Contacts of the helix formed by residues 111 - 131 (chain B) in PDB entry 4ZDR
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER* 1.3 89.6 + - - +
112B ALA* 1.3 67.4 + - - +
113B GLU* 3.2 16.1 - - + +
114B SER* 3.3 25.2 + - - +
115B LYS* 3.4 10.9 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER 3.8 0.2 + - - -
111B GLN* 1.3 72.9 - - - +
113B GLU* 1.3 63.6 + - - +
115B LYS* 3.1 8.6 + - - +
116B VAL* 3.1 27.5 + - - +
155B ILE* 3.9 9.5 - - + +
159B GLU* 3.5 44.6 - - + +
160B MET* 4.7 0.2 - - - -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 5.2 6.1 + - - -
41B ARG* 4.1 14.3 + - - +
111B GLN* 3.2 15.4 - - + +
112B ALA* 1.3 79.3 - - - +
114B SER* 1.3 63.8 + - - +
116B VAL* 3.3 5.4 + - - +
117B PHE* 3.3 19.2 + - - +
160B MET* 3.4 21.1 - - + +
164B HIS* 3.1 28.9 + - - -
166B ILE* 3.7 20.8 - - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 4.2 15.3 + - - -
38B ASN* 5.7 0.5 + - - -
41B ARG* 4.6 8.8 + - - +
109B ALA* 4.3 11.4 - - - -
110B SER 4.7 0.2 - - - -
111B GLN* 3.3 23.4 + - - +
112B ALA 3.2 0.8 - - - -
113B GLU* 1.3 79.0 - - - +
115B LYS* 1.3 66.2 + - - +
116B VAL 3.2 0.9 + - - -
117B PHE* 3.3 7.1 + - - +
118B TYR* 3.1 40.6 + - - -
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 5.4 6.8 - - + +
109B ALA* 3.8 21.2 - - + +
111B GLN 3.4 6.9 + - - +
112B ALA* 3.1 11.0 + - - +
114B SER* 1.3 78.2 - - - +
116B VAL* 1.3 57.8 + - - +
118B TYR* 4.5 2.6 - - - +
119B LEU* 3.0 39.4 + - + +
155B ILE* 4.7 14.8 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.1 15.6 + - - +
113B GLU 3.5 6.7 - - - +
114B SER 3.1 0.2 - - - -
115B LYS* 1.3 76.0 - - - +
117B PHE* 1.3 57.5 + - - +
119B LEU* 3.2 5.3 + - - +
120B LYS* 2.8 34.2 + - + +
152B ALA* 3.7 18.0 - - + +
155B ILE* 3.5 29.8 - - + -
156B SER* 3.8 13.5 - - - +
160B MET* 3.4 25.1 - - + -
166B ILE* 3.9 11.9 - - + -
170B LEU* 4.2 12.6 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 3.6 61.2 - - + +
42B ASN* 4.8 6.5 - - - -
45B SER* 3.8 23.8 - - - -
113B GLU 3.3 8.9 + - - +
114B SER 3.3 10.3 + - - +
116B VAL* 1.3 79.9 - - - +
118B TYR* 1.3 67.0 + + - +
120B LYS* 3.3 12.5 + - + +
121B MET* 3.0 48.7 + - - +
166B ILE* 3.8 24.6 - - + +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 5.6 5.2 - - + +
36B LEU* 3.7 28.4 + - + +
41B ARG* 3.2 36.9 - - + +
44B LEU* 5.0 2.2 - - + -
101B LEU* 3.6 21.0 - - + +
105B LEU* 3.6 54.5 - - + +
106B ILE* 3.9 17.4 - - + +
109B ALA* 4.6 4.7 - - + -
114B SER* 3.1 38.0 + - - +
115B LYS 4.5 1.6 - - - +
117B PHE* 1.3 84.9 - + - +
119B LEU* 1.3 61.1 + - - +
121B MET* 3.4 11.4 - - - +
122B LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.3 25.4 - - + -
115B LYS* 3.0 26.1 + - + +
116B VAL 3.6 0.4 - - - +
118B TYR* 1.3 75.8 - - - +
120B LYS* 1.3 62.9 + - - +
122B LYS* 3.5 16.5 - - + +
123B GLY 3.1 15.4 + - - -
148B ALA* 3.6 22.8 - - - +
151B GLU* 3.7 34.3 - - + +
152B ALA* 3.5 38.4 - - + +
155B ILE* 4.2 12.6 - - + -
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 2.8 17.1 + - + +
117B PHE* 3.6 12.7 - - + +
119B LEU* 1.3 73.9 - - - +
121B MET* 1.3 53.4 + - - +
123B GLY* 2.6 8.1 + - - -
124B ASP* 2.5 51.7 + - - +
149B TYR* 3.8 11.1 - - + -
152B ALA* 4.0 3.3 - - - +
166B ILE* 5.1 6.7 + - + +
169B GLY* 3.9 16.7 + - - +
170B LEU* 3.9 39.3 - - + +
173B ASN* 3.3 25.8 - - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.4 19.3 - - + +
45B SER* 3.8 34.1 - - - +
48B TYR* 5.1 2.7 - - + -
97B VAL* 4.6 11.4 - - + -
101B LEU* 3.9 14.8 - - + -
105B LEU* 5.5 0.4 - - + -
117B PHE* 3.0 40.1 + - + +
118B TYR* 3.4 19.1 - - - +
120B LYS* 1.3 79.5 - - - +
122B LYS* 1.3 60.5 + - - +
124B ASP* 3.4 10.9 - - - +
125B TYR* 3.0 54.5 + - + +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.7 5.8 - - + +
