Contacts of the helix formed by residues 117 - 137 (chain A) in PDB entry 4C8B
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.9 3.8 + - - +
116A VAL* 1.3 75.2 - - - +
118A TRP* 1.3 68.2 + - - +
119A PRO* 3.2 13.2 - - + -
120A LEU* 3.2 14.3 + - - +
121A ARG* 3.3 8.3 + - - +
305A ALA* 3.7 27.1 + - + +
309A LEU* 5.7 0.8 - - - +
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Residues in contact with TRP 118 (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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116A VAL 3.6 0.8 + - - -
117A ALA* 1.3 72.9 - - - +
119A PRO* 1.3 71.0 - - + +
121A ARG* 3.0 55.8 + - + +
122A PHE* 3.0 31.3 + + + -
223A LEU* 3.8 20.4 - - + -
256A PRO* 4.9 4.5 - - + -
258A ASP* 4.7 8.8 + - + +
259A ILE* 3.5 33.4 - - + -
260A PRO* 3.7 38.0 - - + +
297A PHE* 4.8 2.7 - - + -
1317A EDO 3.9 15.0 - - - -
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA* 3.2 16.4 - - + -
118A TRP* 1.3 94.2 - - + +
120A LEU* 1.3 62.3 + - - +
122A PHE* 3.1 3.3 + - - +
123A ARG 2.9 19.1 + - - -
297A PHE* 3.6 32.3 - - + -
301A THR* 3.9 25.1 - - - +
302A PHE* 3.2 32.7 - - + -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.9 0.7 - - + -
116A VAL* 4.3 11.7 - - + -
117A ALA 3.2 11.2 + - - +
119A PRO* 1.3 80.4 - - - +
121A ARG* 1.3 62.7 + - - +
123A ARG* 3.3 34.0 + - - +
124A ILE* 3.0 39.3 + - + +
158A PHE* 4.1 12.3 - - + +
302A PHE* 4.2 5.5 - - + +
305A ALA* 3.9 19.6 - - + +
306A VAL* 4.1 19.1 - - + -
309A LEU* 3.5 35.0 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 5.4 3.4 - - + -
116A VAL* 2.7 42.0 + - + +
117A ALA 3.3 10.5 + - - +
118A TRP* 3.0 49.0 + - + +
120A LEU* 1.3 78.7 - - - +
122A PHE* 1.3 62.1 + - + +
124A ILE* 3.4 9.9 + - + +
125A LEU* 3.1 28.0 + - - +
222A VAL* 2.9 43.6 + - + +
223A LEU* 3.6 3.7 + - + +
225A ARG* 4.0 15.5 - - - +
1317A EDO 3.4 40.8 + - - -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 3.0 44.6 + + + -
119A PRO 3.1 5.1 + - - +
121A ARG* 1.3 75.3 - - + +
123A ARG* 1.3 60.9 + - - +
125A LEU* 3.2 12.7 + - + +
126A HIS* 2.8 30.7 + - - +
223A LEU* 4.3 17.0 - - + -
259A ILE* 4.5 1.1 - - + -
260A PRO* 3.4 34.5 - - + -
265A MET* 3.6 41.1 - - + -
290A LEU* 5.3 1.8 - - + -
293A VAL* 4.0 10.5 - - + -
294A LEU* 3.9 16.5 - - + +
297A PHE* 3.5 32.8 - + + -
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Residues in contact with ARG 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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119A PRO 2.9 12.1 + - - +
120A LEU* 3.5 24.7 - - - +
121A ARG 3.3 0.2 - - - -
122A PHE* 1.3 77.1 - - - +
124A ILE* 1.3 57.8 + - - +
126A HIS* 3.2 6.1 + - + +
127A GLU* 2.9 55.2 + - + +
157A GLU 2.8 27.7 + - - -
158A PHE 3.1 20.6 + - - -
159A HIS* 3.2 30.0 + - - -
294A LEU* 3.8 10.6 - - + +
302A PHE* 3.9 43.1 - - + +
303A LEU* 5.0 2.6 - - - +
306A VAL* 4.1 7.1 - - - +
156B ASN* 5.6 0.8 + - - -
157B GLU* 4.0 8.7 + - - -
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.2 21.8 - - + -
106A LEU* 4.0 27.6 - - + -
116A VAL* 5.7 0.7 - - + -
120A LEU* 3.0 35.2 + - + +
121A ARG* 3.6 9.4 - - + +
122A PHE 3.2 0.2 - - - -
123A ARG* 1.3 75.4 - - + +
125A LEU* 1.3 60.2 + - - +
127A GLU* 3.2 4.8 + - - +
