Contacts of the helix formed by residues 143 - 161 (chain J) in PDB entry 3EOA
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 143 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 4.7 0.4 - - - -
140J MET 5.7 0.5 - - - +
141J SER 4.9 3.8 - - - +
142J LEU* 1.3 77.8 - - - +
144J PRO* 1.3 73.5 - - + +
145J ASP* 4.2 9.0 - - + +
146J GLU* 3.0 36.1 + - + +
147J PHE* 2.7 29.3 + - - +
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Residues in contact with PRO 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.1 31.6 - - + +
55A GLN* 5.7 1.1 - - - +
100B ILE* 5.5 3.6 - - + -
102B PHE* 3.6 21.8 - - + -
103B TYR* 3.5 25.3 - - + +
107B TYR* 4.9 2.5 - - - +
142J LEU 4.6 0.2 - - - +
143J GLN* 1.3 92.1 - - + +
145J ASP* 1.3 59.2 + - + +
147J PHE* 4.2 5.6 - - + -
148J GLN* 3.0 30.7 + - - +
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Residues in contact with ASP 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 6.1 4.0 - - - +
143J GLN* 4.7 7.0 - - + +
144J PRO* 1.3 81.5 - - + +
146J GLU* 1.3 69.1 + - - +
148J GLN* 3.8 5.4 - - - +
149J LYS* 3.0 52.9 + - - -
293J GLU* 5.2 0.7 - - - +
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Residues in contact with GLU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J SER 3.8 10.2 - - - +
142J LEU* 3.6 11.4 - - + +
143J GLN* 3.2 48.0 + - + +
145J ASP* 1.3 85.5 - - - +
147J PHE* 1.3 61.3 + - - +
148J GLN 3.4 0.2 - - - -
149J LYS* 3.5 8.5 - - + +
150J ILE* 3.5 15.4 + - - +
239J ASP* 4.8 0.5 - - - +
292J PHE* 3.3 58.0 - - + -
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Residues in contact with PHE 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 3.5 36.1 - + - -
136J PHE* 3.8 30.5 - + - -
137J ASP 3.8 19.3 - - - -
142J LEU* 3.9 14.8 - - + +
143J GLN 2.7 21.7 + - - +
144J PRO* 4.0 4.0 - - + +
146J GLU* 1.3 72.0 - - - +
148J GLN* 1.3 63.3 + - - +
149J LYS 3.2 0.2 - - - -
150J ILE* 3.3 17.0 + - + +
151J LEU* 3.3 18.1 + - + +
172J GLN* 3.8 15.9 - - - -
199J VAL* 4.1 8.7 - - + -
201J HIS* 3.5 51.1 - + + -
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Residues in contact with GLN 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 4.4 12.3 + - - +
32B HIS* 3.4 32.5 + - + -
102B PHE* 3.5 21.0 - - + -
144J PRO 3.0 20.8 + - - +
145J ASP* 3.8 6.7 - - - +
147J PHE* 1.3 75.7 - - - +
149J LYS* 1.3 59.5 + - - +
151J LEU* 3.0 22.4 + - - +
152J ASP* 2.9 60.1 + - - +
155J LYS* 4.5 4.8 - - - +
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Residues in contact with LYS 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ASP* 3.0 39.8 + - - +
146J GLU* 3.5 13.2 - - + +
147J PHE 3.2 0.4 - - - -
148J GLN* 1.3 80.8 - - - +
150J ILE* 1.3 55.8 + - - +
152J ASP* 3.4 10.3 + - + +
153J PHE* 3.0 27.0 + - - +
292J PHE* 3.5 34.8 - - + +
293J GLU* 2.8 28.4 + - - +
295J LEU* 4.0 7.6 - - + +
296J LYS* 4.5 15.0 - - + +
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Residues in contact with ILE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J PHE* 3.9 30.3 - - + -
137J ASP* 4.3 10.1 - - + +
142J LEU* 4.0 25.1 - - + -
146J GLU 3.5 16.1 + - - +
147J PHE* 3.3 9.6 + - + +
148J GLN 3.2 0.4 - - - -
149J LYS* 1.3 75.3 - - - +
151J LEU* 1.3 66.6 - - - +
153J PHE* 3.1 5.9 + - - +
154J MET* 3.0 25.7 + - - +
237J ILE* 3.9 36.6 - - + +
238J THR 6.0 0.9 - - - -
239J ASP* 5.8 1.3 - - + -
261J ILE* 4.2 11.0 - - + -
292J PHE* 4.1 9.6 - - + -
295J LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 3.6 37.9 - - + -
136J PHE* 4.1 23.8 - - + -
147J PHE* 3.3 22.6 + - + +
148J GLN* 3.0 18.1 + - - +
150J ILE* 1.3 77.7 - - - +
152J ASP* 1.3 58.8 + - - +
154J MET* 3.4 10.7 + - - +
155J LYS* 3.0 38.8 + - - +
196J LEU* 4.1 34.2 - - + +
199J VAL* 4.3 11.0 - - + -
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Residues in contact with ASP 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 5.5 3.7 + - - -
31B GLY* 5.8 0.5 - - - -
148J GLN* 2.9 43.1 + - - +
149J LYS* 3.6 12.8 - - + +
151J LEU* 1.3 74.7 - - - +
153J PHE* 1.3 60.6 + - - +
155J LYS* 3.5 19.2 + - - +
