Contacts of the helix formed by residues 131 - 154 (chain A) in PDB entry 4L8E
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 VAL 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.0 32.1 - - + +
126A TYR* 3.5 52.5 - - + -
127A ALA 3.9 4.9 - - - +
128A PRO* 3.3 6.2 + - + +
130A VAL* 1.3 85.9 - - + +
132A PRO* 1.3 64.9 - - - +
133A TYR 3.3 2.0 - - - -
134A ALA* 3.2 7.0 + - + +
135A ILE* 3.0 28.4 + - + +
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Residues in contact with PRO 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO 3.4 10.7 - - - +
129A GLU* 3.6 14.4 - - - +
130A VAL 3.4 8.1 - - - +
131A VAL* 1.3 90.1 - - - +
133A TYR* 1.3 74.5 + - + +
135A ILE* 3.4 6.6 - - + +
136A LYS* 3.2 25.5 + - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL 3.3 0.6 - - - -
132A PRO* 1.3 91.3 - - + +
134A ALA* 1.3 58.9 + - - +
136A LYS* 3.8 10.0 - - + +
137A ARG* 3.0 30.5 + - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.5 44.4 - - + -
131A VAL* 3.2 10.6 + - + +
133A TYR* 1.3 76.2 - - - +
135A ILE* 1.3 67.4 + - - +
137A ARG* 3.3 4.6 + - - +
138A TYR* 3.0 36.8 + - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 4.8 15.4 - - + +
124A ASN* 4.2 19.3 - - - +
126A TYR 6.1 0.2 - - - +
128A PRO* 4.0 33.7 - - + +
131A VAL* 3.0 27.2 + - + +
132A PRO* 3.4 14.1 - - + +
134A ALA* 1.3 76.9 - - - +
136A LYS* 1.3 59.0 + - - +
138A TYR* 4.6 2.0 - - - +
139A THR* 2.7 48.9 + - - +
182A LYS* 5.4 8.3 - - + -
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO 3.2 19.0 + - - +
133A TYR* 3.8 10.1 - - + +
135A ILE* 1.3 79.0 - - - +
137A ARG* 1.3 63.8 + - - +
139A THR* 3.8 4.3 - - - -
140A GLU* 3.0 53.9 + - + +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 5.7 4.6 - - - -
133A TYR 3.0 18.1 + - - +
134A ALA* 3.6 5.8 - - - +
136A LYS* 1.3 77.7 - - - +
138A TYR* 1.3 97.6 + - + +
140A GLU* 3.4 6.5 + - - +
141A GLU* 2.9 29.6 + - + +
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Residues in contact with TYR 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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116A MET* 3.9 30.9 - - + +
119A GLN* 3.7 26.2 - - + +
120A ASN* 4.0 24.0 - - + +
123A PHE* 3.7 34.8 - + + -
134A ALA* 3.0 30.9 + - + +
135A ILE* 4.6 1.6 - - - +
137A ARG* 1.3 108.7 + - + +
139A THR* 1.3 56.1 + - - +
141A GLU* 4.0 6.5 - - + +
142A SER* 2.6 39.0 + - - -
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASN* 4.4 12.5 + - - +
135A ILE* 2.7 38.0 + - - +
136A LYS* 3.8 4.9 - - - -
138A TYR* 1.3 77.4 - - - +
140A GLU* 1.3 65.3 + - + +
142A SER* 3.2 4.2 + - - -
143A GLN* 3.0 42.6 + - + +
181A GLN 5.7 3.9 + - - +
182A LYS* 5.8 9.4 - - + +
183A ILE* 5.1 0.8 - - + +
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Residues in contact with GLU 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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136A LYS* 3.0 58.3 + - + +
137A ARG* 3.9 4.9 - - - +
139A THR* 1.3 77.8 - - + +
141A GLU* 1.3 57.9 + - - +
143A GLN* 3.3 18.0 + - - +
144A ARG* 3.0 25.6 + - - +
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Residues in contact with GLU 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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112A GLY* 5.8 0.5 - - - -
116A MET* 3.7 37.2 - - + +
137A ARG* 2.9 19.6 + - + +
138A TYR* 4.0 9.6 - - + +
140A GLU* 1.3 73.2 - - - +
142A SER* 1.3 67.5 + - - +
144A ARG* 2.8 46.4 + - - +
145A LEU* 3.0 33.5 + - + +
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Residues in contact with SER 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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116A MET 4.6 1.4 + - - -
117A LEU* 3.2 29.5 + - - +
120A ASN* 2.9 26.8 + - - +
138A TYR 2.6 24.5 + - - -
139A THR* 3.2 5.8 + - - -
141A GLU* 1.3 74.9 - - - +
143A GLN* 1.3 62.0 + - - +
145A LEU* 3.3 5.9 + - - +
146A TYR* 3.0 28.9 + - - -
183A ILE* 4.1 14.8 - - - -
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Residues in contact with GLN 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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139A THR* 3.0 30.6 + - + +
140A GLU* 3.5 21.9 - - - +
141A GLU 3.2 0.2 - - - -
142A SER* 1.3 75.9 - - - +
144A ARG* 1.3 62.8 + - - +
146A TYR 3.4 0.9 + - - -
147A LYS* 3.0 21.7 + - - +
182A LYS 5.7 3.0 + - - -
183A ILE* 4.0 15.6 - - + +
188A TYR* 3.3 25.2 + - - +
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Residues in contact with ARG 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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108A TRP* 5.2 3.8 - - - +
112A GLY* 6.2 0.2 - - - -
140A GLU 3.0 13.7 + - - +
141A GLU* 2.8 47.0 + - - +
143A GLN* 1.3 76.0 - - - +
145A LEU* 1.3 77.9 + - - +
147A LYS* 3.2 12.4 + - + +
