Contacts of the helix formed by residues 109 - 130 (chain A) in PDB entry 2VN9
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 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 4.1 3.4 - - - -
108A TYR* 1.3 79.3 - - - +
110A GLU* 1.3 64.7 + - - +
111A ALA* 3.4 11.4 + - - +
112A ASP* 2.6 27.2 + - - +
113A ALA* 3.1 20.1 + - - +
280A SER 3.4 11.5 + - - -
281A MET* 3.5 14.4 - - - -
282A MET 3.3 19.3 - - - -
284A ARG* 4.6 5.8 - - - -
1313A EPE 3.4 14.0 - - - -
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Residues in contact with GLU 110 (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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109A SER* 1.3 71.5 - - - +
111A ALA* 1.3 60.9 + - - +
113A ALA* 3.3 5.1 + - - -
114A SER* 2.8 26.7 + - - -
208A LEU* 3.9 18.8 - - + -
240A THR 4.0 1.0 - - - +
241A VAL* 3.1 16.0 - - + +
242A THR* 2.9 45.6 + - - -
245A ALA* 4.3 4.9 - - - -
271A TRP* 3.0 27.0 + - + +
279A ALA* 3.9 1.3 - - - -
280A SER* 3.1 36.1 + - - +
282A MET 4.5 0.6 + - - -
284A ARG* 4.5 15.1 + - - +
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Residues in contact with ALA 111 (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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109A SER* 3.2 9.8 - - - +
110A GLU* 1.3 76.0 - - - +
112A ASP* 1.3 57.2 + - - +
115A HIS* 3.0 24.1 + - - +
275A ARG* 3.1 13.2 - - - +
279A ALA* 3.5 21.5 - - + +
280A SER 3.1 11.5 + - - +
281A MET* 4.9 4.7 - - + -
1313A EPE 3.6 39.5 - - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.3 10.3 + - - +
107A TYR 4.6 0.4 - - - -
108A TYR* 3.5 21.3 - - + -
109A SER* 2.6 38.8 + - - +
111A ALA* 1.3 75.0 - - - +
113A ALA* 1.3 64.7 + - - +
115A HIS* 3.1 8.3 + - - +
116A CYS* 3.1 28.8 + - - -
1313A EPE 3.0 52.8 + - - -
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Residues in contact with ALA 113 (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 TYR* 3.4 25.5 - - + +
109A SER 3.1 7.5 + - - +
110A GLU 3.3 7.2 + - - +
112A ASP* 1.3 78.7 - - - +
114A SER* 1.3 57.2 + - - +
116A CYS* 3.5 7.9 + - - +
117A ILE* 3.0 33.4 + - - +
204A LEU* 5.1 0.2 - - + -
207A LEU* 4.2 10.5 - - + +
208A LEU* 3.8 26.7 - - + -
271A TRP* 3.8 3.6 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU 2.8 21.0 + - - -
111A ALA* 4.2 0.2 - - - -
113A ALA* 1.3 70.5 - - - +
115A HIS* 1.3 55.5 + - - +
117A ILE 3.7 0.2 - - - -
118A GLN* 2.8 35.5 + - - +
271A TRP* 2.7 45.5 + - - -
272A ILE* 3.6 12.5 + - - +
275A ARG* 3.5 24.7 + - - +
279A ALA* 4.4 0.4 - - - -
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Residues in contact with HIS 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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111A ALA 3.0 14.2 + - - +
112A ASP* 3.3 13.2 - - - +
114A SER* 1.3 75.1 - - - +
116A CYS* 1.3 64.4 + - - +
118A GLN* 3.5 6.6 + - - +
119A GLN* 3.1 58.3 + - + +
150A GLY* 5.7 3.6 + - - -
151A ALA 5.4 4.2 + - - -
275A ARG* 3.7 33.7 + - - +
1313A EPE 6.3 2.9 - - + -
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Residues in contact with CYS 116 (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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98A LEU* 3.7 43.7 - - + -
102A ILE* 4.9 5.2 - - - -
105A ARG* 4.8 10.8 - - - -
108A TYR* 5.5 0.4 - - - -
112A ASP 3.1 16.4 + - - -
113A ALA* 3.6 9.9 - - - +
115A HIS* 1.3 78.9 - - - +
