Contacts of the helix formed by residues 116 - 139 (chain B) in PDB entry 4B5G
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 ALA 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY 3.8 9.1 - - - +
114B SER 3.6 0.6 - - - -
115B SER* 1.3 81.7 - - - +
117B GLU* 1.3 65.3 + - - +
118B GLU* 3.3 21.8 - - - +
119B ARG* 3.2 14.9 + - + +
120B GLN 3.2 15.8 + - - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 1.3 73.1 - - - +
118B GLU* 1.3 67.2 + - + +
120B GLN* 3.1 17.1 + - - +
121B GLN* 2.9 57.3 + - + +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 3.3 21.0 - - - +
117B GLU* 1.3 83.1 - - + +
119B ARG* 1.3 60.8 + - + +
121B GLN* 3.3 10.5 + - - +
122B VAL* 2.9 32.3 + - + +
125B ARG* 4.6 1.9 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.2 26.0 + - - -
92B GLU* 3.2 24.5 + - - -
94B ARG* 3.8 6.5 - - - +
111B PRO* 4.4 8.7 - - - +
112B SER 3.6 16.5 + - - +
113B GLY* 3.7 6.7 - - - -
115B SER* 4.3 3.4 - - - -
116B ALA* 3.2 27.0 + - + +
117B GLU 3.1 0.2 - - - -
118B GLU* 1.3 78.7 - - + +
120B GLN* 1.3 64.1 + - - +
122B VAL* 3.0 38.9 - - - +
123B LYS* 2.9 23.4 + - - +
35W C 3.8 24.4 + - - +
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY* 2.9 24.8 - - - +
116B ALA 3.2 5.2 + - - +
117B GLU* 3.1 26.8 + - - +
119B ARG* 1.3 78.0 - - - +
121B GLN* 1.3 58.3 + - - +
123B LYS* 3.1 15.2 - - - +
124B TYR* 2.9 62.8 + - + -
169B SER* 2.6 28.5 + - - -
172B LEU* 4.4 9.3 - - + +
175B GLU* 2.6 29.4 + - - -
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 2.9 45.9 + - + +
118B GLU* 3.5 11.0 - - - +
119B ARG 3.1 0.4 - - - -
120B GLN* 1.3 74.5 - - - +
122B VAL* 1.3 64.9 + - - +
124B TYR* 3.0 22.2 + - - +
125B ARG* 2.9 37.5 + - + +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.2 21.7 - - + -
92B GLU* 5.2 2.2 - - - +
111B PRO* 4.8 5.4 - - + -
118B GLU* 2.9 17.8 + - + +
119B ARG* 3.0 60.3 - - - +
121B GLN* 1.3 75.7 - - - +
123B LYS* 1.3 57.0 + - - +
125B ARG* 3.1 34.8 + - - +
126B PHE* 2.9 22.9 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 19.1 - - + -
111B PRO* 3.3 31.2 + - + +
112B SER* 4.9 0.4 - - - +
113B GLY 3.9 12.0 - - - +
119B ARG 2.9 13.2 + - - +
120B GLN* 3.1 27.6 - - - +
122B VAL* 1.3 79.5 - - - +
124B TYR* 1.3 55.0 + - - +
126B PHE* 3.1 9.2 + - - +
127B LEU* 2.9 32.2 + - + +
151B ASN* 3.1 28.6 + - - +
152B ILE* 3.9 14.1 - - - +
169B SER* 3.8 11.1 + - - -
170B GLY 3.9 3.6 - - - +
175B GLU* 3.3 19.4 + - - +
36W 3DR 5.3 1.2 - - - -
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Residues in contact with TYR 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 GLN* 2.9 60.4 + - + -
121B GLN* 3.0 23.8 + - - +
123B LYS* 1.3 74.6 - - + +
125B ARG* 1.3 59.7 + - + +
127B LEU* 3.2 17.0 + - + +
128B ASP* 2.9 42.2 + - - +
172B LEU* 3.9 18.9 - - + +
174B GLU* 4.8 20.8 + - + +
175B GLU* 3.9 20.6 + - + +
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Residues in contact with ARG 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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88B GLU* 3.0 29.1 + - - +
