Contacts of the helix formed by residues 130 - 152 (chain C) in PDB entry 3SF4
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 ASP 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 3.9 21.3 - - + +
125C SER* 2.9 22.1 + - - +
128C LEU* 3.0 12.5 - - + +
129C ASN* 1.3 73.2 - - - +
131C LYS* 1.3 57.9 + - - +
132C VAL* 3.0 16.6 + - - +
133C GLY* 2.9 26.1 + - - -
134C GLU* 2.8 28.6 + - - +
48F GLN* 5.8 0.5 + - - -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ASN* 3.2 16.9 + - - +
130C ASP* 1.3 73.6 + - - +
132C VAL* 1.3 57.6 + - + +
134C GLU* 2.9 30.8 + - - +
135C ALA* 3.0 24.8 + - - +
184C LEU* 3.4 33.3 - - + +
188C LEU* 4.2 21.9 - - + +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 3.0 16.2 - - - +
131C LYS* 1.3 74.1 - - + +
133C GLY* 1.3 70.7 + - - +
135C ALA* 3.5 2.2 + - - +
136C ARG* 3.1 49.3 + - - +
188C LEU* 4.2 25.4 - - + -
48F GLN* 5.7 0.7 - - - +
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Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C HIS* 3.4 16.6 + - - -
125C SER* 3.3 11.7 - - - -
130C ASP* 2.9 28.4 + - - -
132C VAL* 1.3 78.2 - - - +
134C GLU* 1.3 64.1 + - - +
136C ARG* 3.3 6.8 + - - +
137C ALA* 2.9 19.6 + - - +
48F GLN* 5.0 4.9 - - - -
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.6 18.8 - - + +
125C SER* 3.4 15.1 - - - -
126C ARG* 2.8 40.9 + - + +
130C ASP 2.8 15.6 + - - +
131C LYS* 2.9 42.9 + - - +
133C GLY* 1.3 76.1 - - - +
135C ALA* 1.3 62.8 + - - +
137C ALA* 3.1 4.6 + - - +
138C LEU* 3.0 31.0 + - + +
184C LEU* 3.7 10.7 - - + +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS 3.0 18.4 + - - +
132C VAL* 3.8 4.7 - - - +
134C GLU* 1.3 76.7 - - - +
136C ARG* 1.3 62.5 + - + +
138C LEU* 3.2 7.1 + - - +
139C TYR* 3.0 11.6 + - - +
181C ASN* 2.8 27.9 - - - +
184C LEU* 3.4 22.8 - - + +
185C VAL* 4.1 16.4 - - + -
188C LEU* 4.3 7.4 - - + -
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Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C HIS* 4.5 7.6 - - + -
132C VAL* 3.1 31.9 + - - +
133C GLY 3.6 4.3 - - - +
135C ALA* 1.3 77.3 - - + +
137C ALA* 1.3 62.3 + - - +
139C TYR* 3.3 8.7 + - - +
140C ASN* 3.0 30.1 + - - +
46F VAL* 5.5 7.0 - - + +
48F GLN* 2.6 52.4 - - + +
61F ASP* 3.0 38.1 + - - +
62F LEU* 3.2 37.0 - - + +
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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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118C CYS 4.1 3.3 - - - +
121C HIS* 3.7 13.0 - - + -
122C LEU* 3.5 40.4 - - + +
133C GLY 2.9 16.1 + - - +
134C GLU 3.1 3.8 + - - +
136C ARG* 1.3 77.1 - - - +
138C LEU* 1.3 58.6 + - - +
140C ASN* 3.1 12.9 + - - +
141C LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.6 32.8 - - + -
126C ARG* 4.0 9.6 - - - +
134C GLU* 3.0 24.5 + - + +
135C ALA* 3.4 5.8 - - - +
137C ALA* 1.3 78.2 - - - +
139C TYR* 1.3 58.1 + - - +
141C LEU* 3.4 4.0 + - - +
142C GLY* 3.0 22.3 + - - -
177C PHE* 3.5 32.8 - - + +
180C GLU* 3.8 39.9 - - + +
181C ASN* 3.8 12.1 - - + +
184C LEU* 4.2 17.3 - - + -
