Contacts of the helix formed by residues 114 - 139 (chain B) in PDB entry 3G4C
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 PRO 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR 4.9 0.2 - - - +
113B ILE* 1.3 92.3 - - + +
115B PRO* 1.3 68.9 - - + +
116B GLU* 4.2 15.7 - - + +
117B ARG* 2.9 38.6 + - + +
118B VAL* 3.3 9.4 + - - +
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.7 35.5 - - + +
106B LEU* 4.1 28.7 - - + +
111B THR* 5.6 5.6 - - + +
113B ILE 3.6 2.9 - - - +
114B PRO* 1.3 86.3 - - + +
116B GLU* 1.3 66.1 + - - +
118B VAL* 3.6 4.2 + - + +
119B THR* 3.2 28.9 + - - -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.4 28.0 - - + +
114B PRO* 3.0 13.7 + - + +
115B PRO* 1.3 89.9 - - - +
117B ARG* 1.3 59.5 + - - +
119B THR* 3.6 9.5 + - - +
120B GLU* 3.0 25.8 + - - +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.3 13.2 - - + -
114B PRO* 2.9 29.7 + - + +
116B GLU* 1.3 78.3 - - - +
118B VAL* 1.3 55.7 + - - +
120B GLU* 3.2 17.0 + - + +
121B LYS* 2.7 66.9 + - - +
124B GLU* 6.0 0.2 - - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO* 6.3 0.9 - - + -
106B LEU* 3.4 33.9 - - + -
111B THR* 4.3 4.3 - - + -
113B ILE* 3.8 26.0 - - + +
114B PRO 3.3 6.4 + - - +
115B PRO* 3.7 3.6 - - + +
117B ARG* 1.3 77.5 - - - +
119B THR* 1.3 63.7 + - - +
121B LYS* 3.4 2.4 + - - +
122B ILE* 3.0 42.1 + - + +
136C LEU* 4.1 15.0 - - + +
141C VAL* 3.5 31.9 - - + -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.8 19.2 - - + +
101B PRO* 2.6 26.4 + - - +
102B SER 3.9 8.8 + - - -
103B PRO* 3.9 8.4 - - + +
106B LEU* 6.0 0.3 - - - +
115B PRO 3.2 15.7 + - - -
116B GLU* 3.7 8.7 - - - +
118B VAL* 1.3 80.3 - - - +
120B GLU* 1.3 58.0 + - - +
122B ILE* 3.5 10.3 + - - +
123B SER* 3.2 27.8 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU 3.0 15.9 + - - +
117B ARG* 3.2 24.7 + - + +
119B THR* 1.3 75.2 - - - +
121B LYS* 1.3 60.7 + - - +
122B ILE 3.2 0.2 - - - -
123B SER* 3.5 7.2 + - - -
124B GLU* 2.8 46.7 + - + +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.5 16.6 - - + -
117B ARG* 2.7 42.2 + - - +
118B VAL 3.8 4.5 - - - +
120B GLU* 1.3 74.5 - - + +
122B ILE* 1.3 60.9 + - - +
124B GLU* 3.7 17.1 + - - +
125B ILE* 3.3 16.3 + - - +
132C THR* 3.8 21.7 - - + +
135C GLU* 3.6 33.4 + - + +
136C LEU* 4.4 21.3 - - + -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 4.3 8.3 - - + -
101B PRO* 4.1 31.6 - - + -
118B VAL* 3.0 39.8 + - + +
119B THR* 3.8 7.0 - - - +
120B GLU 3.2 0.2 - - - -
121B LYS* 1.3 73.8 - - - +
123B SER* 1.3 60.4 + - - +
125B ILE* 3.3 4.7 + - - +
126B VAL* 3.0 32.1 + - - +
153B ASN* 3.8 25.1 - - - +
136C LEU* 4.1 12.8 - - + -
145C VAL* 4.7 10.8 - - + +
148C ILE* 4.7 6.1 - - + -
149C VAL* 3.8 26.7 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.7 29.7 - - - +
