Contacts of the helix formed by residues 135 - 159 (chain C) in PDB entry 4PAR
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 ASN 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 3.3 27.6 - - - +
133C PRO 4.0 0.4 + - - -
134C GLN* 1.3 74.6 - - - +
136C LEU* 1.3 58.9 + - - +
137C GLU* 3.0 13.8 + - + +
138C ASN* 2.8 40.0 + - - +
139C ILE* 3.7 1.6 - - - +
6D SER* 3.7 33.1 - - - +
7D SER* 4.5 0.4 + - - -
10D THR* 3.6 7.9 - - - -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.4 32.8 - - + +
134C GLN 4.4 0.2 - - - -
135C ASN* 1.3 72.1 - - - +
137C GLU* 1.3 61.7 + - - +
138C ASN 3.6 0.2 - - - -
139C ILE* 3.9 13.7 - - + -
140C HIS* 2.9 44.8 + - + +
6D SER 5.1 0.2 + - - -
9D LEU* 3.9 28.1 - - + +
10D THR* 3.3 26.5 - - + +
13D VAL* 4.0 10.8 - - + -
14D ILE* 6.0 2.5 - - + -
40D PHE* 3.9 32.8 - - + -
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Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ASN* 3.0 15.4 + - + +
136C LEU* 1.3 79.7 - - - +
138C ASN* 1.3 60.8 + - + +
140C HIS* 3.1 6.6 + - - +
141C GLN* 2.9 50.6 + - + +
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Residues in contact with ASN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C GLN* 2.9 48.0 + - - +
135C ASN* 2.8 33.6 + - - +
137C GLU* 1.3 80.3 - - + +
139C ILE* 1.3 63.8 + - - +
141C GLN* 3.3 15.2 - - + +
142C GLN* 2.9 46.7 + - + +
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 5.4 7.6 - - + -
28C TYR* 4.9 5.8 - - + -
29C VAL* 5.1 5.6 - - + -
123C VAL* 4.5 11.7 - - + -
124C ASN 4.9 2.9 - - - +
125C VAL* 4.4 24.2 - - + +
134C GLN* 3.5 24.9 - - + +
135C ASN 3.7 9.4 - - - +
136C LEU* 3.5 22.2 + - + +
137C GLU 3.1 0.8 - - - -
138C ASN* 1.3 87.9 - - - +
140C HIS* 1.3 64.0 + - + +
142C GLN* 3.2 14.8 + - - +
143C ILE* 2.9 45.4 + - + +
10D THR* 5.2 3.1 - - + -
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Residues in contact with HIS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 2.7 26.3 + + - -
32C ARG* 3.5 40.7 + - - +
136C LEU* 2.9 37.9 + - + +
137C GLU* 3.5 5.1 - - - +
139C ILE* 1.3 78.1 - - + +
141C GLN* 1.3 57.1 + - - +
143C ILE* 3.8 5.1 - - - +
144C ASP* 2.9 41.1 + - - +
38D ASN* 3.8 6.7 + - - -
40D PHE* 3.5 33.4 - + - -
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Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLU* 2.9 44.0 + - + +
138C ASN* 3.3 17.7 - - + +
139C ILE 3.1 0.2 - - - -
140C HIS* 1.3 74.2 - - - +
142C GLN* 1.3 64.7 + - + +
144C ASP* 3.2 10.4 + - - +
145C LYS* 2.9 27.2 + - - +
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Residues in contact with GLN 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ARG 3.7 5.1 - - - +
123C VAL* 3.3 19.9 - - + +
124C ASN* 3.1 45.1 + - - +
134C GLN* 4.1 0.2 + - - -
138C ASN* 2.9 42.6 + - + +
139C ILE* 3.4 11.7 - - - +
141C GLN* 1.3 74.3 - - + +
143C ILE* 1.3 62.4 + - - +
145C LYS* 3.0 30.7 + - - +
146C ILE* 2.9 28.8 + - - +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 5.0 1.8 - - + -
29C VAL* 4.2 23.8 - - + -
32C ARG* 3.7 39.3 - - + +
