Contacts of the helix formed by residues 130 - 151 (chain A) in PDB entry 4WNF
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.3 20.6 - - + +
125A SER* 2.7 24.8 + - - +
128A LEU* 4.7 8.7 - - + +
129A ASN* 1.3 71.8 - - - +
131A LYS* 1.3 61.6 + - - +
132A VAL* 3.6 13.1 + - - +
133A GLY* 3.1 26.6 + - - -
134A GLU* 2.8 30.1 + - - +
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Residues in contact with LYS 131 (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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129A ASN* 3.8 29.3 + - - +
130A ASP* 1.3 72.6 + - - +
132A VAL* 1.3 66.1 + - - +
134A GLU* 3.4 20.6 + - - +
135A ALA* 2.9 26.5 + - - +
184A LEU* 4.0 20.2 - - + +
188A LEU* 4.1 17.7 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 3.6 10.5 - - - +
131A LYS* 1.3 80.5 - - + +
133A GLY* 1.3 64.2 + - - +
135A ALA* 3.3 3.1 + - - +
136A ARG* 3.1 41.2 + - + +
188A LEU* 4.1 24.8 - - + +
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Residues in contact with GLY 133 (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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121A HIS* 3.6 11.8 + - - -
125A SER* 3.8 11.4 + - - -
130A ASP* 3.1 23.1 + - - -
131A LYS 3.4 0.2 - - - -
132A VAL* 1.3 77.2 - - - +
134A GLU* 1.3 65.1 + - - +
136A ARG* 3.4 8.2 + - - +
137A ALA* 3.1 24.1 + - - +
1003B GLU* 5.1 2.5 - - - -
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Residues in contact with GLU 134 (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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122A LEU* 3.6 18.2 - - + +
125A SER* 3.6 14.3 - - - -
126A ARG* 3.0 39.9 + - + +
129A ASN* 6.2 0.5 - - - -
130A ASP 2.8 19.0 + - - +
131A LYS* 3.2 25.5 + - - +
133A GLY* 1.3 78.7 - - - +
135A ALA* 1.3 62.2 + - - +
137A ALA* 3.5 2.9 + - - +
138A LEU* 3.2 29.3 + - + +
184A LEU* 4.4 15.2 - - + +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS 2.9 15.5 + - - +
132A VAL 3.7 4.3 - - - +
133A GLY 3.3 0.2 - - - -
134A GLU* 1.3 75.5 - - - +
136A ARG* 1.3 65.8 + - + +
138A LEU* 2.9 20.9 + - - +
139A TYR 3.0 3.6 + - - -
181A ASN* 3.0 32.6 + - - +
184A LEU* 3.8 20.2 - - + -
185A VAL* 3.8 12.6 - - + -
188A LEU* 4.7 4.5 - - + -
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Residues in contact with ARG 136 (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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96A LYS* 6.1 0.8 - - - +
121A HIS* 4.5 0.4 - - + -
132A VAL* 3.1 32.8 - - + +
133A GLY* 3.7 5.6 - - - +
135A ALA* 1.3 76.1 - - + +
137A ALA* 1.3 51.7 + - - +
139A TYR* 3.0 9.9 + - - +
140A ASN* 2.7 40.7 + - - +
181A ASN* 4.9 0.4 - - - +
196A ARG* 4.8 10.2 - - - +
1001B THR* 3.7 35.3 - - - +
1002B MET 4.3 8.7 + - - -
1003B GLU* 2.9 46.1 + - - +
1004B THR* 5.2 4.9 + - - +
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Residues in contact with ALA 137 (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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118A CYS* 4.3 3.1 - - - +
121A HIS* 3.5 28.0 - - + +
122A LEU* 3.7 31.4 - - + +
133A GLY 3.1 13.3 + - - +
134A GLU 3.7 5.6 - - - +
136A ARG* 1.3 78.3 - - - +
138A LEU* 1.3 57.3 + - - +
140A ASN* 3.2 4.6 + - - +
141A LEU* 2.8 37.6 + - - +
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Residues in contact with LEU 138 (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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122A LEU* 3.9 21.1 - - + -
126A ARG* 4.1 2.0 - - - +