101B LEU* 3.6 12.3 - - + +
102B GLU* 3.0 40.0 + - - +
106B ILE* 3.7 16.4 - - + +
118B TYR 2.9 18.2 + - - +
119B LEU* 3.5 13.9 - - + +
121B MET* 1.3 71.9 - - - +
123B GLY* 1.3 68.9 + - - +
125B TYR 3.3 0.9 + - - -
126B TYR* 3.0 50.8 + - + -
144B GLN* 4.5 9.6 + - - -
148B ALA* 3.9 15.5 - - + -
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU 3.1 9.2 + - - -
120B LYS 2.6 11.9 + - - -
122B LYS* 1.3 71.5 - - - +
124B ASP* 1.3 59.8 + - - -
127B ARG* 3.0 9.4 + - - +
145B SER* 2.7 44.7 + - - -
148B ALA* 3.6 7.5 - - - +
149B TYR* 3.4 14.4 - - - -
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 2.5 30.2 + - - +
121B MET* 3.4 14.3 - - - +
123B GLY* 1.3 70.7 - - - +
125B TYR* 1.3 66.2 + - + +
127B ARG* 3.1 9.0 + - - +
128B TYR* 3.1 46.7 + - - +
149B TYR* 2.5 32.7 + - - -
173B ASN* 3.0 31.2 + - - +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 4.3 3.4 + - - -
48B TYR* 3.2 37.8 + + + +
49B LYS* 3.2 8.3 + - - +
52B VAL* 3.9 14.8 - - + -
93B ILE* 5.5 0.4 - - + -
94B CYS* 3.8 25.8 - - + +
97B VAL* 4.1 26.0 - - + -
98B LEU* 4.0 23.6 - - + -
121B MET* 3.0 51.2 + - + +
124B ASP* 1.3 79.5 - - + +
126B TYR* 1.3 66.2 + - - +
127B ARG 3.1 0.9 - - - -
128B TYR* 3.3 29.3 + + - -
129B LEU* 3.1 25.1 + - - +
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 5.8 1.1 - - - -
98B LEU* 3.5 31.1 - - + +
102B GLU* 4.8 3.5 + - - +
122B LYS* 3.0 44.4 + - + +
125B TYR* 1.3 76.3 - - - +
127B ARG* 1.3 52.3 + - - +
129B LEU* 3.2 20.9 + - + +
130B ALA* 2.7 30.1 + - - +
141B ILE* 3.3 20.2 - - + +
144B GLN* 3.5 53.4 + - + +
145B SER* 3.5 22.2 - - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY 3.0 13.9 + - - +
124B ASP* 3.1 18.5 + - - +
126B TYR* 1.3 75.4 - - - +
128B TYR* 1.3 68.4 + - + +
130B ALA* 3.4 7.8 + - - +
131B GLU* 3.0 44.5 + - - +
145B SER* 3.3 8.0 + - - +
149B TYR* 2.6 29.0 + - - -
173B ASN* 4.0 12.6 + - - +
176B VAL* 3.4 22.1 - - - +
177B PHE* 3.8 29.2 - - + +
180B GLU* 4.3 1.2 + - - -
181B ILE* 3.7 18.1 - - + +
237B ARG* 4.1 0.6 - - - +
302B SO4 2.9 43.4 + - - -
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LYS* 5.8 4.0 - - - +
52B VAL* 3.8 28.2 - - + +
56B ARG* 3.5 47.8 + - + -
90B LEU* 4.5 5.5 - - + +
94B CYS* 3.7 15.5 - - - -
124B ASP* 3.1 32.3 + - - +
125B TYR* 3.7 34.4 - + - +
126B TYR 3.3 0.4 - - - -
127B ARG* 1.3 92.5 - - + +
129B LEU* 1.3 68.2 + - - +
131B GLU* 3.1 19.0 + - - +
132B VAL* 3.3 14.0 - - - +
302B SO4 3.2 15.9 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 6.3 0.7 - - + -
91B ARG* 3.9 35.3 + - + +
94B CYS* 3.9 19.5 - - + -
95B ASN* 3.9 17.3 - - - +
98B LEU* 3.6 28.0 - - + -
125B TYR 3.1 12.9 + - - +
126B TYR* 3.2 22.2 + - + +
128B TYR* 1.3 76.4 - - - +
130B ALA* 1.3 62.6 + - - +
132B VAL* 3.0 19.1 + - + +
133B ALA* 3.2 13.0 + - - +
141B ILE* 3.6 21.4 - - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR 2.7 19.9 + - - +
127B ARG* 3.5 10.3 - - - +
129B LEU* 1.3 71.9 - - - +
131B GLU* 1.3 61.8 + - - +
132B VAL 3.2 1.2 + - - -
133B ALA* 3.6 11.7 + - - +
138B LYS* 4.0 18.2 + - - -
141B ILE* 3.4 15.0 - - + +
142B VAL* 4.0 25.6 - - + -
145B SER* 5.4 0.9 - - - -
181B ILE* 4.0 17.8 - - + +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 3.0 46.4 + - - +
59B TRP* 3.9 17.7 - - + -
60B ARG* 5.5 1.0 + - - -
90B LEU* 6.1 0.7 - - + -
127B ARG* 3.0 36.1 + - - +
128B TYR* 3.3 16.1 - - - +
129B LEU 3.0 0.8 + - - -
130B ALA* 1.3 76.1 - - - +
132B VAL* 1.3 64.1 + - + +
133B ALA 5.5 0.2 - - - -
180B GLU* 4.0 12.0 - - - +
181B ILE* 4.0 15.4 - - + +
237B ARG* 4.9 0.3 + - - -
239B MET* 6.1 0.2 - - - +
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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