Contacts of the helix formed by residues 135 - 160 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 5.4 3.6 - - - +
134A GLN* 1.3 86.1 - - - +
136A LEU* 1.3 64.9 + - - +
137A GLU* 3.7 10.3 + - + +
138A ASN* 3.0 33.5 + - - +
139A ILE* 3.4 10.3 + - - +
6B SER* 3.7 28.9 - - - +
7B SER 5.2 0.4 - - - +
10B THR* 3.7 2.7 - - - -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.8 29.4 - - + +
135A ASN* 1.3 72.5 - - - +
137A GLU* 1.3 57.1 + - - +
139A ILE* 3.4 10.2 + - + +
140A HIS* 2.9 47.4 + - + +
6B SER* 5.1 1.8 + - - -
9B LEU* 3.8 34.9 - - + +
10B THR* 3.3 33.1 + - + +
13B VAL* 3.8 20.2 - - + -
14B ILE* 5.5 2.0 - - + -
40B PHE* 4.3 18.8 - - + -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 3.1 10.8 + - + +
136A LEU* 1.3 79.0 - - - +
138A ASN* 1.3 57.8 + - - +
140A HIS* 3.4 8.7 + - - +
141A GLN* 2.9 54.8 + - + +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 2.8 33.2 - - - +
135A ASN* 3.0 24.4 + - - +
137A GLU* 1.3 74.9 - - - +
139A ILE* 1.3 65.3 + - - +
141A GLN* 3.0 20.1 + - - +
142A GLN* 2.4 58.1 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.5 14.1 - - + -
28A TYR* 4.7 9.0 - - + -
29A VAL* 4.7 7.6 - - + -
123A VAL* 4.4 10.8 - - + -
124A ASN 4.5 11.7 - - - +
125A VAL* 4.1 33.2 - - + +
134A GLN* 4.7 8.1 - - + +
135A ASN 3.4 11.4 + - - +
136A LEU* 3.4 13.4 + - + +
138A ASN* 1.3 77.3 + - - +
140A HIS* 1.3 69.1 + - + +
142A GLN* 3.2 10.8 + - - +
143A ILE* 2.9 38.8 + - + +
10B THR* 4.7 12.3 - - + -
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.8 30.6 + + - -
32A ARG* 3.3 43.7 + - - +
136A LEU* 2.9 34.7 + - + +
137A GLU* 3.5 8.0 - - - +
139A ILE* 1.3 79.7 - - + +
141A GLN* 1.3 56.7 + - + +
143A ILE* 3.3 3.9 + - - +
144A ASP* 2.9 39.2 + - - +
38B ASN* 4.2 2.6 + - - -
40B PHE* 3.4 34.5 - + - -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 2.9 45.0 + - + +
138A ASN* 3.0 21.0 + - - +
140A HIS* 1.3 73.2 - - + +
142A GLN* 1.3 66.4 + - + +
144A ASP* 3.0 12.0 + - - +
145A LYS* 3.0 25.8 + - - +
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG 4.1 2.8 - - - +
123A VAL* 3.4 18.2 - - + -
124A ASN* 2.9 53.0 + - - +
134A GLN* 3.7 1.0 + - - -
138A ASN* 2.4 47.1 + - - +
139A ILE* 3.4 9.5 - - - +
141A GLN* 1.3 74.7 - - + +
143A ILE* 1.3 61.5 + - - +
145A LYS* 2.9 50.0 + - - +
146A ILE* 3.0 10.9 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 5.1 1.1 - - + -
29A VAL* 4.1 32.5 - - + +
32A ARG* 4.1 28.0 - - + +
33A ILE* 3.5 33.4 - - + +
123A VAL* 4.7 6.3 - - + -
139A ILE* 2.9 36.0 + - + +
140A HIS* 3.6 7.2 - - - +
142A GLN* 1.3 75.3 - - - +
144A ASP* 1.3 61.7 + - - +
146A ILE* 3.2 8.8 + - - +
147A ILE* 2.9 42.1 + - + +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 4.6 2.8 + - - -
36A LEU* 3.8 24.4 - - - +
140A HIS* 2.9 28.5 + - - +
141A GLN* 3.0 13.2 + - - +
143A ILE* 1.3 76.1 - - - +
145A LYS* 1.3 62.6 + - - +
147A ILE* 3.2 12.1 + - - +
148A GLU* 3.0 25.4 + - - +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 5.6 4.0 - - - -
122A ARG 4.3 10.7 + - - -
141A GLN 3.0 12.8 + - - +
142A GLN* 2.9 47.1 + - - +
144A ASP* 1.3 74.9 - - - +
146A ILE* 1.3 75.5 + - + +
148A GLU* 3.1 9.5 + - - +
149A GLU* 2.9 27.6 + - + +
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.2 10.8 - - + -
71A ILE* 3.7 35.4 - - + -
121A PHE* 3.7 34.5 - - + -
122A ARG 4.2 5.6 - - - +
123A VAL* 3.7 30.7 - - + -
142A GLN 3.0 17.3 + - - +
143A ILE* 3.4 10.1 - - - +
145A LYS* 1.3 85.8 - - - +
147A ILE* 1.3 57.6 + - - +
149A GLU* 3.1 10.4 + - - +
150A ILE* 2.9 35.5 + - + +
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.2 19.7 - - + +
36A LEU* 3.5 38.1 - - + +
37A LEU* 4.3 17.0 - - + +