33C ILE* 3.7 30.5 - - + -
36C LEU* 4.6 0.2 - - + -
123C VAL* 4.9 5.6 - - + -
139C ILE* 2.9 42.3 + - + +
140C HIS* 3.8 4.5 - - + +
142C GLN* 1.3 75.3 - - - +
144C ASP* 1.3 60.0 + - - +
146C ILE* 3.2 9.6 + - - +
147C ILE* 2.9 43.0 + - + +
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Residues in contact with ASP 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 4.8 2.5 + - - -
36C LEU* 3.8 24.6 - - - +
140C HIS* 2.9 31.3 + - - +
141C GLN* 3.2 10.6 + - - +
143C ILE* 1.3 77.2 - - - +
145C LYS* 1.3 56.9 + - - +
147C ILE* 3.3 8.6 + - - +
148C GLU* 2.9 29.3 + - - +
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Residues in contact with LYS 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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121C PHE* 5.5 5.1 - - - +
122C ARG 4.6 8.9 + - - -
141C GLN 2.9 14.0 + - - +
142C GLN* 3.0 48.7 + - - +
144C ASP* 1.3 76.3 - - - +
146C ILE* 1.3 67.4 + - - +
148C GLU* 3.4 15.8 + - - +
149C GLU* 2.9 30.8 + - - +
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 4.3 7.6 - - + -
71C ILE* 3.6 38.4 - - + -
121C PHE* 4.1 33.2 - - + -
122C ARG 4.6 4.3 - - - +
123C VAL* 3.6 30.5 - - + -
142C GLN 2.9 20.9 + - - +
143C ILE* 3.3 10.5 - - - +
145C LYS* 1.3 87.0 - - - +
147C ILE* 1.3 57.2 + - + +
149C GLU* 3.0 9.1 + - - +
150C ILE* 2.9 37.3 + - + +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 3.8 28.5 - - + +
36C LEU* 3.5 35.9 - - + +
37C LEU* 4.1 25.8 - - + +
143C ILE* 2.9 34.9 + - + +
144C ASP* 3.7 7.9 - - - +
146C ILE* 1.3 74.7 - - - +
148C GLU* 1.3 63.8 + - - +
150C ILE* 3.1 10.7 + - + +
151C LYS* 2.9 36.4 + - + +
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Residues in contact with GLU 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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144C ASP 2.9 17.2 + - - +
145C LYS* 3.6 14.9 - - - +
147C ILE* 1.3 77.5 - - - +
149C GLU* 1.3 58.4 + - - +
151C LYS* 3.3 8.1 + - - +
152C THR* 2.9 42.9 + - + +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 5.2 1.6 - - + -
119C LYS* 5.7 5.6 + - - +
121C PHE* 3.5 37.7 - - + -
145C LYS 2.9 15.1 + - - +
146C ILE 3.4 8.7 - - - +
148C GLU* 1.3 78.1 - - - +
150C ILE* 1.3 57.5 + - - +
152C THR* 2.5 25.8 + - - +
153C ALA* 2.9 17.2 + - - +
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Residues in contact with ILE 150 (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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33C ILE* 4.5 4.5 - - + -
37C LEU* 4.0 24.5 - - + -
42C LEU* 4.2 7.2 - - + -
64C PHE* 3.6 32.1 - - + -
67C LEU* 3.7 22.2 - - + +
69C ILE* 4.5 19.7 - - + -
71C ILE* 4.0 15.9 - - + -
121C PHE* 6.0 0.4 - - + -
146C ILE* 2.9 25.1 + - + +
147C ILE* 3.1 14.1 + - - +
149C GLU* 1.3 73.8 - - + +
151C LYS* 1.3 60.5 + - - +
153C ALA* 3.1 8.1 + - - +
154C LYS* 2.9 25.5 + - - +
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Residues in contact with LYS 151 (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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36C LEU 5.2 3.4 + - - -