128A ILE* 2.9 42.6 + - + +
154A LEU* 4.3 10.1 - - + -
158A PHE* 4.2 12.8 - - + +
160A VAL* 3.7 26.4 - - + +
222A VAL* 5.3 5.2 - - + -
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Residues in contact with LEU 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 ARG 3.1 20.3 + - - +
122A PHE* 3.7 18.2 - - + +
124A ILE* 1.3 73.9 - - + +
126A HIS* 1.3 64.8 + - - +
128A ILE* 3.4 5.9 + - + -
129A ALA* 3.2 13.7 + - - +
215A TYR* 2.8 33.6 + - + +
218A ILE* 4.6 5.4 - - + -
219A THR* 3.6 48.2 - - + +
222A VAL* 4.0 29.4 - - + -
223A LEU* 4.5 13.9 - - + -
265A MET* 5.3 4.5 - - - -
290A LEU* 4.5 7.0 - - + -
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Residues in contact with HIS 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 PHE 2.8 17.9 + - - +
123A ARG* 3.5 7.9 + - - +
125A LEU* 1.3 77.2 - - - +
127A GLU* 1.3 59.5 + - - +
129A ALA* 3.1 7.1 + - - +
130A LEU* 2.9 44.0 + - + +
287A LEU* 3.5 23.7 - - + +
290A LEU* 4.1 21.7 - - + +
291A GLU* 4.4 18.9 + - + +
294A LEU* 3.9 29.4 - - + +
41B ARG* 5.3 3.0 + - - +
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Residues in contact with GLU 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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77A TYR* 3.6 39.6 + - + +
123A ARG* 2.9 36.4 + - + +
124A ILE* 3.8 4.0 - - - +
126A HIS* 1.3 77.8 - - + +
128A ILE* 1.3 65.6 + - - +
130A LEU* 3.3 11.9 + - + +
131A GLY* 3.0 17.8 + - - -
158A PHE 4.4 1.2 - - - +
159A HIS* 2.6 36.3 + - - -
160A VAL* 2.8 42.5 + - + +
162A ILE* 4.8 0.2 - - - +
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Residues in contact with ILE 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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103A LEU* 4.0 18.2 - - + -
124A ILE* 2.9 38.4 + - + +
125A LEU* 3.7 11.7 - - + +
127A GLU* 1.3 74.6 - - - +
129A ALA* 1.3 58.6 + - - +
131A GLY 3.1 1.6 + - - -
132A VAL* 3.0 40.1 + - + +
147A LEU* 5.3 3.4 - - + -
152A ILE* 4.0 34.1 - - + -
160A VAL* 4.0 6.7 - - + -
162A ILE* 3.6 7.5 - - + +
215A TYR* 3.6 22.4 - - + -
218A ILE* 4.2 19.3 - - + -
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Residues in contact with ALA 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 LEU 3.2 9.2 + - - +
126A HIS 3.1 10.3 + - - +
128A ILE* 1.3 77.8 - - - +
130A LEU* 1.3 64.9 + - - +
133A ASN* 3.0 28.6 + - - +
215A TYR* 3.8 17.7 - - + +
283A PHE* 4.1 19.4 - - + -
286A CYS* 5.1 2.9 - - + -
287A LEU* 3.6 22.1 - - + +
290A LEU* 4.4 6.1 - - + -
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Residues in contact with LEU 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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75A PHE* 3.7 9.5 - - + -
77A TYR* 3.7 37.7 - - + +
126A HIS* 2.9 39.9 + - + +
127A GLU* 3.7 11.2 - - + +
128A ILE 3.3 0.2 - - - -
129A ALA* 1.3 76.1 - - - +
131A GLY* 1.3 61.7 + - - +
133A ASN* 3.9 3.0 + - - +
134A TYR* 3.2 21.7 + - - +
287A LEU* 3.5 26.9 - - + -
40B TRP 3.4 24.4 - - - +
41B ARG* 3.7 15.3 - - + +
42B VAL* 4.3 6.7 - - + -
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Residues in contact with GLY 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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75A PHE* 4.7 3.4 - - - -