117A ILE* 1.3 64.9 + - - +
118A GLN 3.1 0.2 - - - -
119A GLN* 3.3 14.0 + - - +
120A ILE* 3.0 27.7 + - - +
153A VAL* 4.7 5.4 - - - +
207A LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 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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113A ALA 3.0 18.6 + - - +
114A SER 4.0 2.5 - - - +
116A CYS* 1.3 75.9 - - - +
118A GLN* 1.3 67.3 + - - +
120A ILE* 3.7 19.0 - - + +
121A LEU* 2.9 44.8 + - + +
200A CYS* 4.2 9.0 - - + +
203A ILE* 4.0 12.8 - - + -
204A LEU* 3.8 29.2 - - + +
207A LEU* 3.7 23.1 - - + -
248A LEU* 5.0 0.2 - - + -
252A MET* 4.7 10.8 - - + -
271A TRP* 4.6 4.0 - - + -
272A ILE* 3.7 13.2 - - + -
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Residues in contact with GLN 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 SER 2.8 19.5 + - - +
115A HIS* 3.6 9.4 + - - +
116A CYS 3.1 0.4 - - - -
117A ILE* 1.3 77.8 - - - +
119A GLN* 1.3 58.9 + - + +
121A LEU* 3.4 5.2 + - - +
122A GLU* 3.0 41.1 + - + +
267A LEU* 3.7 10.2 + - + +
272A ILE* 3.6 40.1 + - + +
273A CYS* 4.7 5.5 - - - +
275A ARG* 2.9 25.6 + - - +
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Residues in contact with GLN 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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72A ASN* 3.6 32.4 + - - +
115A HIS* 3.1 49.1 + - + +
116A CYS* 3.3 11.6 + - - +
118A GLN* 1.3 77.3 - - + +
120A ILE* 1.3 64.3 + - - +
122A GLU* 3.2 6.8 + - - +
123A SER* 3.1 18.0 + - - -
151A ALA 4.1 2.7 + - - +
152A ALA* 3.2 13.2 - - - +
153A VAL* 3.0 39.9 + - + +
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Residues in contact with ILE 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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98A LEU* 4.4 11.4 - - + -
116A CYS* 3.0 21.3 + - + +
117A ILE* 3.3 26.9 + - + +
119A GLN* 1.3 73.8 - - - +
121A LEU* 1.3 58.6 + - + +
123A SER* 2.5 26.3 + - - +
124A VAL* 3.0 18.2 + - + +
137A LEU* 5.2 4.7 - - + -
142A LEU* 3.5 46.2 - - + -
153A VAL* 4.2 10.1 - - + -
155A LEU* 5.9 0.2 - - + -
200A CYS* 4.2 23.1 - - - -
203A ILE* 4.4 9.4 - - + -
207A LEU* 4.8 1.1 - - + -
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Residues in contact with LEU 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 ILE* 2.9 39.0 + - + +
118A GLN 3.6 4.0 - - - +
120A ILE* 1.3 73.8 - - + +
122A GLU* 1.3 59.1 + - - +
124A VAL* 3.9 3.9 - - + +
125A ASN* 2.8 32.8 + - - +
197A MET* 3.5 36.8 - - + -
200A CYS* 4.4 11.7 - - - -
252A MET* 4.1 8.7 - - + -
263A ALA* 4.1 7.8 - - + +
266A ALA* 3.7 34.1 - - + +
267A LEU* 3.7 17.4 - - + +
272A ILE* 4.2 10.5 - - + -
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Residues in contact with GLU 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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70A HIS* 3.7 24.2 + - + -
72A ASN* 4.1 4.9 - - - +
118A GLN* 3.0 32.0 + - + +
119A GLN* 3.2 8.5 + - - +
121A LEU* 1.3 75.3 - - - +
123A SER* 1.3 58.3 + - - +
125A ASN* 3.6 7.9 + - - +
126A HIS* 3.0 28.2 + - - +
267A LEU* 3.5 30.7 - - + +
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Residues in contact with SER 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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70A HIS* 4.1 9.3 - - - -
72A ASN* 3.3 27.4 - - - -
73A ILE* 3.8 12.2 - - - +
119A GLN 3.1 9.6 + - - -
