Contacts of the helix formed by residues 114 - 135 (chain A) in PDB entry 4FG8
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 THR 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.7 19.7 - - + -
113A TYR* 1.3 81.2 - - - +
115A GLU* 1.3 65.2 + - - +
116A ARG* 3.1 12.1 + - - +
117A ASP* 2.9 43.1 + - - +
118A ALA* 3.0 12.0 + - - +
120A ARG* 5.1 0.9 + - - -
282A LEU 3.8 7.2 - - - -
283A ASP* 3.4 24.5 + - - +
284A LYS 3.3 20.2 - - - +
286A ILE* 4.1 7.4 - - - -
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Residues in contact with GLU 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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114A THR* 1.3 72.5 - - - +
116A ARG* 1.3 57.4 + - - +
118A ALA* 3.0 5.9 + - - +
119A SER 2.9 23.9 + - - -
212A LEU* 3.6 28.9 - - + -
244A ASP 4.0 0.7 - - - +
245A ILE* 3.3 15.6 - - + +
246A SER* 2.7 49.8 + - - -
249A ALA* 3.9 4.9 - - - -
275A TRP* 2.8 28.1 + - + -
281A ALA* 3.6 2.0 - - - -
282A LEU* 3.3 34.4 + - + +
284A LYS 4.3 2.2 + - - -
286A ILE* 4.0 7.7 - - + +
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Residues in contact with ARG 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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114A THR* 3.0 10.0 + - - +
115A GLU* 1.3 77.7 - - - +
117A ASP* 1.3 64.4 + - - +
119A SER* 3.5 2.6 + - - -
120A ARG* 3.0 65.2 + - + +
279A ASP* 5.0 13.4 + - - +
281A ALA* 3.5 32.0 + - + +
282A LEU 3.1 8.6 + - - +
283A ASP* 3.2 41.7 + - - +
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Residues in contact with ASP 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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110A LYS* 5.3 9.0 - - - +
112A PHE* 4.3 5.0 - - - +
113A TYR* 3.8 23.0 - - + -
114A THR* 2.9 38.3 + - - +
116A ARG* 1.3 74.9 - - - +
118A ALA* 1.3 63.2 + - - +
120A ARG* 3.3 25.9 + - - +
121A LEU* 3.2 29.5 + - + +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 3.6 22.7 + - - +
114A THR 3.0 8.4 + - - +
115A GLU 3.3 8.7 - - - +
117A ASP* 1.3 77.2 - - - +
119A SER* 1.3 56.8 + - - +
121A LEU* 3.3 9.5 + - - +
122A ILE* 2.9 32.0 + - + +
208A ALA* 5.6 0.4 - - - +
211A LEU* 4.2 11.1 - - + +
212A LEU* 3.6 25.6 - - + -
275A TRP* 3.9 6.7 - - + -
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Residues in contact with SER 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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115A GLU 2.9 11.3 + - - -
116A ARG* 3.7 8.3 - - - -
117A ASP 3.3 0.2 - - - -
118A ALA* 1.3 75.7 - - - +
120A ARG* 1.3 59.0 + - - +
122A ILE* 3.2 1.7 + - - -
123A PHE* 2.9 29.9 + - - +
275A TRP* 2.6 54.2 + - - -
276A ILE* 3.7 12.3 + - - +
281A ALA* 4.0 8.7 - - - +
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Residues in contact with ARG 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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114A THR* 5.1 0.6 + - - -
116A ARG* 3.0 61.7 + - + +
117A ASP* 3.5 27.6 + - - +
119A SER* 1.3 75.3 - - - +
121A LEU* 1.3 61.9 + - + +
123A PHE* 3.4 10.5 + - - +
124A GLN* 3.3 32.0 + - - +
283A ASP* 5.9 0.2 + - - -
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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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103A LEU* 3.9 24.7 - - + -
107A ILE* 4.8 1.6 - - + -
110A LYS* 5.2 2.2 - - - +
113A TYR* 4.5 10.5 - - + +
117A ASP* 3.2 18.8 + - + +
118A ALA* 3.5 8.7 - - - +