148A VAL* 2.9 49.7 + - + +
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Residues in contact with LEU 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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108A TRP* 3.7 32.6 - - + +
112A GLY* 3.8 10.5 - - - +
113A PHE* 3.9 33.4 - - + +
116A MET* 3.6 25.6 - - + -
117A LEU* 4.9 3.8 - - + -
141A GLU* 3.0 35.3 + - + +
142A SER* 3.6 8.1 - - - +
144A ARG* 1.3 94.2 - - - +
146A TYR* 1.3 59.0 + - + +
148A VAL* 3.3 5.5 + - - +
149A LEU* 2.9 28.9 + - - +
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Residues in contact with TYR 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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113A PHE* 3.8 24.9 - + - -
117A LEU* 4.0 8.3 - - + -
142A SER 3.0 27.2 + - - +
143A GLN* 3.4 0.4 + - - -
145A LEU* 1.3 75.3 - - - +
147A LYS* 1.3 57.5 + - - +
149A LEU* 3.6 7.7 - - + +
150A ASN* 2.8 31.4 + - - +
174A TRP 3.7 0.2 + - - -
175A ALA* 3.3 30.2 + - + -
178A TYR* 3.6 12.1 - - + +
181A GLN* 2.7 29.4 + - - -
183A ILE* 3.8 29.8 - - + -
185A LEU* 4.6 2.7 - - + -
188A TYR* 3.6 30.0 - + + -
191A VAL* 4.0 30.4 - - + +
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Residues in contact with LYS 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 GLN 3.0 13.9 + - - +
144A ARG* 3.4 15.7 - - + +
145A LEU 3.2 0.2 - - - -
146A TYR* 1.3 75.5 - - - +
148A VAL* 1.3 60.8 + - + +
150A ASN* 3.7 2.6 - - + +
151A THR* 2.9 43.2 + - - +
188A TYR* 3.6 15.8 - - + -
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Residues in contact with VAL 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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105A TRP* 3.9 28.6 - - + -
108A TRP* 3.9 18.2 - - + +
144A ARG* 2.9 43.8 + - + +
145A LEU* 3.6 7.4 - - - +
147A LYS* 1.3 76.3 - - + +
149A LEU* 1.3 65.2 + - - +
151A THR* 3.3 6.5 + - - +
152A GLN* 3.1 21.0 + - - +
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Residues in contact with LEU 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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105A TRP* 5.4 0.4 - - - -
108A TRP* 4.0 12.5 - - + -
113A PHE* 4.1 16.8 - - + -
145A LEU 2.9 17.0 + - - +
146A TYR* 3.6 7.0 - - + +
148A VAL* 1.3 77.9 - - - +
150A ASN* 1.3 63.1 + - - +
152A GLN* 3.2 6.0 + - - +
153A LEU* 3.0 43.1 + - + +
159A LEU* 3.7 37.9 - - + -
171A VAL* 4.0 23.6 - - + -
175A ALA* 4.6 3.6 - - + -
191A VAL* 3.9 26.5 - - + -
194A TRP* 4.7 2.9 - - + -
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Residues in contact with ASN 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 TYR 2.8 21.7 + - - +
147A LYS* 3.7 4.3 - - - +
148A VAL 3.3 0.2 - - - -
149A LEU* 1.3 74.3 - - - +
151A THR* 1.3 64.4 + - - +
153A LEU* 3.2 1.5 + - - +
154A GLU* 3.0 55.1 + - - +
187A ASP 4.9 2.0 + - - -
188A TYR* 3.0 26.8 - - + +
189A PRO* 4.2 10.3 - - - +
190A ALA* 2.9 31.6 + - - +
191A VAL* 3.2 14.2 + - + +
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Residues in contact with THR 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 LYS* 2.9 29.6 + - - +
148A VAL* 3.7 7.9 - - - +
149A LEU 3.3 0.2 - - - -
150A ASN* 1.3 81.4 + - - +
152A GLN* 1.3 61.8 + - - +
154A GLU* 3.4 27.2 + - - +
155A LYS* 3.5 27.3 - - - +
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Residues in contact with GLN 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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101A GLU* 4.4 6.5 + - - +
105A TRP* 3.5 35.1 + - + -
148A VAL 3.1 12.6 + - - +
149A LEU 3.8 6.7 - - - +
151A THR* 1.3 77.0 - - - +
153A LEU* 1.3 58.3 + - - +
154A GLU 3.1 0.4 - - - -
155A LYS* 2.9 33.4 + - - +
156A THR* 3.0 45.3 + - - +
159A LEU* 3.6 26.0 - - + -
160A GLY* 3.9 11.1 - - - +
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Residues in contact with LEU 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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149A LEU* 3.0 42.2 + - + +
150A ASN 3.2 0.6 + - - -
152A GLN* 1.3 73.4 - - - +
154A GLU* 1.3 62.0 + - - +
155A LYS 3.2 0.2 - - - -
156A THR 3.2 16.4 - - - +
157A PRO* 4.1 4.3 - - - +
158A TYR 3.8 25.6 - - - +
159A LEU* 3.8 10.3 - - + +
190A ALA* 3.9 22.2 - - + +
191A VAL* 4.1 12.1 - - - -
194A TRP* 3.6 53.4 - - + +
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Residues in contact with GLU 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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150A ASN* 3.0 35.2 + - - +
151A THR* 3.5 21.4 + - - +
152A GLN 3.1 0.4 - - - -
153A LEU* 1.3 76.7 - - - +
155A LYS* 1.3 61.0 + - + +
189A PRO* 5.6 2.9 - - - +
190A ALA* 4.0 13.0 - - + -
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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