119B THR* 3.2 16.7 + - - +
120B GLU* 3.6 8.3 - - - -
122B ILE* 1.3 78.0 - - - +
124B GLU* 1.3 62.2 + - - +
126B VAL* 3.6 1.3 - - - +
127B ASP* 3.0 36.7 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 6.0 0.5 - - - -
120B GLU* 2.8 39.2 + - + +
121B LYS* 3.7 19.9 + - - +
122B ILE 3.2 0.2 - - - -
123B SER* 1.3 75.0 - - - +
125B ILE* 1.3 63.2 + - - +
127B ASP* 3.2 5.1 + - - +
128B LYS* 3.0 54.0 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LYS 3.3 6.1 + - - +
122B ILE 3.3 6.7 + - - +
124B GLU* 1.3 78.8 - - + +
126B VAL* 1.3 67.2 + - + +
128B LYS* 3.3 14.6 + - + +
129B ALA* 2.8 30.5 + - + +
151B PRO* 5.1 1.6 - - + -
125C ILE* 4.8 2.9 - - + +
128C LYS* 3.7 16.2 - - + -
129C ALA* 3.5 31.0 - - + +
132C THR* 3.3 31.4 - - + +
149C VAL* 3.8 35.9 - - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 4.3 3.8 - - + +
98B PHE* 3.3 40.1 - - + -
100B ILE* 4.3 6.7 - - + -
122B ILE* 3.0 22.3 + - + +
123B SER* 3.6 6.5 - - - +
125B ILE* 1.3 79.3 - - + +
127B ASP* 1.3 66.9 + - - +
129B ALA* 3.4 2.1 + - - +
130B TYR* 2.9 28.6 + - - +
151B PRO* 4.1 12.3 - - + -
153B ASN* 3.4 37.2 - - - +
149C VAL* 5.8 1.3 - - + -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 2.5 39.4 + - - -
123B SER* 3.0 24.2 + - - +
124B GLU* 3.7 5.3 - - - +
126B VAL* 1.3 75.2 - - - +
128B LYS* 1.3 65.8 + - + +
130B TYR* 3.5 0.9 + - - +
131B ARG* 3.1 25.8 + - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 3.0 51.0 + - - +
125B ILE* 3.7 14.6 - - + +
127B ASP* 1.3 77.7 - - + +
129B ALA* 1.3 62.2 + - - +
131B ARG* 3.7 4.9 - - - +
132B THR* 3.0 28.3 + - - -
125C ILE* 4.2 6.3 - - + -
128C LYS* 4.1 36.5 - - + +
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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
----------------------------------------------------------
125B ILE* 2.8 25.4 + - + +
126B VAL 3.7 3.4 - - - +
128B LYS* 1.3 73.4 - - - +
130B TYR* 1.3 58.9 + - - +
132B THR* 3.4 3.3 + - - -
133B TYR* 2.9 27.9 + - - +
149B VAL* 3.6 26.6 - - - +
150B LEU* 4.3 2.0 - - - -
151B PRO* 3.8 17.5 - - + -
125C ILE* 3.9 16.8 - - + +
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Residues in contact with TYR 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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93B LYS* 5.0 1.7 - - - +
94B LEU 2.7 26.8 + - - -
95B SER* 4.1 3.2 - - - -
96B TYR* 3.5 52.4 + + + +
98B PHE* 4.1 13.9 - + + -
126B VAL 2.9 17.9 + - - +
127B ASP 4.1 2.2 - - - +
129B ALA* 1.3 74.2 - - - +
131B ARG* 1.3 60.1 + - - +
133B TYR* 3.2 26.0 + + - +
134B LEU* 2.8 66.5 + - + +
150B LEU* 3.8 16.3 - - + +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 3.1 18.6 + - - +
128B LYS* 3.7 6.7 - - - +
130B TYR* 1.3 74.4 - - - +
132B THR* 1.3 53.6 + - - +
134B LEU* 3.0 14.1 + - - +