143A ILE* 2.9 38.2 + - + +
144A ASP* 3.2 11.6 + - - +
146A ILE* 1.3 74.5 - - - +
148A GLU* 1.3 59.7 + - + +
150A ILE* 3.3 10.6 + - - +
151A LYS* 2.9 51.2 + - + +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP 3.0 15.8 + - - +
145A LYS* 3.1 11.6 + - - +
147A ILE* 1.3 78.7 - - + +
149A GLU* 1.3 57.2 + - + +
151A LYS* 3.3 20.4 + - - +
152A THR* 2.9 35.0 + - - +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.5 3.2 - - + +
121A PHE* 3.6 41.0 - - + -
145A LYS* 2.9 18.1 + - + +
146A ILE* 3.1 9.4 + - - +
148A GLU* 1.3 75.6 - - + +
150A ILE* 1.3 57.7 + - - +
152A THR* 3.2 17.3 - - - +
153A ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.3 7.2 - - + -
37A LEU* 4.0 15.9 - - + -
42A LEU* 3.6 30.3 - - + -
64A PHE* 3.4 35.7 - - + -
67A LEU* 3.3 17.0 - - + +
69A ILE* 4.4 16.2 - - + -
71A ILE* 4.2 3.1 - - + -
121A PHE* 5.9 0.4 - - + -
146A ILE* 2.9 34.9 + - + +
147A ILE* 3.4 11.0 - - - +
149A GLU* 1.3 76.6 - - + +
151A LYS* 1.3 57.8 + - - +
153A ALA 3.3 1.2 + - - -
154A LYS* 2.9 25.8 + - - +
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 5.1 4.8 + - - -
37A LEU* 4.2 27.9 + - + +
39A ASP* 6.3 0.2 - - - -
42A LEU* 6.2 0.2 - - - -
147A ILE* 2.9 35.1 + - + +
148A GLU* 3.3 24.5 + - - +
150A ILE* 1.3 76.3 - - - +
152A THR* 1.3 58.9 + - - +
154A LYS* 3.3 11.8 + - + +
155A ASN* 2.9 37.5 + - - +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 2.9 20.1 + - - +
149A GLU* 3.2 28.3 - - - +
151A LYS* 1.3 74.1 - - - +
153A ALA* 1.3 65.4 + - + +
155A ASN* 3.6 10.5 - - - +
156A LYS* 2.9 37.3 + - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.8 18.4 - - + +
69A ILE* 4.1 13.0 - - + -
149A GLU 2.9 18.4 + - - +
150A ILE 3.3 4.2 + - - +
152A THR* 1.3 76.6 - - + +
154A LYS* 1.3 65.5 + - - +
156A LYS* 3.1 22.7 - - + +
157A LEU* 3.0 28.0 + - + +
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 2.4 35.2 + - - +
41A THR* 3.5 15.6 + - - +
42A LEU* 3.6 22.0 - - + -
67A LEU* 3.9 11.1 - - + +
150A ILE 2.9 14.7 + - - +
151A LYS* 3.4 13.9 - - + +
153A ALA* 1.3 75.4 - - - +
155A ASN* 1.3 62.1 + - - +
157A LEU* 3.3 6.6 + - - +
158A ILE* 2.9 41.1 + - + +
163A PHE* 3.9 23.3 - - + -
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 2.9 30.5 + - - +
152A THR* 3.6 9.9 - - - +
154A LYS* 1.3 77.6 - - - +
156A LYS* 1.3 65.8 + - - +
157A LEU 3.0 1.8 - - - -
158A ILE* 3.1 19.1 - - + +
159A GLU* 2.9 32.7 + - - +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 2.9 19.0 + - - +
153A ALA* 3.1 31.4 + - + +
155A ASN* 1.3 76.0 - - - +
157A LEU* 1.3 71.5 + - + +
159A GLU* 3.5 21.9 - - - +
160A ALA* 3.4 19.6 - - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 3.5 28.0 - - + +
67A LEU* 4.6 11.2 - - + -
153A ALA* 3.0 22.6 + - + +
154A LYS* 3.6 5.8 - - - +
155A ASN 3.0 0.2 - - - -
156A LYS* 1.3 92.0 - - + +
158A ILE* 1.3 64.6 + - - +
159A GLU 3.2 0.2 - - - -
160A ALA 3.3 1.4 + - - -
161A SER 3.2 3.3 + - - -
162A THR* 3.1 45.1 + - - +
163A PHE* 3.5 24.8 + - + -
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 2.9 32.3 + - + +
155A ASN* 3.1 30.7 - - + +
157A LEU* 1.3 75.7 - - - +
159A GLU* 1.3 74.4 + - + +
161A SER* 3.0 20.7 + - - +
163A PHE* 3.5 37.2 - - + +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN* 2.9 22.2 + - - +
156A LYS* 3.5 20.2 - - - +
158A ILE* 1.3 83.0 - - + +
160A ALA* 1.3 63.2 + - + +
161A SER* 3.1 10.8 + - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LYS 3.4 16.2 - - - +
157A LEU* 3.3 5.5 + - - +
158A ILE 3.2 0.4 - - - -
159A GLU* 1.3 80.3 - - + +
161A SER* 1.3 70.0 + - - +
162A THR* 3.1 21.7 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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