Contacts of the helix formed by residues 111 - 132 (chain D) in PDB entry 1IB1
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 GLN 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D SER* 1.3 107.5 + - - +
112D ALA* 1.3 61.3 + - - +
113D GLU* 4.1 9.4 - - + +
114D SER* 3.1 18.8 + - - +
115D LYS* 2.9 30.9 + - - +
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLN* 1.3 72.0 - - - +
113D GLU* 1.3 60.7 - - - +
115D LYS* 3.6 15.9 - - - +
116D VAL* 2.9 33.3 + - - +
155D ILE* 3.6 15.3 - - + +
159D GLU* 3.5 42.8 - - + +
160D MET* 3.9 3.2 - - + +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASN* 4.5 8.5 + - - +
41D ARG* 3.6 21.7 + - - -
111D GLN* 3.2 7.0 - - + +
112D ALA* 1.3 78.5 - - - +
114D SER* 1.3 60.6 + - - +
116D VAL* 3.1 22.4 - - - +
117D PHE* 3.2 13.0 + - - +
160D MET* 4.3 10.4 - - + +
164D HIS* 3.2 28.1 + - + +
166D ILE* 3.4 22.5 - - + +
211D TYR* 4.6 3.3 + - - -
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 4.7 6.2 + - - -
41D ARG* 3.5 19.2 + - - +
109D ALA* 4.0 17.7 - - - -
110D SER* 4.7 1.0 + - - -
111D GLN* 3.1 27.2 + - - +
113D GLU* 1.3 76.5 - - - +
115D LYS* 1.3 65.3 + - - +
117D PHE* 3.2 1.2 + - - +
118D TYR* 3.0 40.0 + - - -
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Residues in contact with LYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 5.2 3.0 - - - +
109D ALA* 3.4 28.0 + - + +
110D SER 2.8 32.9 + - - -
111D GLN 2.9 13.2 + - - +
112D ALA* 3.2 16.7 + - - +
114D SER* 1.3 77.5 - - - +
116D VAL* 1.3 56.3 + - - +
118D TYR* 4.2 2.0 - - - +
119D LEU* 3.0 38.9 + - + +
155D ILE* 4.1 24.2 - - + -
159D GLU* 5.5 2.9 - - - -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ALA 2.9 21.2 + - - +
113D GLU 3.1 9.6 - - - +
115D LYS* 1.3 74.2 - - - +
117D PHE* 1.3 65.5 + - - +
119D LEU* 3.8 0.8 - - - +
120D LYS* 2.9 29.1 + - - +
152D ALA* 3.5 31.4 - - + +
155D ILE* 5.0 4.9 - - + +
156D SER* 3.5 22.0 - - - +
160D MET* 3.2 22.4 - - + -
166D ILE* 3.5 18.6 - - + -
170D LEU* 3.8 9.9 - - + -
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ARG* 3.6 46.9 - - + +
42D ASN* 5.2 0.7 - - - -
45D SER* 3.7 22.9 - - - -
113D GLU 3.3 14.8 - - - +
114D SER 3.2 5.3 + - - +
116D VAL* 1.3 83.5 - - - +
118D TYR* 1.3 71.4 + + - +
120D LYS* 3.2 14.8 + - + +
121D MET* 2.9 37.3 + - + +
166D ILE* 4.0 30.7 - - + -
87H GLU* 3.7 28.5 - - + -
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 5.6 4.2 - - - +
36D LEU* 4.0 12.6 + - - +
41D ARG* 3.3 45.2 - - + +
44D LEU* 5.0 4.5 - - + -
101D LEU* 3.8 14.3 - - + +
105D LEU* 3.6 60.1 - - + +
106D ILE* 3.6 21.6 - - + +
109D ALA* 4.3 5.4 - - + -
114D SER* 3.0 34.3 + - - +
115D LYS* 4.4 1.6 - - - +
117D PHE* 1.3 82.7 - + - +
119D LEU* 1.3 59.6 + - - +
121D MET* 3.5 11.7 - - - +
