Contacts of the helix formed by residues 140 - 162 (chain A) in PDB entry 4HYJ
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 THR 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A SER* 2.5 32.6 + - - +
133A ILE* 4.2 2.5 + - - +
136A ALA* 3.5 28.5 - - + -
138A GLY 3.4 4.6 + - - +
139A PHE* 1.3 94.7 - - - +
141A GLN* 1.3 61.8 + - - +
142A LEU* 4.1 3.8 - - - -
143A GLY* 2.7 24.1 + - - -
144A LEU 3.1 8.3 + - - -
202A LEU* 4.0 3.1 - - - +
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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
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139A PHE* 3.6 16.7 - - + -
140A THR* 1.3 69.3 - - - +
142A LEU* 1.3 58.7 + - + +
143A GLY 3.1 1.6 - - - -
144A LEU* 2.8 20.9 + - - +
145A TRP* 2.8 55.6 + - + +
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Residues in contact with LEU 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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128A ILE* 3.8 22.2 - - + +
132A SER* 3.8 27.1 - - - +
140A THR* 4.1 2.0 - - - +
141A GLN* 1.3 80.3 - - - +
143A GLY* 1.3 62.3 + - - +
145A TRP* 4.3 8.1 - - + -
146A SER* 2.9 46.7 + - - +
311A LFA 4.3 13.5 - - + -
113B THR* 6.0 2.7 - - + -
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Residues in contact with GLY 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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129A GLY* 4.0 13.7 - - - -
132A SER* 4.0 0.4 + - - -
133A ILE* 4.1 7.0 - - - -
140A THR* 2.7 27.0 + - - -
141A GLN 3.1 0.2 - - - -
142A LEU* 1.3 74.5 - - - +
144A LEU* 1.3 57.7 + - - +
147A TYR* 3.4 11.4 + - - +
198A TYR* 2.7 31.7 + - - -
202A LEU* 4.0 6.2 - - - +
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Residues in contact with LEU 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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139A PHE* 3.9 32.1 - - + -
140A THR 3.1 3.4 + - - -
141A GLN* 2.8 15.7 + - + +
143A GLY* 1.3 72.1 - - - +
145A TRP* 1.3 95.5 + - + +
147A TYR* 3.3 8.9 - - + +
148A LEU* 3.2 43.0 + - + +
202A LEU* 4.1 19.1 - - + -
203A PHE* 4.7 9.4 - - + -
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Residues in contact with TRP 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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141A GLN* 2.8 64.7 + - + +
142A LEU* 4.1 8.7 - - + +
144A LEU* 1.3 91.5 - - + +
146A SER* 1.3 66.2 + - - +
148A LEU* 3.1 28.8 + - + +
149A ILE* 3.0 35.3 + - + +
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Residues in contact with SER 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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125A GLY* 3.3 31.3 - - - -
128A ILE* 3.8 6.2 - - - +
129A GLY* 3.6 18.8 + - - -
142A LEU* 2.9 37.8 + - - +
145A TRP* 1.3 75.8 - - - +
147A TYR* 1.3 52.9 + - - +
149A ILE* 3.4 7.0 + - - +
150A GLY* 2.8 31.5 + - - -
198A TYR* 4.5 0.2 - - - -
311A LFA 4.3 12.7 - - - +
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Residues in contact with TYR 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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143A GLY 3.4 14.9 + - - +
144A LEU* 3.3 13.9 + - + +
146A SER* 1.3 79.5 - - - +
148A LEU* 1.3 68.4 + - + +
150A GLY* 3.0 2.9 + - - -
151A CYS* 2.7 58.4 + - - -
195A PRO* 2.6 44.1 + - + +
196A ILE* 4.6 0.3 - - - -
198A TYR* 3.2 36.0 + + + -
199A ALA* 3.7 18.8 - - + +
202A LEU* 4.8 9.2 - - + -
203A PHE* 6.2 1.3 - + - -
301A RET 3.6 15.6 - - + +
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Residues in contact with LEU 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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144A LEU* 3.2 21.9 + - + +
145A TRP* 3.1 39.1 + - + +
147A TYR* 1.3 96.2 - - + +
149A ILE* 1.3 59.8 + - + +
151A CYS* 3.2 10.2 + - + +
152A PHE* 2.9 28.8 + - - +
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Residues in contact with ILE 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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121A ILE* 3.8 24.2 - - + +
145A TRP* 3.0 22.7 + - + +
146A SER* 3.6 7.4 - - - +
148A LEU* 1.3 76.3 - - + +
150A GLY* 1.3 63.6 + - - +
152A PHE* 3.1 10.5 + - - +
153A ALA* 3.0 21.5 + - - +
306A LFA 3.8 18.1 - - + +
311A LFA 4.1 31.2 - - + -
317B LFA 6.5 0.2 - - + -
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Residues in contact with GLY 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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121A ILE 4.7 2.0 - - - -
122A MET* 3.5 26.9 - - - +
125A GLY* 5.3 0.4 - - - -
146A SER 2.8 15.3 + - - -
147A TYR 3.4 4.3 - - - -
149A ILE* 1.3 78.2 - - - +
151A CYS* 1.3 55.4 + - - +
153A ALA* 3.3 5.1 + - - +
154A TRP* 2.9 23.2 + - - +
301A RET 3.5 18.4 - - - -
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Residues in contact with CYS 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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147A TYR* 2.7 52.0 + - - -
148A LEU* 3.5 14.1 - - + +