120A ILE* 2.5 26.9 + - - +
122A GLU* 1.3 77.7 - - - +
124A VAL* 1.3 57.1 + - - +
126A HIS* 3.4 3.5 + - - +
127A CYS* 3.0 33.3 + - - -
142A LEU* 5.8 0.3 - - - +
155A LEU* 3.8 18.6 - - - +
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Residues in contact with VAL 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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120A ILE* 3.0 21.0 + - + +
121A LEU* 3.9 7.2 - - - +
123A SER* 1.3 80.3 + - - +
125A ASN* 1.3 60.2 + - - +
127A CYS* 3.3 9.1 + - - +
128A HIS* 2.9 63.2 + - + +
134A HIS* 6.2 0.4 - - + -
137A LEU* 3.6 31.2 - - + -
155A LEU* 4.8 2.2 - - + -
196A ASP* 4.0 10.1 - - + +
197A MET* 4.1 16.6 - - - -
200A CYS* 4.2 9.6 - - - -
263A ALA* 4.2 1.6 - - + -
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Residues in contact with ASN 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 LEU 2.8 23.3 + - - +
122A GLU* 3.8 9.2 + - - +
124A VAL* 1.3 74.6 - - - +
126A HIS* 1.3 56.8 + - - +
128A HIS* 3.7 4.7 - - - +
129A LEU* 2.8 57.7 + - - +
263A ALA* 3.8 13.5 - - + +
264A SER* 2.8 34.3 + - - -
267A LEU* 4.3 15.9 - - + +
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Residues in contact with HIS 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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67A LEU 5.2 1.2 + - - -
68A LEU* 4.2 14.1 - - + -
69A LYS 3.4 27.4 + - - -
70A HIS* 3.6 36.3 - + + +
73A ILE* 4.2 3.6 - - + -
122A GLU 3.0 18.5 + - - +
123A SER 3.6 4.9 - - - +
124A VAL 3.3 0.2 - - - -
125A ASN* 1.3 74.3 - - - +
127A CYS* 1.3 66.8 + - - +
129A LEU* 3.5 13.5 + - + +
130A ASN* 2.9 56.2 + - - -
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Residues in contact with CYS 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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68A LEU* 4.1 12.6 - - - -
73A ILE* 4.0 7.4 - - - -
123A SER 3.0 22.5 + - - -
124A VAL* 3.3 11.0 - - - +
126A HIS* 1.3 76.7 - - - +
128A HIS* 1.3 56.4 + - + +
130A ASN* 3.0 14.4 + - - -
132A ILE* 2.8 43.4 + - + +
134A HIS* 5.3 5.2 - - - +
155A LEU* 3.8 14.6 - - - -
158A PHE* 3.6 32.8 - - - -
196A ASP* 5.6 0.7 - - - +
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Residues in contact with HIS 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 VAL* 2.9 42.6 + - + +
125A ASN* 3.8 7.4 - - - +
126A HIS 3.3 0.2 - - - -
127A CYS* 1.3 74.2 - - + +
129A LEU* 1.3 61.5 + - - +
131A GLY 3.0 10.7 + - - -
132A ILE 3.2 20.2 - - - +
133A VAL* 4.4 0.4 - - - -
193A LYS* 3.2 77.8 + - + +
196A ASP* 2.9 27.5 + - + +
197A MET* 4.5 8.9 - - + +
263A ALA* 4.5 9.5 + - + +
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Residues in contact with LEU 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 ASN* 2.8 48.1 + - - +
126A HIS* 3.7 15.7 - - + +
128A HIS* 1.3 71.5 - - - +
130A ASN* 1.3 64.0 + - - +
131A GLY 3.3 0.7 + - - -
193A LYS* 5.5 0.4 - - - +
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Residues in contact with ASN 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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67A LEU* 3.7 31.0 - - + +
68A LEU* 4.0 16.1 - - + +
126A HIS* 2.9 55.8 + - - +
127A CYS 3.0 5.7 + - - +
129A LEU* 1.3 81.9 - - - +
131A GLY* 1.3 61.5 + - - +
132A ILE* 3.3 12.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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