122D LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ILE* 4.2 24.5 - - + -
115D LYS* 3.0 26.2 + - + +
117D PHE 3.3 0.2 - - - -
118D TYR* 1.3 72.8 - - - +
120D LYS* 1.3 61.5 + - - +
122D LYS* 3.2 22.2 + - + +
123D GLY 3.0 21.7 + - - -
148D ALA* 3.4 25.4 - - + +
151D GLU* 3.8 41.3 - - + +
152D ALA* 3.7 21.1 - - + +
155D ILE* 4.4 8.5 - - + -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 4.6 2.6 - - - +
116D VAL 2.9 18.8 + - - +
117D PHE* 3.4 13.1 + - + +
119D LEU* 1.3 75.2 - - - +
121D MET* 1.3 56.6 + - - +
123D GLY* 3.0 2.3 + - - -
124D ASP* 2.7 58.0 + - - +
149D TYR* 3.5 9.7 - - + -
152D ALA* 4.2 0.4 - - - +
166D ILE* 4.5 10.1 - - + +
169D GLY* 3.9 16.2 - - - -
170D LEU* 3.6 46.9 - - + +
173D ASN* 3.5 19.1 - - + +
32H LEU* 4.1 20.7 - - - +
87H GLU* 5.5 2.2 + - - -
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Residues in contact with MET 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 4.6 18.4 - - + +
45D SER* 4.1 27.6 - - - +
48D TYR* 4.7 3.6 - - + -
97D VAL* 4.2 12.6 - - + -
101D LEU* 3.9 24.1 - - + +
117D PHE* 2.9 29.9 + - + +
118D TYR* 3.5 19.3 - - - +
120D LYS* 1.3 78.2 - - - +
122D LYS* 1.3 61.8 + - - +
124D ASP* 3.9 10.8 - - - -
125D TYR* 3.0 60.6 + - + +
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.0 5.6 - - + +
101D LEU* 3.5 17.5 - - + -
102D GLU* 3.0 34.9 + - - +
106D ILE* 4.6 8.0 - - + +
118D TYR 2.9 14.6 + - - +
119D LEU* 3.3 23.0 - - + +
120D LYS 3.1 0.2 - - - -
121D MET* 1.3 76.0 - - - +
123D GLY* 1.3 65.3 + - - +
125D TYR 3.6 0.2 + - - -
126D TYR* 3.1 56.5 + - + -
144D GLN* 5.0 9.7 + - - +
148D ALA* 3.7 19.2 - - + +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU 3.0 12.9 + - - -
120D LYS 3.0 3.6 + - - -
122D LYS* 1.3 77.1 - - - +
124D ASP* 1.3 62.6 + - - +
126D TYR 3.4 0.7 + - - -
127D ARG* 3.0 13.5 + - - +
145D SER* 2.9 40.1 + - - -
148D ALA* 3.7 2.9 - - - +
149D TYR* 3.4 19.1 - - - -
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 3.8 10.2 + - - -
120D LYS* 2.7 37.9 + - - +
121D MET* 3.3 14.1 - - - +
123D GLY* 1.3 76.2 - - - +
125D TYR* 1.3 67.2 + - + +
127D ARG* 3.0 25.4 + - - +
128D TYR* 3.0 30.3 + - - +
149D TYR* 2.7 28.0 + - - -
173D ASN* 2.8 23.9 + - - +
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 4.4 2.1 + - - -
48D TYR* 3.3 36.2 - - + +
49D LYS* 3.3 14.1 + - + +
52D VAL* 4.1 13.9 - - + -
93D ILE* 4.9 1.3 - - + -
94D CYS* 3.6 22.4 - - + +
97D VAL* 3.6 35.4 - - + -
98D LEU* 3.7 26.5 - - + -
121D MET* 3.0 43.3 + - + +
123D GLY 3.5 0.2 - - - -
124D ASP* 1.3 83.0 - - + +
126D TYR* 1.3 59.9 + - - +
128D TYR* 3.8 26.5 - + - -
129D LEU* 2.9 28.2 + - - +
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.8 33.3 - - + +
102D GLU* 5.2 3.3 + - - -
122D LYS* 3.1 54.5 + - + +