134A GLU* 3.2 31.4 + - + +
135A ALA* 2.9 15.8 + - - +
137A ALA* 1.3 78.0 - - - +
139A TYR* 1.3 54.3 + - - +
141A LEU* 3.8 2.6 - - - +
142A GLY* 3.1 21.1 + - - -
177A PHE* 3.2 38.1 - - + +
180A GLU* 3.5 43.1 - - + +
181A ASN* 4.0 19.3 - - + +
184A LEU* 4.5 7.9 - - + -
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Residues in contact with TYR 139 (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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135A ALA 3.0 10.6 + - - +
136A ARG* 3.4 8.5 - - - +
138A LEU* 1.3 74.5 - - - +
140A ASN* 1.3 66.2 + - - +
142A GLY* 3.1 3.3 + - - -
143A ASN* 3.0 48.4 + - - +
178A TYR* 3.7 19.3 - + - -
181A ASN* 4.2 15.6 - - - +
193A ALA 5.6 0.4 - - - -
196A ARG* 3.5 28.5 - - + +
197A ALA* 3.8 25.8 - - + -
200A ASN* 3.1 25.2 + - - -
998B GLU* 3.5 3.8 - - - +
999B PRO 3.0 26.3 + - - -
1001B THR* 3.9 28.3 - - + -
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Residues in contact with ASN 140 (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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99A GLY* 4.7 4.0 - - - -
103A ASN* 3.2 38.5 + - - +
106A LYS* 5.2 0.2 - - - +
118A CYS* 4.2 9.6 - - + -
121A HIS* 3.9 17.2 + - - -
136A ARG 2.7 21.3 + - - +
137A ALA* 3.5 5.8 - - - +
139A TYR* 1.3 76.3 - - - +
141A LEU* 1.3 62.8 + - - +
143A ASN* 3.2 18.6 + - - +
144A VAL* 3.1 21.2 + - - +
1001B THR* 3.1 19.9 + - - +
1003B GLU* 3.8 18.4 + - - -
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Residues in contact with LEU 141 (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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115A ILE* 3.9 13.9 - - + +
118A CYS* 3.3 33.4 - - + +
119A GLN* 3.8 18.4 - - + +
122A LEU* 3.7 30.3 - - + -
137A ALA 2.8 23.4 + - - +
138A LEU 3.8 3.8 - - - +
140A ASN* 1.3 73.1 - - - +
142A GLY* 1.3 69.1 + - - +
144A VAL* 3.0 16.0 + - + +
145A TYR* 3.1 32.2 + - + -
177A PHE* 3.9 26.7 - - + -
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Residues in contact with GLY 142 (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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138A LEU 3.1 9.0 + - - -
139A TYR 3.1 8.1 + - - -
141A LEU* 1.3 76.5 - - - +
143A ASN* 1.3 55.9 + - - +
146A HIS* 2.9 25.6 + - - +
174A ALA* 3.3 17.6 - - - +
177A PHE* 3.7 18.2 - - - +
178A TYR* 3.4 18.8 - - - -
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Residues in contact with ASN 143 (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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103A ASN* 5.6 0.8 + - - +
106A LYS* 3.8 26.1 - - + +
139A TYR* 3.0 38.3 + - - +
140A ASN* 3.5 13.6 + - - +
141A LEU 3.2 0.4 - - - -
142A GLY* 1.3 75.0 - - - +
144A VAL* 1.3 53.9 + - - +
146A HIS* 3.4 6.1 - - - +
147A ALA* 2.7 35.2 + - - +
178A TYR* 2.7 30.6 + - - -
200A ASN* 3.1 17.4 + - - +
997B MET* 6.0 2.0 - - + -
998B GLU 5.7 0.4 + - - -
999B PRO 5.6 0.2 - - - -
1000B GLU* 4.4 10.1 - - - +
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Residues in contact with VAL 144 (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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103A ASN* 5.3 1.1 - - - +
106A LYS* 4.0 25.8 - - + -
111A PHE* 3.9 21.4 - - + +
114A ALA* 4.2 8.7 - - + -
115A ILE* 3.5 33.0 - - + -
118A CYS* 4.0 22.2 - - + -
140A ASN 3.1 17.3 - - - +
141A LEU* 3.0 7.4 + - - +
143A ASN* 1.3 71.7 - - - +
145A TYR* 1.3 56.6 + - + +
146A HIS 3.0 0.9 - - - -
147A ALA* 3.0 3.3 + - - +
