Contacts of the helix formed by residues 122 - 143 (chain A) in PDB entry 3LQ5
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LYS 5.1 0.9 - - - +
121A PHE* 1.3 76.7 - - - +
123A LEU* 1.3 65.3 + - - +
124A SER* 2.9 20.5 + - - -
125A GLU* 3.2 34.6 + - + +
126A ILE* 3.0 22.8 + - - +
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Residues in contact with LEU 123 (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 THR* 1.3 74.3 + - - +
124A SER* 1.3 56.5 + - - +
126A ILE* 3.3 4.1 + - + +
127A LYS* 2.9 46.4 + - - +
223A TRP* 3.8 35.0 - - + +
285A ASP* 3.3 36.6 - - + +
314A PHE* 4.8 5.4 - - + -
319A PRO* 3.3 35.9 - - + -
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Residues in contact with SER 124 (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 THR* 2.9 9.7 + - - -
123A LEU* 1.3 78.3 - - - +
125A GLU* 1.3 61.6 + - - +
127A LYS* 4.6 0.9 - - - -
128A ARG* 3.3 6.9 + - - +
319A PRO* 2.9 23.3 - - - +
320A MET 2.9 24.7 + - - -
321A PRO* 3.3 8.1 - - - +
322A SER* 2.8 41.5 + - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS 3.5 18.7 - - - +
121A PHE* 3.8 14.8 - - + -
122A THR* 3.2 37.5 + - + +
124A SER* 1.3 77.7 - - - +
126A ILE* 1.3 62.3 + - - +
128A ARG* 3.2 4.6 + - - +
129A VAL* 3.1 25.5 + - - +
322A SER* 3.9 10.8 - - - +
323A ASP 3.8 15.5 - - - +
324A LEU* 4.0 11.3 - - + +
325A LYS 3.8 6.4 + - - -
326A GLY* 3.0 38.5 + - - +
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Residues in contact with ILE 126 (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 PHE* 3.6 28.0 - - + +
122A THR 3.0 18.4 + - - +
123A LEU* 3.3 8.9 + - + +
125A GLU* 1.3 72.7 - - - +
127A LYS* 1.3 68.8 + - - +
128A ARG 3.0 2.4 + - - -
129A VAL* 3.3 2.3 + - - +
130A MET* 3.1 29.4 + - + +
222A MET* 3.7 38.6 - - + +
223A TRP* 3.5 57.4 - - + +
314A PHE* 4.6 2.5 - - + -
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Residues in contact with LYS 127 (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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123A LEU* 2.9 38.6 + - + +
124A SER 3.9 2.5 - - - +
125A GLU 3.5 0.2 - - - -
126A ILE* 1.3 75.3 - - - +
128A ARG* 1.3 56.0 + - - +
130A MET 3.5 0.2 + - - -
131A GLN* 2.9 25.5 + - - +
285A ASP* 4.1 5.2 + - - -
314A PHE* 2.9 60.5 + - + +
315A PHE* 3.3 13.2 - - + -
317A SER* 2.9 37.1 + - - +
318A ASP 3.7 7.3 + - - -
319A PRO* 2.9 20.5 + - - +
320A MET 4.5 0.2 - - - -
321A PRO* 3.8 24.9 - - + -
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Residues in contact with ARG 128 (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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124A SER 3.3 4.9 + - - +
125A GLU 3.2 8.7 + - - +
126A ILE 3.0 0.6 - - - -
127A LYS* 1.3 76.2 - - - +
129A VAL* 1.3 68.6 + - - +
131A GLN* 2.9 40.4 + - - +
132A MET* 2.8 55.8 + - + +
321A PRO* 3.9 14.8 - - - +
322A SER 3.1 34.3 - - - +
323A ASP* 4.1 12.3 + - - -
324A LEU* 3.7 17.7 - - + -
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Residues in contact with VAL 129 (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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110A LEU* 5.0 10.1 - - + -
121A PHE* 4.9 5.8 - - + -
125A GLU 3.1 7.8 + - - +
126A ILE 3.7 6.5 - - - +
128A ARG* 1.3 80.2 - - - +
130A MET* 1.3 66.2 + - - +
132A MET* 3.3 13.4 + - + +
133A LEU* 2.9 32.2 + - + +
157A ILE* 4.2 18.2 - - + -
