Contacts of the helix formed by residues 137 - 154 (chain F) in PDB entry 5X6E
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 ASN 137 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASP 4.5 3.0 + - - +
136F ILE* 1.3 105.0 + - + +
138F GLY* 1.3 64.2 + - - +
139F LYS 3.7 0.5 + - - -
140F LEU* 3.7 8.9 + - + +
141F GLY* 3.1 27.6 + - - +
216F ARG 4.9 1.4 - - - +
217F TYR* 3.7 36.5 - - + +
17H T 4.2 2.4 + - - -
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Residues in contact with GLY 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LYS* 4.5 13.6 - - - +
134F PHE 3.1 10.5 + - - +
135F SER 3.6 8.5 + - - -
136F ILE 3.5 3.2 + - - -
137F ASN* 1.3 78.4 - - - +
139F LYS* 1.3 60.6 + - - -
142F SER* 3.0 29.5 + - - -
17H T 4.1 4.3 - - - -
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE 4.9 1.4 + - - -
135E SER* 2.4 36.2 + - - +
137E ASN 5.2 5.4 - - - -
138E GLY* 5.1 6.3 - - - +
138F GLY* 1.3 69.9 - - - -
140F LEU* 1.3 61.1 + - - +
142F SER* 3.0 7.9 + - - +
143F ILE* 2.9 34.6 + - - +
178F SER 3.7 16.0 + - - +
179F GLY 4.0 6.3 - - - -
180F ILE* 4.1 25.5 - - + +
189F ILE* 5.6 4.3 - - + -
17H T 3.2 41.1 + - - +
18H G 3.5 25.4 - - - +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ASN* 4.0 7.2 - - + +
138F GLY 3.4 0.4 - - - -
139F LYS* 1.3 77.9 - - - +
141F GLY* 1.3 60.8 + - - +
143F ILE* 3.7 5.4 + - + +
144F CYS* 3.1 43.3 + - - -
189F ILE* 5.0 17.3 - - + -
193F LEU* 5.2 7.4 - - + -
196F GLU* 4.8 4.9 - - - +
213F TYR* 4.5 5.4 - - - +
217F TYR* 3.5 30.7 - - + +
16H T 5.3 8.1 - - - +
17H T 3.5 21.0 + - - +
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Residues in contact with GLY 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ASP 3.8 14.8 - - - +
137F ASN* 3.1 33.5 + - - -
138F GLY 3.7 1.8 - - - -
140F LEU* 1.3 75.6 - - - +
142F SER* 1.3 52.8 + - - +
144F CYS* 3.4 4.5 + - - +
145F GLY* 2.7 33.1 + - - -
217F TYR* 4.2 11.7 - - - +
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Residues in contact with SER 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ASP 4.3 0.6 + - - -
134F PHE* 3.1 52.8 + - - +
138F GLY 3.0 16.4 + - - -
139F LYS* 3.3 13.7 + - - +
141F GLY* 1.3 77.5 - - - +
143F ILE* 1.3 57.1 + - - +
146F GLN* 2.9 25.6 + - - +
178F SER* 3.7 24.0 + - - -
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F LYS 2.9 19.5 + - - +
140F LEU* 3.9 4.9 - - + +
142F SER* 1.3 73.0 - - - +
144F CYS* 1.3 57.2 + - - +
146F GLN* 3.1 4.5 + - - +
147F LEU* 2.8 58.2 + - + +
174F LEU* 3.7 23.8 - - + +
178F SER* 3.2 25.4 - - - +
180F ILE* 3.6 20.2 - - + -
186F VAL* 4.5 11.4 - - + -
189F ILE* 4.2 30.3 - - + -
193F LEU* 5.1 3.6 - - + -
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Residues in contact with CYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 3.1 33.1 + - - +
141F GLY 3.6 4.0 - - - +
143F ILE* 1.3 81.0 - - - +
145F GLY* 1.3 56.7 + - - +
147F LEU* 4.3 4.9 - - - -
148F LEU* 3.0 31.0 + - - +
193F LEU* 5.8 2.9 - - - -
196F GLU* 4.9 1.6 - - - -
213F TYR* 4.2 11.9 - - - -
214F LEU* 3.7 28.0 - - + +
217F TYR* 3.5 39.7 - - + -
218F ALA* 4.6 2.4 - - - +
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ASP* 5.4 0.2 - - - -
134F PHE* 3.7 15.5 - - - -
141F GLY 2.7 21.4 + - - -
142F SER 3.6 1.8 - - - -
143F ILE 3.1 0.4 - - - -
144F CYS* 1.3 73.0 - - - +
146F GLN* 1.3 60.8 - - - +
148F LEU* 3.2 5.0 + - - +
149F ILE* 3.0 27.6 + - - +
218F ALA* 3.9 19.4 - - - +
221F LEU* 3.9 2.9 - - - +
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Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLN* 6.0 1.0 - - - +
62F TYR* 4.7 6.5 - - - +
130F LYS* 3.4 28.5 + - - +
134F PHE* 3.7 3.6 - - + -
142F SER 2.9 19.5 + - - +
143F ILE* 3.7 3.4 - - - +