120A ARG* 1.3 74.0 - - + +
122A ILE* 1.3 63.7 + - - +
124A GLN* 3.1 15.0 + - - +
125A VAL* 3.1 28.3 + - + +
149A TYR* 3.6 26.2 - - + +
156A SER 5.8 0.4 - - - +
158A ILE* 4.0 26.3 - - + +
211A LEU* 4.1 23.3 - - + -
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Residues in contact with ILE 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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118A ALA* 2.9 22.1 + - + +
119A SER* 3.8 4.5 - - - +
121A LEU* 1.3 72.1 - - - +
123A PHE* 1.3 55.3 + - - +
125A VAL* 3.2 10.4 + - + +
126A LEU* 2.8 39.8 + - + +
204A ILE* 4.0 18.4 - - + +
207A ILE* 4.1 9.9 - - + -
208A ALA* 4.0 29.4 - - + +
211A LEU* 3.9 22.2 - - + -
252A PHE* 3.8 21.5 - - + -
275A TRP* 4.5 4.3 - - + -
276A ILE* 3.8 19.3 - - + -
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Residues in contact with PHE 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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77A ASN* 6.2 0.2 - - - -
119A SER* 2.9 13.5 + - - +
120A ARG* 3.4 13.0 - - - +
122A ILE* 1.3 75.2 - - - +
124A GLN* 1.3 70.2 + - + +
126A LEU* 3.8 4.3 - - - +
127A ASP* 3.0 51.4 + - + +
271A LEU* 3.8 17.5 - - + -
276A ILE* 3.8 34.0 - - + +
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Residues in contact with GLN 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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77A ASN* 2.9 41.2 + - - +
120A ARG* 3.3 25.9 + - - +
121A LEU* 3.1 18.8 + - - +
123A PHE* 1.3 90.0 - - + +
125A VAL* 1.3 57.9 + - - +
127A ASP* 3.5 5.0 + - - +
128A ALA* 3.0 29.5 + - - +
156A SER 5.1 1.8 + - - -
157A LYS* 3.2 13.0 - - - +
158A ILE* 2.9 31.8 + - + +
160A ILE* 5.4 0.4 - - - -
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Residues in contact with VAL 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* 3.1 16.9 + - + +
122A ILE* 3.6 15.7 - - + +
124A GLN* 1.3 73.9 - - - +
126A LEU* 1.3 61.6 + - - +
128A ALA* 3.3 0.7 + - - +
129A VAL* 2.8 36.8 + - + +
142A LEU* 4.9 7.0 - - + -
147A LEU* 4.0 33.4 - - + -
158A ILE* 4.7 9.4 - - + -
160A ILE* 4.1 15.0 - - + -
204A ILE* 3.6 29.8 - - + -
207A ILE* 5.6 3.4 - - + -
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Residues in contact with LEU 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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122A ILE* 2.8 39.3 + - + +
123A PHE 3.8 0.4 - - - +
125A VAL* 1.3 72.0 - - - +
127A ASP* 1.3 58.4 + - - +
129A VAL* 3.0 3.3 + - - +
130A LYS* 2.9 31.5 + - - +
201A CYS* 5.9 0.7 - - - -
204A ILE* 3.6 32.1 - - + -
252A PHE* 4.0 5.4 - - + -
256A LEU* 4.8 4.0 - - + -
267A CYS* 4.1 17.0 - - - +
270A ALA* 3.7 43.7 - - + -
271A LEU* 3.6 25.1 - - + +
276A ILE* 4.0 9.2 - - + -
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Residues in contact with ASP 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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75A HIS* 3.0 23.4 + - + -
76A PRO* 5.8 0.7 - - - +
77A ASN* 4.4 4.6 - - - +
123A PHE* 3.0 40.6 + - + +
124A GLN* 3.5 7.9 - - - +
126A LEU* 1.3 75.5 - - - +
128A ALA* 1.3 60.9 + - - +
130A LYS* 3.6 3.7 + - - +
131A TYR* 3.2 22.2 + - - +
271A LEU* 4.2 12.2 - - + +
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Residues in contact with ALA 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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75A HIS* 3.8 10.9 - - + -
77A ASN* 4.0 10.3 - - + +