150A GLY* 1.3 69.8 - - - +
152A PHE* 1.3 57.2 + - - +
154A TRP* 3.2 13.9 + - + +
155A ILE* 2.8 48.3 + - + +
195A PRO* 4.4 4.5 - - - -
301A RET 3.5 15.2 - - - +
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Residues in contact with PHE 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 LEU 2.9 12.8 + - - +
149A ILE* 3.1 12.8 + - - +
151A CYS* 1.3 73.3 - - - +
153A ALA* 1.3 65.1 + - - +
155A ILE* 3.2 11.4 + - + +
156A TYR* 2.9 28.0 + + + +
306A LFA 3.6 33.2 - - + -
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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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118A ALA* 3.2 30.2 - - - +
121A ILE* 4.0 11.2 - - + -
122A MET* 3.7 11.4 - - + +
149A ILE 3.0 12.2 + - - +
150A GLY 3.4 8.7 - - - +
152A PHE* 1.3 73.8 - - - +
154A TRP* 1.3 63.9 + - - +
156A TYR* 3.1 5.5 + - - +
157A ILE* 2.9 26.7 + - - +
306A LFA 3.8 15.9 - - + +
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Residues in contact with TRP 154 (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 MET* 3.6 26.1 - - - -
150A GLY 2.9 14.0 + - - +
151A CYS* 3.3 19.7 - - + +
153A ALA* 1.3 75.9 - - - +
155A ILE* 1.3 73.1 + - + +
157A ILE* 3.1 11.2 + - + +
158A ILE* 3.0 36.3 + - + +
187A ILE* 3.1 21.7 + - + -
188A LEU* 3.7 16.4 - - + -
191A TRP* 3.9 19.6 - + + +
192A ALA* 3.6 40.8 - - + -
195A PRO* 3.9 11.9 - - + -
301A RET 3.6 20.6 - - + -
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Residues in contact with ILE 155 (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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151A CYS* 2.8 35.6 + - + +
152A PHE* 3.7 8.7 - - + +
154A TRP* 1.3 85.3 - - + +
156A TYR* 1.3 62.8 + - - +
158A ILE* 3.2 15.3 + - + +
159A TYR* 2.9 24.2 + - + +
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Residues in contact with TYR 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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114A LYS* 3.6 29.9 - - - +
118A ALA* 3.6 19.1 - - + -
152A PHE* 2.9 20.9 + + + +
153A ALA* 3.2 11.7 - - - +
155A ILE* 1.3 75.9 - - - +
157A ILE* 1.3 61.8 + - - +
159A TYR* 3.2 21.7 + + - +
160A LEU* 3.1 53.6 + - + +
306A LFA 3.4 51.9 - - + +
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Residues in contact with ILE 157 (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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94A LEU* 4.1 23.8 - - + -
115A LEU* 4.1 20.6 - - + +
118A ALA* 3.6 14.6 - - + -
119A ASP* 3.8 37.9 - - + +
122A MET* 4.4 8.3 - - + -
153A ALA 2.9 18.2 + - - +
154A TRP* 3.1 16.1 + - + +
156A TYR* 1.3 79.1 - - - +
158A ILE* 1.3 62.9 + - - +
160A LEU* 3.1 6.5 + - - +
161A LEU* 3.1 22.7 + - + +
187A ILE* 3.9 22.7 - - + -
191A TRP* 4.9 3.8 - - + -
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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
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154A TRP* 3.0 49.3 + - + +
155A ILE* 3.2 17.7 + - + +
157A ILE* 1.3 76.7 - - - +
159A TYR* 1.3 56.8 + - - +
161A LEU* 3.2 6.6 + - - -
162A PHE* 2.9 56.0 + - + +
187A ILE* 4.0 21.3 - - + +
188A LEU* 4.1 24.2 - - + -
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Residues in contact with TYR 159 (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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155A ILE* 2.9 14.2 + - + +
156A TYR* 3.3 27.4 - + - +
157A ILE 3.2 0.2 - - - -
158A ILE* 1.3 78.7 - - - +
160A LEU* 1.3 75.5 + - + +
162A PHE* 3.4 2.1 + - - -
163A THR* 2.6 65.2 + - + +
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Residues in contact with LEU 160 (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 LEU* 4.3 11.7 - - + -
114A LYS* 3.6 26.9 - - + -
115A LEU* 3.6 30.3 - - + +
156A TYR* 3.1 50.7 + - + +
157A ILE* 3.1 6.5 + - - +
159A TYR* 1.3 92.7 - - + +
161A LEU* 1.3 59.7 + - - +
163A THR* 3.8 3.1 - - - +
164A ASN* 2.9 36.2 + - + +
165A VAL* 2.9 10.8 + - - -
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Residues in contact with LEU 161 (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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94A LEU* 4.9 0.7 - - + -
97A PHE* 3.7 40.6 - - + -
115A LEU* 4.2 16.8 - - + -
157A ILE* 3.1 17.0 + - + +
158A ILE* 3.2 7.2 + - - +
160A LEU* 1.3 76.1 - - - +
162A PHE* 1.3 56.3 + - + +
163A THR 3.2 0.2 - - - -
165A VAL* 3.3 25.7 - - + +
166A THR* 2.8 34.8 + - - -
184A ARG* 3.6 21.7 - - + +
187A ILE* 3.6 39.3 - - + -
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Residues in contact with PHE 162 (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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158A ILE* 2.9 49.2 + - + +
159A TYR* 4.4 2.2 - - - +
161A LEU* 1.3 78.2 - - + +
163A THR* 1.3 65.6 + - + +
166A THR* 3.3 19.0 + - - +
184A ARG* 3.2 67.2 + - + -
185A LEU* 4.3 9.0 - - + -
187A ILE* 6.4 0.2 - - + -
188A LEU* 3.9 31.9 - - + -
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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