG 3.5 5.1 + - - -
106C GLY 3.3 19.3 - - - -
108C TYR 3.6 1.0 + - - -
109C THR 3.4 1.4 - - - -
110C ILE* 1.3 78.1 - - - +
112C LYS* 1.3 52.3 + - - +
113C GLU 2.6 5.0 + - - -
114C ILE* 2.5 32.8 + - - +
115C ILE* 3.1 9.2 + - - -
149C PHE* 4.2 13.9 - - - -
152C LEU* 4.4 6.5 - - - -
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TYR 3.2 20.1 + - - +
109C THR 4.1 5.2 - - - +
111C GLY* 1.3 71.2 - - - +
113C GLU* 1.3 76.3 + - - +
114C ILE 3.4 0.5 + - - -
115C ILE* 3.7 22.0 + - + +
116C ASP* 4.4 6.1 + - - +
152C LEU* 4.3 8.8 - - - +
105E MET* 3.8 38.4 - - + -
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Residues in contact with GLU 113 (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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109C THR 4.5 9.6 - - - +
110C ILE* 3.8 14.7 + - + +
111C GLY 2.6 5.9 + - - -
112C LYS* 1.3 96.1 + - - +
114C ILE* 1.3 66.9 + - + +
116C ASP* 5.1 3.0 + - - +
117C LEU* 5.4 2.6 + - - +
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 4.9 3.8 - - + -
69C ASP 5.9 0.9 - - - +
70C LEU* 4.8 17.9 - - + -
93C ILE* 4.4 17.7 - - + -
94C THR 4.5 13.7 - - - +
95C GLY* 4.7 13.7 - - - +
110C ILE 4.1 4.7 + - - +
111C GLY 2.5 15.3 + - - +
113C GLU* 1.3 80.8 - - + +
115C ILE* 1.3 62.6 + - - +
116C ASP 3.4 2.7 - - - -
117C LEU* 3.2 19.0 + - + +
118C VAL* 3.1 25.5 + - + +
149C PHE* 3.6 26.0 - - + -
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLY 3.1 7.1 + - - +
112C LYS* 3.8 13.2 - - + +
113C GLU 3.7 0.4 - - - -
114C ILE* 1.3 77.1 - - - +
116C ASP* 1.3 74.6 + - - +
118C VAL 3.2 0.5 + - - -
119C LEU* 2.8 70.0 + - + +
149C PHE* 3.9 19.3 - - + -
152C LEU* 3.4 37.0 - - + +
153C LEU* 4.7 6.3 - - + -
156C ARG* 3.7 31.6 - - + +
105E MET* 6.3 2.5 - - + -
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Residues in contact with ASP 116 (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 LYS 4.4 6.3 + - - +
113C GLU 5.1 2.4 + - - +
114C ILE 3.4 0.6 - - - -
115C ILE* 1.3 86.8 - - - +
117C LEU* 1.3 60.5 + - - +
119C LEU* 4.0 5.1 - - - +
120C ASP* 3.3 26.3 + - - +
156C ARG* 3.5 28.0 + - - +
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Residues in contact with LEU 117 (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 ILE* 4.7 11.3 - - + +
113C GLU 5.4 2.4 + - - +
114C ILE* 3.2 27.4 + - + +
115C ILE 3.2 0.8 - - - -
116C ASP* 1.3 77.5 - - - +
118C VAL* 1.3 65.4 + - + +
120C ASP* 4.2 10.4 - - - +
121C ARG* 3.5 50.3 + - - +
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Residues in contact with VAL 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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7C ILE* 5.9 0.2 - - + -
66C VAL* 4.5 5.8 - - + -
68C VAL* 3.3 38.4 - - + -
93C ILE* 4.2 17.3 - - + -
114C ILE* 3.1 19.8 + - + +
115C ILE 3.8 4.0 - - - +
117C LEU* 1.3 74.7 - - - +
119C LEU* 1.3 61.2 + - - +
121C ARG* 2.7 24.9 + - - +
122C ILE* 3.0 28.4 + - + +
149C PHE* 3.7 22.0 - - + -
153C LEU* 4.8 11.2 - - + -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 2.8 36.8 + - + +
116C ASP* 4.0 4.9 - - - +
118C VAL* 1.3 78.3 - - - +
120C ASP* 1.3 59.9 + - - +
122C ILE* 3.4 17.2 - - + +
123C ARG* 3.4 20.3 + - - +
153C LEU* 3.7 23.6 - - + +
156C ARG* 3.2 51.6 - - + +
157C LEU* 4.7 3.4 - - + +
160C ASP* 3.2 24.7 - - + +
161C TYR* 4.8 2.4 + - + -