163A LEU* 3.9 8.4 - - + +
218A ILE* 6.4 0.4 - - + -
222A MET* 4.0 33.4 - - + -
324A LEU* 3.9 25.4 - - + -
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Residues in contact with MET 130 (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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126A ILE* 3.1 24.9 + - + +
127A LYS 3.8 3.6 - - - +
129A VAL* 1.3 88.3 - - + +
131A GLN* 1.3 61.6 + - - +
133A LEU* 3.2 21.8 + - + +
134A LEU* 2.8 47.0 + - + +
215A ALA* 3.9 11.9 - - + +
218A ILE* 4.9 4.5 - - - -
219A MET* 3.3 59.9 - - + -
222A MET* 4.6 4.9 - - + +
295A LEU* 4.9 1.6 - - + -
314A PHE* 4.5 2.7 - - + -
315A PHE* 4.0 14.8 - - + -
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Residues in contact with GLN 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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127A LYS 2.9 17.8 + - - +
128A ARG* 2.9 28.2 + - - +
130A MET* 1.3 79.2 - - - +
132A MET* 1.3 63.1 + - - +
135A ASN* 2.9 25.7 + - + +
310A LEU* 3.5 25.4 + - + +
315A PHE* 3.6 33.7 + - + +
316A TRP* 4.7 13.1 - - - -
321A PRO* 3.9 18.5 - - - +
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Residues in contact with MET 132 (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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77A ASN* 3.3 31.8 - - - +
128A ARG* 2.8 51.9 + - + +
129A VAL* 3.7 30.1 - - + +
131A GLN* 1.3 71.4 - - - +
133A LEU* 1.3 58.6 + - - +
135A ASN* 3.4 2.4 + - - -
136A GLY* 2.9 24.1 + - - -
157A ILE* 5.5 1.8 - - + -
161A GLY 3.8 20.4 - - - +
162A VAL* 4.0 6.1 - - - -
163A LEU* 3.3 39.3 - - + +
324A LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 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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110A LEU* 5.7 0.4 - - + -
129A VAL* 2.9 17.2 + - + +
130A MET* 3.7 21.3 - - + +
132A MET* 1.3 75.4 - - - +
134A LEU* 1.3 66.0 + - + +
136A GLY* 3.3 1.8 + - - +
137A LEU* 3.0 33.0 + - + +
150A MET* 5.2 3.6 - - - -
155A VAL* 4.0 32.8 - - + -
163A LEU* 3.4 15.2 - - + +
165A LEU* 4.1 15.9 - - + +
215A ALA* 3.7 29.2 - - + -
218A ILE* 4.6 19.5 - - + -
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Residues in contact with LEU 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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130A MET* 2.8 29.0 + - + +
133A LEU* 1.3 82.7 - - + +
135A ASN* 1.3 59.7 + - - +
137A LEU* 3.5 6.7 + - + +
138A TYR* 3.1 26.7 + - - +
212A LEU* 3.9 27.4 - - + -
215A ALA* 4.2 9.6 - - + -
291A LEU* 4.6 5.6 - - + -
295A LEU* 5.0 5.8 - - + -
306A SER* 4.0 10.2 + - - +
309A ALA* 3.9 24.0 - - + -
310A LEU* 3.7 20.7 - - + +
315A PHE* 3.8 28.3 - - + -
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Residues in contact with ASN 135 (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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75A HIS* 3.8 21.7 + - - -
77A ASN* 3.8 10.8 + - - +
131A GLN* 2.9 19.1 + - + +
132A MET* 3.5 6.7 - - - +
134A LEU* 1.3 75.6 - - - +
136A GLY* 1.3 65.9 + - - +
138A TYR* 3.2 13.1 + - - +
139A TYR* 3.0 23.6 + - - +
310A LEU* 3.9 19.6 - - + +
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Residues in contact with GLY 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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75A HIS* 4.5 4.5 - - - -
77A ASN* 3.8 21.5 - - - +
78A VAL* 4.4 1.4 - - - +