89B PHE* 3.6 13.3 - - + -
118B GLU 4.6 2.2 + - - -
121B GLN* 2.9 24.0 + - - +
122B VAL* 3.1 43.9 - - - +
124B TYR* 1.3 75.7 - - + +
126B PHE* 1.3 57.3 + - - +
128B ASP* 3.4 8.1 + - - +
129B ALA* 3.0 31.5 + - - +
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Residues in contact with PHE 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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84B MET* 3.7 30.5 - - + +
89B PHE* 3.4 38.5 - + + -
94B ARG* 4.6 11.0 - - + -
95B PHE* 6.2 0.2 - - + -
108B LEU* 4.1 19.5 - - + -
109B TYR 4.9 1.8 - - - -
110B LEU* 3.6 30.3 - - + -
111B PRO* 3.5 29.2 - - + -
122B VAL 2.9 14.3 + - - +
123B LYS* 3.1 10.1 + - - +
125B ARG* 1.3 74.7 - - - +
127B LEU* 1.3 61.0 + - + +
129B ALA* 3.3 0.7 + - - +
130B PHE* 2.9 54.3 + + + +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.8 27.1 - - + -
123B LYS* 2.9 23.4 + - + +
124B TYR* 3.2 27.3 + - + +
126B PHE* 1.3 76.8 - - + +
128B ASP* 1.3 61.8 - - - +
131B TYR* 2.9 34.7 + - - +
152B ILE* 4.3 15.0 - - + -
174B GLU* 5.3 1.1 - - + +
175B GLU* 4.8 7.4 - - + -
178B TRP* 3.4 64.3 + - + +
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 2.9 26.0 + - - +
125B ARG* 3.9 8.6 - - - +
127B LEU* 1.3 80.7 - - - +
129B ALA* 1.3 58.7 + - - +
131B TYR* 4.4 4.2 - - - +
132B PRO* 3.8 14.6 - - - +
178B TRP* 5.1 5.2 + - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 5.0 4.8 - - + +
86B ILE* 4.3 27.6 - - + -
89B PHE* 4.4 6.7 - - + -
125B ARG 3.0 17.9 + - - +
126B PHE 4.1 2.0 - - - +
128B ASP* 1.3 78.9 - - - +
130B PHE* 1.3 62.6 + - - +
131B TYR 3.4 1.1 - - - -
132B PRO* 3.5 10.6 - - - +
133B MET* 4.7 6.9 + - - +
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 3.9 25.1 - - + -
95B PHE* 4.2 14.4 - + - -
108B LEU* 3.6 29.2 - - + -
110B LEU* 5.3 0.7 - - + -
126B PHE* 2.9 36.5 + + + +
127B LEU* 4.3 1.3 - - - +
129B ALA* 1.3 76.7 - - - +
131B TYR* 1.3 65.7 + - - +
132B PRO* 3.5 0.4 - - - -
133B MET* 3.5 10.7 + - + -
134B LEU* 3.3 50.9 + - + +
137B MET* 4.2 22.0 - - + -
146B VAL* 4.8 7.2 - - + -
150B TRP* 4.3 13.2 - + - -
178B TRP* 4.3 9.9 - + - -
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Residues in contact with TYR 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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127B LEU 2.9 19.1 + - - +
128B ASP* 4.6 4.0 - - - +
130B PHE* 1.3 77.4 - - - +
132B PRO* 1.3 73.1 - - + +
134B LEU* 3.1 18.0 + - + +
135B GLU* 3.2 20.2 + - - +
178B TRP* 3.8 28.9 - + - +
181B LYS* 3.7 33.3 + - + +
182B VAL* 4.1 14.4 - - + -
185B LYS* 4.3 9.2 - - - +
186B LEU* 3.4 33.7 - - + +
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Residues in contact with PRO 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP 3.8 13.5 - - - +
129B ALA* 3.5 17.5 - - - +
131B TYR* 1.3 101.2 - - + +
133B MET* 1.3 58.7 + - - +
135B GLU* 3.2 14.6 + - + +