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Residues in contact with TYR 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 ALA 3.0 6.5 + - - +
136C ARG* 3.7 9.6 - - - +
138C LEU* 1.3 77.9 - - - +
140C ASN* 1.3 62.8 + - - +
142C GLY* 3.3 2.3 + - - -
143C ASN* 3.0 46.1 + - - +
178C TYR* 4.0 11.5 - + - -
181C ASN* 3.6 34.9 + - - +
193C ALA 5.4 0.4 - - - -
196C ARG* 3.5 44.8 - - + +
197C ALA* 4.0 2.0 - - - -
200C ASN* 3.0 23.7 + - - -
42F GLU* 3.9 3.1 - - - +
43F CYS 2.6 24.2 + - - -
46F VAL* 3.6 27.1 - - + -
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Residues in contact with ASN 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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99C GLY* 4.4 7.1 - - - -
103C ASN* 3.3 28.0 + - - +
118C CYS* 3.9 17.3 - - + -
121C HIS* 3.8 24.5 + - - -
136C ARG* 3.0 23.9 + - - +
137C ALA* 3.1 6.9 + - - +
139C TYR* 1.3 78.5 - - - +
141C LEU* 1.3 57.0 + - - +
143C ASN* 3.2 8.6 + - - +
144C VAL* 2.9 34.9 + - - +
46F VAL* 3.6 26.1 + - - +
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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
----------------------------------------------------------
115C ILE* 4.0 16.4 - - + +
118C CYS* 3.5 31.9 - - + +
119C GLN* 3.9 15.7 - - + +
122C LEU* 3.7 22.2 - - + -
137C ALA 2.9 18.9 + - - +
138C LEU* 3.7 1.3 - - - +
139C TYR 3.3 0.2 - - - -
140C ASN* 1.3 73.8 - - - +
142C GLY* 1.3 66.6 + - - +
144C VAL* 3.8 3.3 - - + +
145C TYR* 3.0 46.3 + - + -
177C PHE* 3.4 43.1 - - + -
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU 3.0 12.0 + - - -
139C TYR 3.3 4.5 + - - -
140C ASN 3.2 0.2 - - - -
141C LEU* 1.3 77.8 - - - +
143C ASN* 1.3 55.7 + - - +
146C HIS* 3.0 28.4 + - - +
174C ALA* 3.5 11.6 - - - +
177C PHE* 3.7 17.5 - - - +
178C TYR* 3.3 22.7 + - - -
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Residues in contact with ASN 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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103C ASN* 5.2 2.0 - - - +
106C LYS* 3.8 6.5 + - + +
139C TYR* 3.0 37.4 + - - -
140C ASN* 3.2 11.2 + - - +
142C GLY* 1.3 77.3 - - - +
144C VAL* 1.3 56.8 + - + +
146C HIS* 3.3 3.6 + - - +
147C ALA* 3.0 29.6 + - - +
178C TYR* 2.5 30.7 + - - -
200C ASN* 3.2 14.6 + - - -
44F MET* 3.2 47.4 + - + +
45F CYS* 4.9 0.2 - - - +
46F VAL* 4.8 1.6 - - - +
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY 4.9 1.6 - - - +
103C ASN* 5.6 3.8 - - - +
106C LYS* 3.8 27.6 - - + -
111C PHE* 3.9 6.9 - - + +
114C ALA* 3.9 21.1 - - + -
115C ILE* 3.4 30.5 - - + +
118C CYS* 3.9 23.6 - - - -
140C ASN* 2.9 22.1 + - + +
141C LEU* 3.8 7.0 - - - +
143C ASN* 1.3 75.5 - - + +
145C TYR* 1.3 59.0 + - - +
147C ALA* 3.3 4.0 + - - +
148C LYS* 2.9 26.5 + - - +
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Residues in contact with TYR 145 (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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115C ILE* 3.4 45.3 - - + +
141C LEU* 3.0 29.8 + - + +
144C VAL* 1.3 74.8 - - - +
146C HIS* 1.3 55.7 + - - +