135B GLU* 2.7 65.7 + - - +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS 3.0 11.6 + - - -
129B ALA 3.5 5.6 - - - -
131B ARG* 1.3 77.8 - - - +
133B TYR* 1.3 54.6 + - - +
135B GLU* 3.1 15.2 + - - +
136B LEU* 2.8 54.5 + - + +
149B VAL* 4.3 0.2 - - + -
121C LYS* 4.3 18.7 + - + +
124C GLU* 6.1 0.5 - - - +
125C ILE* 2.8 45.1 - - + +
128C LYS* 5.7 1.4 + - - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 5.1 0.5 + - - -
92B SER 4.0 4.3 + - - -
93B LYS* 3.8 5.2 - - + -
94B LEU* 3.1 37.9 + - + +
129B ALA 2.9 14.9 + - - +
130B TYR* 3.2 38.4 - + - +
132B THR* 1.3 76.0 - - - +
134B LEU* 1.3 71.0 + - + +
136B LEU* 3.3 4.8 + - - +
137B ILE* 3.1 55.0 + - + +
143B ARG* 4.5 5.0 - - - +
146B ALA* 3.4 21.8 - - + -
147B ARG* 3.6 27.9 - - + +
149B VAL* 4.1 9.4 - - + +
150B LEU* 3.6 18.4 - - + -
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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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93B LYS* 5.1 9.6 - - + -
130B TYR* 2.8 64.8 + - + +
131B ARG* 3.5 13.5 - - - +
133B TYR* 1.3 82.0 - - + +
135B GLU* 1.3 66.4 + - + +
137B ILE* 3.4 7.9 + - + +
138B GLU* 3.0 42.2 + - + +
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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
----------------------------------------------------------
131B ARG* 2.7 46.8 + - - +
132B THR* 3.5 13.0 + - - +
134B LEU* 1.3 70.1 - - - +
136B LEU* 1.3 65.7 + - - +
138B GLU* 3.4 14.7 + - - +
139B SER* 3.1 28.3 + - - +
121C LYS* 2.4 44.4 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 2.8 38.0 + - + +
133B TYR 3.7 4.3 - - - +
135B GLU* 1.3 73.9 - - - +
137B ILE* 1.3 62.6 + - - +
139B SER* 3.1 8.9 + - - -
141B VAL* 3.1 35.1 + - + +
146B ALA* 3.8 31.2 - - + +
149B VAL* 4.5 2.9 - - + -
113C ILE* 4.9 4.9 - - + -
118C VAL* 4.1 23.3 - - + -
121C LYS* 4.1 27.8 - - + -
122C ILE* 3.9 26.0 - - + -
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS* 4.5 11.7 - - + -
133B TYR* 3.1 54.7 + - + +
134B LEU* 3.7 9.6 - - + +
135B GLU 3.3 0.2 - - - -
136B LEU* 1.3 74.4 - - - +
138B GLU* 1.3 61.4 + - + +
140B GLY* 3.0 20.6 + - - -
141B VAL 3.9 10.2 + - - +
143B ARG* 3.8 33.0 - - + +
146B ALA* 3.9 14.4 - - + -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.0 37.4 + - + +
135B GLU* 3.7 12.9 + - - +
136B LEU 3.3 0.2 - - - -
137B ILE* 1.3 79.4 - - + +
139B SER* 1.3 59.9 + - - +
140B GLY 3.2 1.5 + - - -
112C THR* 4.2 8.7 - - - +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 3.1 13.8 + - - +
136B LEU* 3.1 11.2 + - - -
138B GLU* 1.3 76.2 - - - +
140B GLY* 1.3 57.3 + - - +
141B VAL* 3.5 4.5 - - - -
110C LYS 3.9 0.3 - - - +
111C THR* 2.8 11.0 - - - -
112C THR* 2.8 50.2 + - - +
113C ILE* 3.8 30.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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