136B ALA* 2.8 24.6 + - - +
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Residues in contact with MET 133 (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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81B GLN* 6.4 0.2 - - - +
84B MET* 4.4 20.2 - - + +
129B ALA 4.7 4.4 + - - +
130B PHE* 3.5 19.2 + - + +
131B TYR 3.2 0.6 - - - -
132B PRO* 1.3 79.4 - - - +
134B LEU* 1.3 60.3 + - - +
136B ALA* 3.0 15.2 + - + +
137B MET* 2.8 50.2 + - + +
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Residues in contact with LEU 134 (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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130B PHE* 3.3 46.2 + - + +
131B TYR* 3.1 10.0 + - + +
133B MET* 1.3 79.3 - - - +
135B GLU* 1.3 60.5 + - - +
137B MET* 3.4 12.9 + - - +
138B LYS* 3.3 16.6 + - - +
146B VAL* 4.6 5.6 - - + -
150B TRP* 4.4 12.1 - - + -
178B TRP* 3.9 24.7 - - + -
182B VAL* 4.0 21.1 - - + -
186B LEU* 4.8 5.2 - - + -
188B TRP* 3.3 42.2 + - + +
224B MET* 6.2 0.2 - - + -
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Residues in contact with GLU 135 (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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131B TYR* 3.2 17.2 + - - +
132B PRO* 3.2 17.5 + - + +
133B MET 3.2 0.4 - - - -
134B LEU* 1.3 77.1 - - - +
136B ALA* 1.3 65.3 + - - +
138B LYS* 3.3 13.6 + - - +
139B ASN* 3.3 28.3 + - - +
186B LEU* 3.6 31.4 - - + +
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Residues in contact with ALA 136 (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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132B PRO 2.8 13.0 + - - +
133B MET* 3.0 25.7 + - + +
135B GLU* 1.3 76.5 - - - +
137B MET* 1.3 63.0 + - + +
139B ASN* 3.1 16.0 + - - +
140B GLU* 3.1 22.8 + - + +
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.3 7.6 - - + -
97B ARG* 3.9 18.6 - - - +
106B ILE* 3.7 32.8 - - + -
130B PHE* 4.2 27.1 - - + -
133B MET* 2.8 36.9 + - + +
134B LEU* 3.7 9.0 - - - +
135B GLU 3.3 0.2 - - - -
136B ALA* 1.3 73.4 - - + +
138B LYS* 1.3 63.0 + - - +
140B GLU* 3.3 26.1 + - - +
141B GLY 4.3 1.7 + - - -
142B ARG* 4.9 2.9 - - - +
144B ILE* 3.5 22.7 - - + +
146B VAL* 4.3 15.7 - - + -
188B TRP* 3.9 13.2 - - + -
226B THR* 5.3 1.2 - - - +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU 3.3 9.1 + - - +
135B GLU* 3.3 12.2 + - - +
136B ALA 3.2 0.6 - - - -
137B MET* 1.3 78.9 - - - +
139B ASN* 1.3 89.3 + - - +
140B GLU 3.2 3.6 + - - -
141B GLY* 3.6 9.9 + - - -
142B ARG 5.2 0.2 + - - -
186B LEU* 3.1 43.7 - - + +
187B GLY 6.1 0.2 - - - -
188B TRP* 4.5 12.9 - - + +
226B THR* 5.5 8.1 - - + -
227B PRO* 6.1 5.8 - - + -
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 3.3 26.6 + - - +
136B ALA* 3.1 11.7 + - - +
138B LYS* 1.3 106.8 + - - +
140B GLU* 1.3 63.3 + - - +
141B GLY* 3.2 2.4 + - - -
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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