77A TYR* 4.1 12.8 - - - -
78A ILE* 3.9 10.0 - - - +
127A GLU 3.0 12.8 + - - -
128A ILE 3.1 3.3 + - - -
130A LEU* 1.3 74.9 - - - +
132A VAL* 1.3 64.6 + - - +
134A TYR* 3.2 13.3 + - - +
135A LEU* 3.2 16.5 + - - +
162A ILE* 3.7 16.2 - - - -
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Residues in contact with VAL 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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128A ILE* 3.0 19.9 + - + +
131A GLY* 1.3 74.4 - - - +
133A ASN* 1.3 62.4 + - - +
135A LEU* 3.0 17.6 + - + +
136A HIS* 2.9 37.2 + - + +
144A HIS* 5.4 0.9 - - + -
147A LEU* 3.8 26.0 - - + -
162A ILE* 3.6 14.6 - - + -
211A ASP* 3.9 10.1 - - + +
283A PHE* 3.4 41.1 - - + -
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Residues in contact with ASN 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 ALA 3.0 20.1 + - - +
130A LEU 3.9 2.8 + - - +
132A VAL* 1.3 78.1 - - - +
134A TYR* 1.3 61.9 + - - +
136A HIS* 3.2 6.1 + - - +
137A ASN* 2.9 45.2 + - - +
283A PHE* 4.0 14.5 - - + +
284A LEU* 3.7 23.4 + - - +
287A LEU* 3.8 23.9 - - + +
39B ASP 2.8 28.3 + - - -
40B TRP* 4.0 10.1 + - - +
41B ARG* 4.6 0.2 - - - +
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Residues in contact with TYR 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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72A LYS 4.5 6.8 + - - -
73A ALA* 4.1 13.2 - - - -
74A ARG 3.3 25.7 + - - -
75A PHE* 3.5 43.5 - + + -
78A ILE* 4.8 1.1 - - + -
130A LEU 3.2 11.1 + - - +
131A GLY 3.2 9.7 + - - +
133A ASN* 1.3 79.0 - - - +
135A LEU* 1.3 74.0 + - + +
137A ASN* 3.1 15.8 + - - +
138A MET* 3.3 33.7 + - + +
11B PRO* 4.0 20.3 - - - +
40B TRP* 3.6 42.0 - + + -
82B LEU* 5.1 1.8 + - + +
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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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73A ALA* 4.0 26.7 - - + -
78A ILE* 4.0 22.2 - - + -
131A GLY 3.2 13.0 + - - +
132A VAL* 3.0 16.0 + - + +
134A TYR* 1.3 78.0 - - + +
136A HIS* 1.3 62.1 + - + +
138A MET* 3.2 20.7 + - - +
142A LEU* 2.9 45.4 + - + +
144A HIS* 4.4 33.9 - - + +
162A ILE* 5.1 2.7 - - + -
1000A 0LI 4.2 15.0 - - - -
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Residues in contact with HIS 136 (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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132A VAL* 2.9 19.5 + - + +
133A ASN* 3.2 10.7 + - - +
135A LEU* 1.3 78.0 - - + +
137A ASN* 1.3 61.4 + - - +
141A PRO* 3.4 25.5 - - + +
142A LEU 3.3 17.5 - - - -
143A LEU* 3.7 17.8 - - + +
208A ILE 4.6 12.4 + - - -
211A ASP* 2.7 32.7 + - + -
212A ILE 5.4 0.4 - - - -
283A PHE* 3.6 36.2 + + + +
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN* 2.9 47.3 + - - +
134A TYR* 3.1 7.9 + - - +
136A HIS* 1.3 79.5 - - - +
138A MET* 1.3 63.9 + - - +
139A THR* 4.4 3.5 + - - -
284A LEU* 5.7 4.8 - - - +
39B ASP* 3.8 28.1 + - + +
40B TRP* 4.5 19.0 + - + +
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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
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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