78A ILE* 3.6 27.6 - - + +
124A GLN 3.0 17.2 + - - +
127A ASP* 1.3 76.2 - - - +
129A VAL* 1.3 64.6 + - - +
131A TYR* 3.3 3.5 + - - +
132A LEU* 3.0 26.3 + - + +
160A ILE* 3.6 21.3 - - + -
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Residues in contact with VAL 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 VAL* 2.8 29.0 + - + +
126A LEU 3.0 2.7 + - - +
128A ALA* 1.3 73.4 - - - +
130A LYS* 1.3 56.7 + - - +
132A LEU* 3.2 14.4 + - + +
133A HIS* 2.8 55.6 + - + +
139A HIS* 5.5 0.4 - - + -
142A LEU* 3.7 30.1 - - + -
160A ILE* 4.7 4.9 - - + -
200A ASP* 3.9 13.5 - - + +
204A ILE* 3.9 12.3 - - + -
267A CYS* 3.6 10.3 - - - -
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Residues in contact with LYS 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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126A LEU 2.9 19.8 + - - +
127A ASP* 3.9 4.3 - - - +
129A VAL* 1.3 70.6 - - - +
131A TYR* 1.3 61.5 + - - +
133A HIS* 3.3 6.0 + - + +
134A ASP* 2.9 54.3 + - - +
267A CYS* 3.8 21.0 - - + -
268A GLU* 2.6 42.4 - - - +
271A LEU* 4.1 13.5 - - + -
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Residues in contact with TYR 131 (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 LYS 3.4 10.4 + - - -
73A ILE* 4.0 6.7 - - + -
74A LYS* 3.0 41.4 + - - +
75A HIS* 3.6 26.2 - + + -
78A ILE* 3.8 16.6 - - + -
127A ASP* 3.2 16.4 + - - +
128A ALA 3.6 2.2 - - - +
129A VAL 3.2 0.2 - - - -
130A LYS* 1.3 80.6 - - - +
132A LEU* 1.3 63.7 + - - +
134A ASP* 3.3 16.6 + - + +
135A LEU* 3.3 44.9 + - + +
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Residues in contact with LEU 132 (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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73A ILE* 3.9 38.6 - - + -
78A ILE* 3.9 14.6 - - + -
128A ALA* 3.0 19.0 + - + +
129A VAL* 3.2 15.9 + - + +
131A TYR* 1.3 75.1 - - + +
133A HIS* 1.3 57.5 + - + +
135A LEU* 2.9 16.8 + - + +
137A ILE* 2.7 57.3 + - + +
139A HIS* 4.1 31.0 - - + +
160A ILE* 5.5 5.4 - - + -
162A ASP 5.6 1.1 - - - +
163A PHE* 4.5 7.0 - - - +
200A ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 133 (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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129A VAL* 2.8 38.8 + - + +
130A LYS* 3.3 7.8 + - + +
132A LEU* 1.3 72.7 - - + +
134A ASP* 1.3 60.3 + - - +
136A GLY* 2.9 18.1 + - - +
137A ILE 3.2 21.8 - - - +
138A VAL* 4.4 0.7 - - - -
197A LYS* 3.2 61.6 + - + +
200A ASP* 2.9 28.0 + - + +
201A CYS* 4.4 5.1 - - - -
267A CYS* 4.1 16.2 - - - +
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Residues in contact with ASP 134 (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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130A LYS* 2.9 48.5 + - - +
131A TYR* 3.6 10.8 - - + +
132A LEU 3.2 0.4 - - - -
133A HIS* 1.3 78.5 - - - +
135A LEU* 1.3 63.8 + - + +
136A GLY 3.2 0.8 + - - -
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Residues in contact with LEU 135 (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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69A VAL* 4.7 13.3 - - + +
72A LYS* 4.4 11.2 - - + +
73A ILE* 3.7 32.1 - - + +
131A TYR* 3.3 51.1 + - + +
132A LEU* 2.9 14.0 + - + +
134A ASP* 1.3 80.5 - - + +
136A GLY* 1.3 61.3 + - - +
137A ILE* 3.6 11.6 + - + +
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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