Contacts of the helix formed by residues 113 - 134 (chain A) in PDB entry 3UJG
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 SER 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 5.9 1.8 - - - +
112A PHE* 1.3 77.6 - - - +
114A GLU* 1.3 65.5 + - - +
115A ASP* 3.0 9.1 + - - +
116A GLU* 3.1 34.9 + - - +
117A ALA* 2.9 21.9 + - - +
211A LEU* 4.6 0.9 - - - -
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Residues in contact with GLU 114 (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 SER* 1.3 73.8 - - - +
115A ASP* 1.3 63.8 + - - +
117A ALA* 3.8 0.2 - - - +
118A ARG* 3.0 36.5 + - - +
211A LEU* 3.9 14.2 - - + +
245A HIS 4.4 4.0 - - - +
246A ILE* 3.4 12.3 - - + +
247A SER* 2.6 53.6 + - - -
250A CYS* 4.2 9.2 - - - -
276A TRP* 2.9 31.4 + - + +
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Residues in contact with ASP 115 (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 SER* 3.1 7.5 + - - +
114A GLU* 1.3 83.7 - - - +
116A GLU* 1.3 59.9 + - + +
118A ARG* 3.4 19.2 + - - +
119A PHE* 3.1 25.8 + - - +
279A LYS* 5.1 6.1 + - - -
280A ASN* 3.9 18.7 + - - -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG 5.1 0.2 - - - +
112A PHE* 3.8 29.6 - - + -
113A SER* 3.1 35.0 + - - +
115A ASP* 1.3 73.6 - - + +
117A ALA* 1.3 66.0 + - - +
119A PHE* 3.2 15.0 + - - +
120A PHE* 3.2 32.1 + - + -
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Residues in contact with ALA 117 (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 PHE* 4.1 3.7 - - + +
113A SER 2.9 16.7 + - - +
114A GLU 3.8 1.8 - - - +
116A GLU* 1.3 77.8 - - - +
118A ARG* 1.3 56.8 + - - +
120A PHE 3.5 0.2 + - - -
121A PHE* 3.0 29.3 + - - +
207A LEU* 4.3 5.3 - - + +
210A MET* 3.8 29.9 - - + +
211A LEU* 3.4 32.1 - - + -
276A TRP* 4.2 2.9 - - + -
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Residues in contact with ARG 118 (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 GLU* 3.0 30.0 + - - +
115A ASP* 3.7 32.7 + - - +
116A GLU 3.2 0.8 - - - -
117A ALA* 1.3 73.5 - - - +
119A PHE* 1.3 67.3 + - - +
121A PHE* 3.8 0.3 - - - +
122A GLN* 3.1 43.3 + - + +
247A SER* 5.9 0.2 - - - -
276A TRP* 2.7 75.3 + - + +
277A PHE 4.7 0.2 - - - +
279A LYS* 3.0 58.0 + - - +
280A ASN* 4.4 8.3 - - - +
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Residues in contact with PHE 119 (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 ASP 3.1 13.2 + - - +
116A GLU* 3.4 11.4 - - - +
118A ARG* 1.3 79.4 - - - +
120A PHE* 1.3 83.5 + + - +
122A GLN* 3.4 24.2 + - - +
123A GLN* 3.4 30.8 + - + +
153A ALA* 5.0 4.9 - - + -
154A PRO* 3.2 41.5 - - + -
282A PRO* 5.7 9.6 - - + -
285A LEU* 5.3 1.7 - - + +
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Residues in contact with PHE 120 (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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102A LEU* 5.5 0.9 - - + -
112A PHE* 4.0 31.2 - + - -
116A GLU* 3.2 29.4 + - + +
119A PHE* 1.3 90.9 - + - +
121A PHE* 1.3 58.4 + - - +
123A GLN* 3.1 24.5 + - - +
124A LEU 2.9 23.6 + - - -
148A LEU* 3.7 24.7 - - + -
154A PRO* 3.7 36.1 - - + -
156A LEU* 3.2 28.5 - - + +
210A MET* 3.7 18.4 - - - -
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Residues in contact with PHE 121 (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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117A ALA 3.0 19.4 + - - +