156J ASP* 3.1 36.9 + - - +
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Residues in contact with PHE 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J PHE* 4.7 7.2 - + - -
149J LYS 3.0 13.6 + - - +
150J ILE* 3.1 8.5 + - - +
152J ASP* 1.3 73.0 - - - +
154J MET* 1.3 68.6 + - + +
156J ASP* 3.4 8.1 + - - +
157J VAL* 3.2 45.7 + - + +
235J ILE* 5.0 2.2 - - + -
237J ILE* 4.2 20.0 - - + -
259J ILE* 4.2 17.0 - - + -
295J LEU* 3.4 47.8 - - + -
298J LEU* 3.8 33.2 - - + -
299J PHE* 4.2 13.9 - - + -
302J LEU* 4.4 10.1 - - + -
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Residues in contact with MET 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J PHE* 3.6 51.3 - - + -
136J PHE* 3.7 37.2 - - + -
150J ILE* 3.0 21.1 + - - +
151J LEU* 3.6 12.1 - - - +
153J PHE* 1.3 74.6 - - + +
155J LYS* 1.3 64.9 + - - +
157J VAL* 3.4 3.1 + - - +
158J MET* 3.1 35.4 + - + +
170J ALA* 3.7 24.5 - - + -
196J LEU* 4.0 15.9 - - + -
237J ILE* 4.0 9.4 - - + -
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Residues in contact with LYS 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 5.7 0.2 + - - -
31B GLY* 3.7 22.6 + - - -
52B HIS* 6.1 0.2 - - - -
148J GLN* 4.5 3.6 - - - +
151J LEU* 3.0 28.1 + - - +
152J ASP* 3.7 24.5 + - - +
154J MET* 1.3 75.5 - - - +
156J ASP* 1.3 52.7 + - - +
158J MET* 3.3 9.7 + - - +
159J LYS* 2.7 51.2 + - - +
192J PRO* 3.8 23.6 - - + +
193J ASP* 2.7 42.7 + - - +
196J LEU* 4.1 19.0 + - + -
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Residues in contact with ASP 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J ASP* 3.1 25.6 + - - +
153J PHE* 3.6 9.1 - - - +
154J MET 3.3 0.2 - - - -
155J LYS* 1.3 73.2 - - - +
157J VAL* 1.3 64.5 + - - +
159J LYS* 3.7 16.4 + - - +
160J LYS 3.1 19.4 + - - -
299J PHE* 3.3 49.1 - - + +
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Residues in contact with VAL 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J LEU* 5.7 4.0 - - + -
134J PHE* 3.8 20.4 - - + -
153J PHE* 3.2 42.3 + - + +
154J MET 3.8 5.4 - - - +
156J ASP* 1.3 75.3 - - - +
158J MET* 1.3 62.8 + - - +
160J LYS* 3.5 3.2 + - + +
161J LEU* 3.1 48.1 + - + +
168J PHE* 4.6 2.7 - - + -
299J PHE* 4.0 17.5 - - + -
302J LEU* 4.6 14.8 - - + -
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Residues in contact with MET 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J PHE* 3.7 12.1 - - + -
154J MET* 3.1 38.0 + - + +
155J LYS 3.5 4.9 - - - +
157J VAL* 1.3 77.2 - - - +
159J LYS* 1.3 61.2 + - - +
161J LEU 3.4 2.6 + - - -
162J SER* 3.2 21.8 + - - -
168J PHE* 3.6 38.6 - - + -
181J PHE* 3.6 28.3 - - + -
186J TYR* 4.2 13.4 + - + -
192J PRO* 3.8 26.5 - - + -
196J LEU* 3.8 26.7 - - + -
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Residues in contact with LYS 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J LYS* 2.7 44.2 + - - +
156J ASP* 3.3 15.5 + - - +
158J MET* 1.3 73.7 - - - +
160J LYS* 1.3 57.9 + - - +
162J SER* 3.4 20.4 - - - -
191J ASP* 5.2 1.3 - - - -
192J PRO* 4.5 19.7 - - + +
193J ASP* 3.6 24.2 + - - -
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Residues in contact with LYS 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J ASP 3.1 15.0 + - - +
157J VAL* 3.6 11.0 - - + +
159J LYS* 1.3 75.0 - - - +
161J LEU* 1.3 73.4 + - + +
162J SER 3.3 6.3 + - - +
164J THR* 4.9 0.7 + - - -
299J PHE* 3.5 26.7 - - + -
302J LEU* 4.7 11.2 - - + -
303J GLN* 3.7 40.1 + - + +
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Residues in contact with LEU 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 5.5 1.3 - - + -
157J VAL* 3.1 35.1 + - + +
158J MET 3.5 4.5 - - - -
159J LYS 3.3 0.4 - - - -
160J LYS* 1.3 93.7 - - + +
162J SER* 1.3 64.3 + - - +
164J THR* 3.2 23.6 + - + +
166J TYR* 3.8 49.2 - - + +
168J PHE* 3.8 21.4 - - + -
186J TYR* 4.0 7.4 + - - -
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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
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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