123D GLY 3.9 0.2 - - - +
124D ASP 3.3 0.2 - - - -
125D TYR* 1.3 77.1 - - - +
127D ARG* 1.3 51.4 + - - +
129D LEU* 3.3 10.9 + - + -
130D ALA* 2.7 29.5 + - - +
141D ILE* 3.1 28.7 - - + +
144D GLN* 3.1 54.2 + - + -
145D SER* 3.6 20.6 - - - +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 4.0 2.2 - - - +
123D GLY 3.0 10.5 + - - +
124D ASP* 3.0 26.7 + - - +
126D TYR* 1.3 75.3 - - - +
128D TYR* 1.3 74.6 + - - +
130D ALA* 2.9 8.6 + - - +
131D GLU* 2.8 37.4 + - - +
145D SER* 3.9 2.7 + - - +
149D TYR* 2.8 33.9 + - - -
173D ASN* 4.1 9.8 + - - +
176D VAL* 4.6 7.1 - - - +
177D PHE* 3.7 43.3 - - + +
180D GLU* 4.9 1.4 + - - -
181D ILE* 3.7 15.4 - - + +
29H ARG* 3.9 4.4 - - - +
31H TPO 2.4 52.8 + - - +
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Residues in contact with TYR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 3.1 21.0 + - + -
52D VAL* 4.0 27.6 - - + -
56D ARG* 3.6 36.5 - - + +
90D LEU* 5.2 5.7 - - + +
94D CYS* 3.9 10.8 - - - -
124D ASP* 3.0 28.6 + - + +
125D TYR* 3.7 36.1 - + - +
127D ARG* 1.3 102.3 - - - +
129D LEU* 1.3 62.3 + - - +
131D GLU* 3.1 27.9 + - - +
132D VAL* 3.7 9.4 + - - +
31H TPO 2.7 18.4 + - - -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU 5.2 0.2 - - - -
91D ARG* 3.9 38.6 + - + +
94D CYS* 3.4 25.5 - - + -
95D ASN* 4.2 11.0 - - - +
98D LEU* 4.0 25.8 - - + -
125D TYR 2.9 13.5 + - - +
126D TYR* 3.4 20.9 - - + +
128D TYR* 1.3 75.3 - - - +
130D ALA* 1.3 61.5 + - - +
132D VAL* 3.3 12.7 - - + +
133D ALA* 3.2 18.9 + - - +
141D ILE* 4.0 21.8 - - + +
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR 2.7 15.2 + - - +
127D ARG* 2.9 15.2 + - - +
129D LEU* 1.3 74.2 - - - +
131D GLU* 1.3 61.5 + - - +
132D VAL 3.1 2.5 - - - -
133D ALA* 3.2 23.1 + - - +
138D LYS* 4.6 8.8 - - - +
141D ILE* 3.7 10.7 - - + +
142D VAL* 4.1 24.0 - - + +
145D SER* 5.8 0.7 - - - -
181D ILE* 4.2 15.8 - - + +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 2.9 48.2 + - - +
59D TRP* 3.4 26.0 - - + -
60D ARG* 5.8 0.8 + - - -
90D LEU* 6.0 0.5 - - - +
127D ARG* 2.8 20.5 + - - +
128D TYR* 3.1 24.6 + - - +
130D ALA* 1.3 75.6 - - - +
132D VAL* 1.3 62.5 + - + +
180D GLU* 3.8 16.0 - - - +
181D ILE* 4.3 15.3 - - + -
28H ARG* 4.4 5.1 + - - -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.4 41.3 - - + +
87D GLU* 3.8 22.1 - - + +
90D LEU* 3.8 27.4 - - + -
91D ARG* 3.4 31.4 + - - +
128D TYR 4.0 9.0 - - - +
129D LEU* 3.3 17.3 - - + +
131D GLU* 1.3 79.8 - - + +
133D ALA* 1.3 65.6 + - - +
134D ALA* 3.4 3.3 + - - +
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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
------------------------------------------------------------
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