118A ARG 3.3 4.0 + - - +
120A PHE* 1.3 77.5 - - - +
122A GLN* 1.3 63.4 + - + +
124A LEU* 3.2 12.0 + - + +
125A ILE* 3.0 53.2 + - + +
203A CYS* 3.8 32.5 - - + -
204A GLY 4.8 0.2 - - - -
207A LEU* 3.8 31.9 - - + -
210A MET* 4.2 5.6 - - + +
253A LEU* 4.1 10.5 - - + -
257A ILE* 4.3 15.3 - - + -
271A ILE* 3.9 17.3 - - + -
276A TRP* 3.9 22.0 - + + -
277A PHE* 4.1 10.3 - + - -
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Residues in contact with GLN 122 (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 ARG* 3.1 27.7 + - + +
119A PHE* 3.5 22.6 + - - +
120A PHE 3.2 0.2 - - - -
121A PHE* 1.3 77.4 - - + +
123A GLN* 1.3 61.4 - - - +
125A ILE* 3.5 1.7 + - - +
126A SER* 3.0 24.9 + - - -
277A PHE* 3.0 44.3 - - + +
279A LYS 3.2 15.8 - - - +
280A ASN 3.8 10.8 + - - +
281A LEU* 3.5 32.2 - - + -
282A PRO* 4.1 9.1 - - - +
285A LEU* 4.0 9.6 - - + +
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Residues in contact with GLN 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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76A ASN* 3.5 36.6 + - - +
119A PHE* 3.4 31.4 - - + +
120A PHE* 3.2 22.0 - - - +
122A GLN* 1.3 75.7 - - - +
124A LEU* 1.3 64.2 + - - +
126A SER* 3.3 5.5 + - - -
127A GLY* 2.9 19.4 + - - -
153A ALA* 4.6 2.6 - - - +
154A PRO 3.3 17.5 + - - -
155A ARG* 3.4 14.5 - - - +
156A LEU* 3.1 25.4 + - + -
285A LEU* 4.4 12.9 - - + +
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Residues in contact with LEU 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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76A ASN* 5.8 0.2 - - - -
120A PHE 2.9 13.3 + - - +
121A PHE* 3.2 19.5 + - + +
123A GLN* 1.3 74.9 - - - +
125A ILE* 1.3 53.3 - - - +
127A GLY* 2.9 3.6 + - - -
128A VAL* 2.6 56.0 + - + +
143A LEU* 4.3 8.1 - - + -
146A THR* 5.2 3.8 - - + +
156A LEU* 4.0 15.0 - - + +
158A ILE* 3.8 30.0 - - + +
203A CYS* 3.9 35.0 - - + +
206A THR* 4.0 24.9 - - + +
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Residues in contact with ILE 125 (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* 3.0 49.3 + - + +
124A LEU* 1.3 80.2 - - + +
126A SER* 1.3 57.4 + - - +
128A VAL* 4.1 2.6 - - - +
129A SER* 2.9 32.6 + - - -
203A CYS* 4.2 15.0 - - - -
268A ILE* 3.7 31.8 - - + +
271A ILE* 4.0 15.3 - - + -
272A ARG* 3.6 30.7 - - + +
277A PHE* 3.7 18.6 - - + -
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Residues in contact with SER 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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74A HIS* 2.8 28.5 + - - -
122A GLN 3.0 18.5 + - - -
123A GLN 3.5 4.3 - - - -
124A LEU 3.2 0.2 - - - -
125A ILE* 1.3 78.4 - - - +
127A GLY* 1.3 56.6 + - - +
129A SER* 3.7 1.9 - - - -
130A TYR* 3.0 28.4 + - - +
272A ARG* 3.7 17.9 + - - +
277A PHE* 6.1 0.2 - - - -
285A LEU* 3.2 30.4 - - - +
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Residues in contact with GLY 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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74A HIS* 3.6 21.6 + - - -
76A ASN* 4.7 0.4 - - - -
77A ILE* 3.9 10.9 - - - +
123A GLN 2.9 13.4 + - - -
124A LEU 3.3 2.9 - - - -
126A SER* 1.3 74.3 - - - +
128A VAL* 1.3 64.0 + - - +
129A SER 3.1 0.2 - - - -
130A TYR* 3.3 2.6 + - - +
131A CYS* 2.9 28.9 + - - -
158A ILE* 4.4 7.6 - - - -