148C LYS* 3.3 20.5 + - + +
149C GLY* 2.8 30.5 + - - -
170C ALA* 3.5 34.1 - - + +
173C ALA* 3.7 21.8 - - + -
174C ALA* 3.9 12.6 - - + +
177C PHE* 3.4 31.1 - + - -
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Residues in contact with HIS 146 (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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142C GLY 3.0 18.8 + - - +
143C ASN* 3.4 6.7 - - - +
144C VAL 3.2 0.2 - - - -
145C TYR* 1.3 76.3 - - - +
147C ALA* 1.3 62.4 + - - +
149C GLY* 3.0 11.8 + - - -
150C LYS* 3.1 50.7 + - - +
171C LEU* 4.1 6.6 - - + +
174C ALA* 3.9 6.7 - - + +
178C TYR* 3.8 9.4 - + - +
200C ASN* 4.4 2.6 + - + -
203C ASN* 4.1 7.6 - - + +
204C THR* 2.8 42.2 + - + -
207C LEU* 3.9 15.9 - - + +
39F THR* 5.0 0.2 - - - -
41F CYS* 4.1 6.5 - - - -
44F MET* 3.1 23.9 - - + +
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Residues in contact with ALA 147 (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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106C LYS* 3.7 20.2 - - + +
111C PHE* 3.5 23.0 - - + -
143C ASN 3.0 16.5 + - - +
144C VAL 3.6 2.0 - - - +
146C HIS* 1.3 79.0 + - - +
148C LYS* 1.3 59.1 + - - +
150C LYS* 3.1 11.1 + - - +
151C SER* 2.9 28.2 + - - -
44F MET* 5.3 2.2 - - + +
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Residues in contact with LYS 148 (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 PHE* 3.7 32.3 - - + -
112C ASP* 4.3 18.4 + - - -
115C ILE* 5.0 6.7 - - + +
144C VAL* 2.9 18.3 + - + +
145C TYR* 3.5 26.5 - - + +
147C ALA* 1.3 76.9 - - - +
149C GLY* 1.3 64.5 + - - +
151C SER* 2.5 27.1 + - - +
152C PHE* 3.5 26.7 - - + -
166C GLU 5.7 1.0 + - - -
170C ALA* 4.2 15.3 - - + +
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR 2.8 15.7 + - - -
146C HIS 3.0 5.1 + - - -
148C LYS* 1.3 78.7 - - - +
150C LYS* 1.3 60.7 + - - +
152C PHE* 3.9 4.7 + - - +
167C VAL* 3.5 27.3 - - - +
170C ALA* 3.8 13.2 - - - +
171C LEU* 3.8 21.1 - - - -
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Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C HIS* 3.1 48.3 + - + +
147C ALA* 3.1 11.4 + - - +
149C GLY* 1.3 74.0 - - - +
151C SER* 1.3 67.9 + - - +
152C PHE 2.7 13.7 + - - -
207C LEU* 3.7 24.5 - - + -
37F LEU 5.3 4.3 - - - -
39F THR* 3.5 19.4 + - - -
41F CYS* 3.7 9.3 - - - -
44F MET* 4.7 2.8 - - - +
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C PHE* 3.3 36.5 - - - -
147C ALA 2.9 7.9 + - - -
148C LYS* 2.5 22.4 + - - +
150C LYS* 1.3 74.7 - - - +
152C PHE* 1.3 73.6 + - - +
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Residues in contact with PHE 152 (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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148C LYS* 3.5 44.6 - - + -
149C GLY 4.2 1.6 - - - +
150C LYS 2.7 13.5 + - - -
151C SER* 1.3 88.0 + - - +
164C PRO* 5.5 3.4 - - + -
166C GLU* 3.6 51.4 - - + -
167C VAL* 3.4 39.0 - - + -
170C ALA* 5.2 0.7 - - + -
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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