132A MET 2.9 17.1 + - - -
133A LEU 3.3 2.2 + - - -
135A ASN* 1.3 77.5 - - - +
137A LEU* 1.3 57.9 + - - +
139A TYR* 3.4 3.5 + - - +
140A ILE* 3.0 28.8 + - - +
165A LEU* 3.9 15.4 - - - +
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Residues in contact with LEU 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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133A LEU* 3.0 23.6 + - + +
134A LEU* 3.8 14.4 - - + +
135A ASN 3.1 0.2 - - - -
136A GLY* 1.3 71.7 - - - +
138A TYR* 1.3 67.0 + - - +
139A TYR 2.8 3.1 + - - -
140A ILE* 2.9 32.3 + - + +
141A HIS* 3.0 25.7 + - + +
150A MET* 4.3 15.3 - - + -
165A LEU* 4.0 11.6 - - + +
211A ASP* 3.9 44.4 - - + +
212A LEU* 4.5 6.7 - - + -
215A ALA* 4.2 17.3 - - + -
306A SER* 4.5 4.5 - - - -
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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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134A LEU 3.1 12.4 + - - +
135A ASN* 3.5 17.3 - - - +
137A LEU* 1.3 75.1 - - - +
139A TYR* 1.3 68.9 + - + +
141A HIS* 3.9 4.3 - - - +
142A ARG* 2.7 68.0 + - + +
306A SER* 3.2 24.7 + - - +
307A ASP* 3.6 36.9 + - + -
310A LEU* 4.7 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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72A LEU 3.6 8.7 + - - -
73A LEU* 3.6 22.7 - - + -
74A LYS* 2.9 36.0 + - - +
75A HIS* 3.4 46.4 - + + +
78A VAL* 4.1 4.0 - - + -
135A ASN 3.0 9.9 + - - +
136A GLY 3.5 8.5 - - - +
137A LEU 2.8 1.4 + - - -
138A TYR* 1.3 86.1 - - + +
140A ILE* 1.3 69.9 + - + +
142A ARG* 3.3 11.0 + - - +
143A ASN* 3.1 52.9 + - - -
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Residues in contact with ILE 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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73A LEU* 3.8 26.5 - - + -
78A VAL* 4.0 16.6 - - + -
136A GLY 3.0 17.0 - - - +
137A LEU* 2.9 22.6 + - + +
139A TYR* 1.3 77.7 - - + +
141A HIS* 1.3 69.2 + - + +
143A ASN* 2.9 16.9 + - - +
145A ILE* 2.8 35.9 + - + +
147A HIS* 3.8 33.4 - - + +
165A LEU* 4.8 4.0 - - + -
168A PHE* 4.2 13.7 - - + -
211A ASP* 4.5 0.7 - - - +
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Residues in contact with HIS 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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137A LEU* 3.0 30.9 + - + +
138A TYR* 3.9 4.7 - - - +
140A ILE* 1.3 87.4 - - + +
142A ARG* 1.3 57.0 + - - +
144A LYS* 2.9 22.2 + - - +
145A ILE 3.4 17.7 - - - -
146A LEU* 4.4 1.6 - - + -
174A PHE* 3.7 11.2 - - - -
208A PRO* 3.5 49.6 - - + +
211A ASP* 3.2 31.3 + - + +
212A LEU* 4.6 10.4 - - + +
306A SER* 4.7 8.9 + - - +
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Residues in contact with ARG 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 TYR* 2.7 66.5 + - + +
139A TYR* 3.3 12.1 - - - +
140A ILE 3.2 0.2 - - - -
141A HIS* 1.3 76.4 - - - +
143A ASN* 1.3 68.3 + - - +
144A LYS* 3.2 12.3 + - - +
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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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72A LEU* 3.9 29.0 - - + +
73A LEU* 3.8 20.6 - - + -
139A TYR* 3.1 46.4 + - - +
140A ILE 2.9 9.8 + - - +
142A ARG* 1.3 85.8 - - - +
144A LYS* 1.3 73.0 + - - +
145A ILE* 3.1 12.3 + - - +
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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