148A LYS* 2.7 35.0 + - - +
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Residues in contact with TYR 145 (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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115A ILE* 3.5 46.8 - - + +
141A LEU* 3.1 23.5 + - + +
142A GLY 4.0 0.7 - - - +
144A VAL* 1.3 80.0 - - + +
146A HIS* 1.3 64.0 + - - +
148A LYS* 3.8 12.4 - - + +
149A GLY* 3.1 15.9 + - - -
170A ALA* 3.2 43.3 - - + +
171A LEU* 4.3 0.2 - - - +
173A ALA* 3.9 14.1 - - + -
174A ALA 3.9 9.4 - - - +
177A PHE* 3.5 30.7 - + - -
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Residues in contact with HIS 146 (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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142A GLY 2.9 19.0 + - - +
143A ASN 3.4 7.0 - - - +
145A TYR* 1.3 72.9 - - - +
147A ALA* 1.3 69.9 + - - +
149A GLY* 3.1 4.2 + - - -
150A LYS* 2.8 45.7 + - - +
171A LEU* 3.9 6.2 - - - +
174A ALA* 3.9 10.2 - - + +
178A TYR* 4.0 7.9 - - - +
200A ASN 4.7 0.7 - - - -
203A ASN* 4.2 7.2 - - + -
204A THR* 3.1 36.9 + - - +
207A LEU* 3.8 26.1 - - + +
995B MET* 4.2 0.8 - - - -
997B MET* 3.1 36.8 - - + +
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Residues in contact with ALA 147 (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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106A LYS* 4.1 15.5 - - + +
111A PHE* 3.7 20.7 - - + -
143A ASN 2.7 21.3 + - - +
144A VAL 3.5 3.8 - - - +
146A HIS* 1.3 79.1 - - + +
148A LYS* 1.3 62.7 + - - +
150A LYS* 3.2 15.3 + - - +
151A SER* 2.9 26.0 + - - -
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Residues in contact with LYS 148 (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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111A PHE* 3.6 38.1 - - + -
112A ASP* 4.1 14.6 - - - +
115A ILE* 4.4 15.2 - - + +
144A VAL* 2.7 19.0 + - + +
145A TYR* 3.8 13.2 - - + +
147A ALA* 1.3 71.4 - - - +
149A GLY* 1.3 66.2 + - - +
151A SER* 3.0 19.9 + - - -
152A PHE* 3.9 2.9 + - - +
166A GLU* 4.8 7.1 + - - +
170A ALA* 4.5 17.9 - - + +
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Residues in contact with GLY 149 (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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145A TYR 3.1 8.2 + - - -
146A HIS 3.1 5.4 + - - -
148A LYS* 1.3 80.5 - - - +
150A LYS* 1.3 61.9 + - - +
151A SER 3.4 0.3 + - - -
152A PHE* 3.5 10.7 + - - +
167A VAL* 3.4 32.1 - - - +
170A ALA* 4.2 9.4 - - - +
171A LEU* 4.1 14.3 - - - +
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Residues in contact with LYS 150 (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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146A HIS* 2.8 44.4 + - - +
147A ALA* 3.4 14.2 - - - +
149A GLY* 1.3 77.4 - - - +
151A SER* 1.3 60.3 + - - +
152A PHE 3.1 13.7 + - - +
153A GLY 5.1 0.5 - - - +
154A CYS 5.0 6.1 - - - -
155A PRO* 5.1 16.6 - - + +
171A LEU* 4.3 0.8 - - - +
207A LEU* 4.0 28.3 - - + -
995B MET* 4.4 14.8 - - + -
997B MET* 4.3 13.7 - - - +
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Residues in contact with SER 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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111A PHE* 3.3 24.8 - - - -
147A ALA 2.9 12.8 + - - -
148A LYS 3.0 14.5 + - - -
150A LYS* 1.3 75.0 - - - +
152A PHE* 1.3 59.7 + - - +
153A GLY 3.9 4.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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