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Residues in contact with ASP 120 (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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116C ASP 3.3 17.4 + - - +
117C LEU* 4.2 13.6 - - - +
118C VAL 3.0 1.0 - - - -
119C LEU* 1.3 78.5 - - - +
121C ARG* 1.3 68.0 + - - +
123C ARG* 3.3 9.3 + - - +
124C LYS* 3.1 30.8 + - - +
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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
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66C VAL* 5.5 2.7 - - + -
90C GLU* 2.7 59.1 + - - +
91C GLN* 4.8 2.0 - - - +
93C ILE* 3.6 24.1 - - + +
117C LEU* 3.5 42.1 + - - +
118C VAL 2.7 14.2 + - - +
120C ASP* 1.3 79.2 + - - +
122C ILE* 1.3 60.0 + - + +
123C ARG 3.1 2.0 - - - -
124C LYS* 2.9 33.8 + - + +
125C LEU* 3.1 14.6 + - - +
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Residues in contact with ILE 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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5C ILE* 4.2 5.6 - - + +
7C ILE* 4.3 13.0 - - + -
66C VAL* 3.6 39.9 - - + -
118C VAL* 3.0 17.8 + - + +
119C LEU* 3.4 23.3 - - + +
121C ARG* 1.3 76.5 - - + +
123C ARG* 1.3 61.3 + - - +
125C LEU* 3.3 10.1 + - - +
126C ALA* 3.1 25.5 + - - +
135C PHE* 4.8 7.7 - - + -
153C LEU* 4.1 13.2 - - + -
157C LEU* 3.4 30.3 - - + -
161C TYR* 4.3 9.6 + - + +
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Residues in contact with ARG 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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119C LEU 3.4 9.1 + - - +
120C ASP* 3.3 12.7 + - - +
121C ARG 3.1 0.4 - - - -
122C ILE* 1.3 79.0 - - - +
124C LYS* 1.3 60.6 + - - +
125C LEU 3.1 1.8 - - - -
126C ALA* 3.8 3.5 - - + -
127C ASP* 2.8 44.6 + - - +
160C ASP* 4.4 26.1 + - - +
161C TYR* 2.7 38.9 - - - +
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Residues in contact with LYS 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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90C GLU* 3.8 22.0 - - - +
120C ASP* 3.1 19.4 + - - +
121C ARG* 2.9 32.6 + - + +
123C ARG* 1.3 76.5 - - - +
125C LEU* 1.3 59.2 + - - +
127C ASP* 3.9 12.8 - - - +
128C GLN* 3.5 17.0 + - - +
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Residues in contact with LEU 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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5C ILE* 4.4 11.7 - - + -
54C SER* 5.0 4.0 - - - +
62C VAL* 6.1 0.7 - - + -
63C PRO 4.7 4.7 - - - +
64C ARG* 4.0 22.7 - - + -
65C ALA 3.2 36.1 - - - +
66C VAL* 3.7 18.2 - - + -
91C GLN* 4.8 13.0 - - + +
121C ARG 3.1 9.4 + - - +
122C ILE 3.4 9.6 - - - +
123C ARG 3.1 0.2 - - - -
124C LYS* 1.3 76.4 - - - +
126C ALA* 1.3 57.3 + - - +
127C ASP 3.0 8.1 + - - -
128C GLN* 3.4 33.0 + - + +
129C CYS* 3.3 16.8 - - - -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.8 19.3 - - + +
122C ILE 3.1 15.3 + - - +
123C ARG* 3.6 6.0 + - + +
124C LYS 3.6 0.2 - - - -
125C LEU* 1.3 75.0 - - - +
127C ASP* 1.3 63.2 + - - +
128C GLN 3.3 0.4 - - - -
129C CYS* 3.5 23.8 + - - +
132C LEU* 4.0 17.6 - - + +
135C PHE* 5.4 0.4 - - + -
161C TYR* 4.3 17.7 - - + +
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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