37C LEU* 4.3 36.6 + - + +
39C ASP* 6.0 1.3 - - - +
42C LEU* 6.1 0.4 - - + -
147C ILE* 2.9 29.2 + - + +
148C GLU* 3.7 7.2 - - + +
150C ILE* 1.3 76.2 - - - +
152C THR* 1.3 58.1 + - + +
154C LYS* 3.3 9.8 + - + +
155C ASN* 2.8 40.5 + - - +
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Residues in contact with THR 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 GLU* 2.9 26.2 + - + +
149C GLU* 2.5 38.7 + - - +
151C LYS* 1.3 76.1 - - + +
153C ALA* 1.3 55.6 + - - +
155C ASN* 3.4 10.1 + - - +
156C LYS* 2.9 32.8 + - - +
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Residues in contact with ALA 153 (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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67C LEU* 4.4 8.7 - - + +
69C ILE* 3.7 23.8 - - + -
119C LYS* 4.6 10.5 - - - +
149C GLU* 2.9 14.1 + - + +
150C ILE 3.4 8.5 - - - +
152C THR* 1.3 75.3 + - - +
154C LYS* 1.3 64.4 + - - +
156C LYS* 3.0 15.5 + - + +
157C LEU* 3.0 30.7 + - + +
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 2.5 33.7 + - - +
41C THR* 3.3 11.4 + - - +
42C LEU* 4.0 19.7 - - + -
67C LEU* 3.9 18.7 - - + +
150C ILE 2.9 12.4 + - - +
151C LYS* 3.3 13.0 + - + +
153C ALA* 1.3 75.2 - - - +
155C ASN* 1.3 62.9 + - - +
157C LEU* 3.1 4.7 + - - +
158C ILE* 2.9 42.9 + - + +
163C PHE* 3.5 35.8 - - + -
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LYS* 2.8 30.3 + - - +
152C THR* 3.6 9.5 - - - +
154C LYS* 1.3 79.2 - - - +
156C LYS* 1.3 65.1 + - - +
158C ILE* 3.2 31.9 - - + +
159C GLU* 3.3 18.9 + - - +
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Residues in contact with LYS 156 (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 LYS* 5.8 4.2 - - - +
152C THR* 2.9 17.1 + - - +
153C ALA* 3.0 17.4 + - - +
155C ASN* 1.3 77.1 - - - +
157C LEU* 1.3 65.1 + - + +
159C GLU* 3.6 25.1 - - - +
160C ALA* 3.9 10.2 - - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLN* 3.3 26.2 - - + +
67C LEU* 3.9 16.4 - - + +
153C ALA* 3.0 27.0 + - + +
154C LYS* 3.1 8.5 + - - +
156C LYS* 1.3 86.7 - - + +
158C ILE* 1.3 63.1 + - - +
159C GLU 3.3 0.4 - - - -
160C ALA* 3.2 9.3 + - - +
162C THR* 3.2 44.5 + - + -
163C PHE* 3.5 21.9 + - + +
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Residues in contact with ILE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LYS* 2.9 30.6 + - + +
155C ASN* 3.2 31.4 - - + +
157C LEU* 1.3 76.4 - - - +
159C GLU* 1.3 68.8 + - + +
160C ALA 3.2 0.2 - - - -
161C SER* 3.4 14.1 + - - +
163C PHE* 3.5 34.8 - - + +
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Residues in contact with GLU 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ASN* 3.4 18.2 - - - +
156C LYS* 3.6 21.0 - - - +
158C ILE* 1.3 86.6 - - + +
160C ALA* 1.3 60.9 + - + +
161C SER* 3.2 6.5 + - - -
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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
------------------------------------------------------------
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