145F GLY* 1.3 70.8 - - - +
147F LEU* 1.3 63.6 + - - +
149F ILE* 3.1 10.7 + - - +
150F LEU* 2.9 59.3 + - + +
174F LEU* 4.0 18.6 - - + -
177F SER* 3.4 40.0 + - - +
178F SER* 5.2 0.4 - - - -
301F GSH 4.0 13.5 + - - -
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ILE* 2.8 42.7 + - + +
144F CYS* 3.8 10.3 - - - +
146F GLN* 1.3 71.5 - - - +
148F LEU* 1.3 50.3 + - - +
149F ILE 3.2 0.2 + - - -
150F LEU* 3.2 13.1 + - + +
151F THR* 2.7 40.5 + - - +
156F LYS* 5.1 0.3 - - - -
169F LEU* 6.3 1.6 - - + -
174F LEU* 4.0 25.1 - - + -
193F LEU* 4.2 21.5 - - + -
199F ILE* 4.6 15.3 - - + -
206F PHE* 6.0 7.0 - - + -
214F LEU* 4.3 17.0 - - + -
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F CYS 3.0 18.9 + - - +
145F GLY* 3.6 4.3 - - - +
147F LEU* 1.3 76.4 - - - +
149F ILE* 1.3 63.0 + - - +
151F THR* 3.1 20.8 - - - -
152F TYR* 3.2 22.6 + - + +
211F LEU* 4.9 2.2 - - + -
214F LEU* 3.3 44.4 - - + +
215F LYS* 3.6 14.4 - - + +
218F ALA* 4.0 7.9 - - + +
221F LEU* 4.0 16.6 - - + +
222F ASP* 3.8 33.2 - - + +
225F PHE* 4.4 7.9 - - + -
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Residues in contact with ILE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F TYR* 3.7 17.7 - - + +
130F LYS* 4.0 10.3 - - - -
145F GLY 3.0 20.6 + - - +
146F GLN* 3.1 24.8 + - - +
148F LEU* 1.3 73.6 - - + +
150F LEU* 1.3 64.0 + - + +
151F THR 2.9 5.3 + - - -
152F TYR* 3.0 12.1 + - - +
153F VAL* 3.2 17.0 + - + +
221F LEU* 3.8 32.8 - - + -
225F PHE* 4.3 19.9 - - + -
301F GSH 3.5 39.5 - - - +
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F TYR* 4.1 9.6 - - + -
146F GLN* 2.9 49.1 + - + +
147F LEU* 3.7 15.5 - - + +
149F ILE* 1.3 74.8 - - + +
151F THR* 1.3 61.1 + - - +
153F VAL* 4.3 0.4 - - - -
154F TYR* 3.4 62.4 + - + +
156F LYS* 3.6 7.0 + - - -
164F ILE* 6.6 0.2 - - + -
166F LEU* 5.6 2.7 - - + -
169F LEU* 4.4 29.2 - - + -
174F LEU* 5.1 4.7 - - + -
301F GSH 3.9 8.5 - - - +
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Residues in contact with THR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU* 2.7 23.1 + - - +
148F LEU* 3.1 16.6 - - - -
149F ILE 2.9 0.4 - - - -
150F LEU* 1.3 78.8 - - - +
152F TYR* 1.3 68.1 + - + +
155F GLY* 3.4 3.1 - - - -
156F LYS* 2.9 52.7 - - + +
208F VAL* 4.5 7.0 - - + +
211F LEU* 3.5 33.0 - - + -
214F LEU* 3.8 9.4 - - - +
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Residues in contact with TYR 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LEU* 3.2 16.1 + - + -
149F ILE 3.0 3.0 + - - +
151F THR* 1.3 87.8 - - + +
153F VAL* 1.3 65.2 + - - +
155F GLY* 3.3 14.2 - - - -
211F LEU* 3.4 18.9 - - + +
215F LYS* 3.6 11.4 - - - +
222F ASP* 2.2 50.0 + - - +
225F PHE* 3.2 45.8 - + + -
232F THR* 4.1 17.5 - - - +
233F TRP* 3.8 16.4 - + + -
235F LYS* 2.8 37.4 + - + -
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Residues in contact with VAL 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LYS* 4.0 25.1 - - + +
149F ILE* 3.2 20.6 - - + +
152F TYR* 1.3 80.2 - - - +
154F TYR* 1.3 97.5 + - + +
155F GLY 3.4 3.6 + - - -
225F PHE* 4.7 8.5 - - + -
232F THR* 5.2 12.1 - - + -
301F GSH 4.3 37.0 - - + +
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Residues in contact with TYR 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ILE* 4.3 11.2 - - + +
62F TYR* 3.0 34.9 - + - +
63F TYR 4.4 0.3 + - - -
64F LYS* 3.4 43.1 - - + +
150F LEU* 3.4 48.4 + - + +
153F VAL* 1.3 92.2 - - + +
155F GLY* 1.3 50.3 + - - +
156F LYS* 3.4 8.3 + - - -
163F LYS 2.9 23.6 - - - +
164F ILE* 5.8 0.2 - - - -
165F THR* 3.4 23.2 + - - +
166F LEU* 3.4 41.7 - - + -
301F GSH 3.6 5.2 + - - -
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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