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Residues in contact with VAL 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 LEU* 2.6 34.2 + - + +
125A ILE* 4.1 4.9 - - - +
127A GLY* 1.3 71.5 - - - -
129A SER* 1.3 57.3 + - - +
131A CYS* 3.1 6.7 + - - +
132A HIS* 2.8 60.5 + - + +
141A LEU* 4.5 7.2 - - + -
143A LEU* 3.8 18.4 - - + -
158A ILE* 4.8 2.0 - - + +
199A ASP* 4.6 4.5 - - + -
203A CYS* 3.8 27.4 - - - -
268A ILE* 4.1 13.9 - - + -
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Residues in contact with SER 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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125A ILE 2.9 19.9 + - - -
126A SER 3.7 4.2 + - - -
128A VAL* 1.3 78.2 - - - +
130A TYR* 1.3 63.6 + - - +
132A HIS* 3.4 8.6 + - - +
133A ALA* 3.1 21.4 + - - +
268A ILE* 4.0 23.0 - - - +
272A ARG* 4.3 16.1 + - - -
287A ASN 5.8 0.2 + - - -
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Residues in contact with TYR 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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71A SER 3.4 7.8 + - - -
72A LEU* 3.4 12.7 - - + -
73A ARG 2.8 21.3 + - - -
74A HIS* 3.6 30.5 - - + +
77A ILE* 4.6 2.5 - - + -
126A SER 3.0 19.0 + - - +
127A GLY 3.3 4.9 + - - +
129A SER* 1.3 76.3 + - - +
131A CYS* 1.3 72.3 + - - +
133A ALA* 2.9 9.8 + - - +
134A MET* 2.9 44.6 + - + +
290A THR* 4.0 18.4 - - - -
293A THR* 3.9 33.0 - - + +
294A GLN* 2.7 31.6 + - - -
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Residues in contact with CYS 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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72A LEU* 5.4 3.4 - - - -
77A ILE* 3.9 25.6 - - - -
127A GLY 2.9 21.0 + - - +
128A VAL 3.6 6.5 - - - +
130A TYR* 1.3 77.3 - - - +
132A HIS* 1.3 64.1 + - - +
134A MET* 2.9 12.8 + - - +
136A VAL* 2.9 43.1 + - + +
141A LEU* 3.4 33.7 - - + -
158A ILE* 4.9 0.9 - - - -
159A CYS* 4.4 6.7 - - - -
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Residues in contact with HIS 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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128A VAL* 2.8 44.3 + - + +
129A SER* 3.4 7.9 - - - +
131A CYS* 1.3 72.7 - - - +
133A ALA* 1.3 62.5 + - - +
135A GLN* 3.2 10.8 + - - +
136A VAL 3.7 4.6 + - - +
137A CYS* 3.6 11.4 - - + +
141A LEU* 4.6 1.9 - - + +
196A LYS* 3.2 72.5 + - + +
199A ASP* 3.0 30.0 - - + +
268A ILE* 4.4 15.5 - - + +
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Residues in contact with ALA 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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129A SER 3.1 11.4 + - - +
130A TYR* 2.9 11.0 + - - +
132A HIS* 1.3 78.0 - - - +
134A MET* 1.3 60.2 + - - +
135A GLN* 3.1 5.4 + - - +
290A THR* 3.2 32.5 - - + +
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Residues in contact with MET 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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71A SER* 3.3 42.8 - - - +
72A LEU* 3.8 17.7 - - + -
130A TYR* 2.9 40.7 + - + +
131A CYS* 2.9 8.0 + - - +
133A ALA* 1.3 75.0 - - + +
135A GLN* 1.3 69.1 + - - +
136A VAL* 3.2 12.7 + - + +
290A THR* 4.3 12.8 - - - -
294A GLN* 4.0 20.0 - - - +
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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