Contacts of the helix formed by residues 145 - 157 (chain F) in PDB entry 2Q5E
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 TYR 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143F ARG 3.6 0.6 + - - -
144F PRO* 1.3 90.4 - - + +
146F VAL* 1.3 66.7 + - - +
148F GLU* 2.7 40.3 + - + +
149F PHE* 2.8 12.2 + - - +
242F ASP 3.7 9.0 - - - -
243F THR* 3.0 39.0 - - + +
245F LEU* 4.3 5.2 - - + -
246F LEU* 3.6 52.2 - - + +
249F ILE* 6.0 1.6 - - + -
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Residues in contact with VAL 146 (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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112F LEU* 3.8 35.4 - - + +
142F LYS* 3.4 36.1 - - + -
143F ARG 3.3 19.3 - - - +
144F PRO 3.2 3.8 + - - -
145F TYR* 1.3 77.3 - - - +
147F ASP* 1.3 69.3 + - - +
149F PHE* 3.2 1.1 + - + +
150F LEU* 3.0 39.0 + - + +
177F LEU* 4.2 10.3 - - + -
245F LEU* 3.7 17.5 - - + -
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Residues in contact with ASP 147 (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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142F LYS* 2.7 38.1 + - - -
146F VAL* 1.3 78.8 - - - +
148F GLU* 1.3 73.5 + - - +
150F LEU* 3.4 5.3 + - - +
151F ARG* 3.1 41.6 + - - +
177F LEU* 4.1 9.7 - - - +
179F ARG* 3.4 43.5 + - + +
180F CYS* 5.4 1.7 - - - -
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Residues in contact with GLU 148 (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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145F TYR* 2.7 39.0 + - + +
146F VAL 3.8 0.2 + - - -
147F ASP* 1.3 90.7 + - - +
149F PHE* 1.3 64.6 + - - +
151F ARG* 3.4 28.6 + - - +
152F ARG* 3.3 21.8 + - - +
246F LEU* 5.7 3.8 - - + -
249F ILE* 3.6 9.8 - - + +
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Residues in contact with PHE 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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106F ILE* 4.7 3.6 - - + -
112F LEU* 4.6 11.0 - - + -
145F TYR* 2.8 14.5 + - + +
146F VAL* 3.6 3.8 - - - +
148F GLU* 1.3 75.3 - - - +
150F LEU* 1.3 77.0 + - + +
152F ARG* 3.1 4.0 + - - +
153F MET* 2.8 68.4 + - + +
216F LEU* 3.8 29.8 - - + -
245F LEU* 3.5 38.1 - - + -
248F LEU* 3.7 24.2 - - + -
249F ILE* 3.6 20.4 - - + +
252F PHE* 4.1 6.7 - + - -
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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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106F ILE* 4.5 7.4 - - + -
112F LEU* 4.3 9.4 - - + -
146F VAL* 3.0 28.3 + - + +
147F ASP* 4.0 4.9 - - - +
149F PHE* 1.3 93.2 - - + +
151F ARG* 1.3 56.8 + - - +
153F MET* 3.9 2.6 - - + +
154F GLY 2.8 25.5 + - - -
177F LEU* 4.0 33.0 - - + +
178F ASP* 4.5 12.8 - - - +
180F CYS* 6.0 1.1 - - - -
182F VAL* 3.2 26.2 - - + +
183F PHE* 3.9 33.2 - - + -
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Residues in contact with ARG 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 ASP* 3.1 35.7 + - - +
148F GLU* 3.4 33.9 + - - +
150F LEU* 1.3 76.2 - - - +
152F ARG* 1.3 63.2 + - - +
154F GLY* 3.4 1.6 + - - -
155F GLU* 3.1 36.6 + - - +
179F ARG* 5.4 9.7 - - - +
180F CYS* 3.9 30.1 - - - -
182F VAL* 4.5 1.1 - - - +
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Residues in contact with ARG 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 GLU 3.3 12.3 + - - +
149F PHE 3.1 8.5 + - - +
151F ARG* 1.3 77.6 - - - +
153F MET* 1.3 69.1 + - + +
155F GLU* 2.5 56.9 + - - +
156F LEU* 3.1 50.8 + - + +
249F ILE* 3.9 28.3 - - + +
253F GLU* 2.5 33.2 + - - +
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Residues in contact with MET 153 (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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104F VAL* 3.9 18.8 - - + -
106F ILE* 4.7 6.3 - - + -
149F PHE* 2.8 63.1 + - + +
150F LEU* 3.9 5.4 - - + +
152F ARG* 1.3 72.8 - - - +
154F GLY* 1.3 55.4 + - - +
156F LEU* 2.9 5.6 + - - -
157F PHE* 2.7 54.7 + - + +
159F CYS* 3.7 15.3 - - - -
216F LEU* 5.9 0.2 - - + -
249F ILE* 5.7 2.2 - - - -
252F PHE* 3.6 51.4 - - + -
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Residues in contact with GLY 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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97F GLU* 5.5 1.9 - - - +
101F ARG* 3.2 14.1 + - - -
150F LEU 2.8 18.9 + - - -
151F ARG 3.7 2.9 - - - -
152F ARG 3.1 0.2 - - - -
153F MET* 1.3 76.9 - - - +
155F GLU* 1.3 59.6 + - - +
157F PHE 4.1 2.1 - - - +
159F CYS* 4.0 3.4 - - - -
182F VAL* 3.6 25.0 - - - +
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Residues in contact with GLU 155 (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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101F ARG* 3.0 23.0 + - - +
151F ARG* 3.1 36.9 + - - +
152F ARG* 2.5 60.7 + - - +
154F GLY* 1.3 72.6 - - - +
156F LEU* 1.3 60.4 + - + +
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Residues in contact with LEU 156 (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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101F ARG* 3.3 18.6 - - - +
102F ILE 5.2 0.2 + - - -
152F ARG* 3.4 59.0 - - + +
153F MET* 2.9 3.2 + - - -
155F GLU* 1.3 81.3 - - + +
157F PHE* 1.3 82.7 + - + +
249F ILE 5.4 0.2 - - - +
252F PHE* 5.3 1.8 - - + -
253F GLU* 4.1 18.6 - - + +
256F SER* 3.8 38.0 + - - +
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Residues in contact with PHE 157 (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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98F ASP* 3.6 2.8 - - - +
101F ARG* 2.9 28.5 + - - +
102F ILE* 3.3 37.0 - - + +
104F VAL* 3.4 23.1 - - + -
153F MET* 2.7 52.6 + - + +
154F GLY 4.1 2.6 - - - +
156F LEU* 1.3 88.3 - - + +
158F GLU* 1.3 64.3 + - - +
159F CYS* 3.8 7.5 + - - -
214F LEU* 4.4 5.2 - - + -
252F PHE* 3.5 42.6 - + + -
255F LEU 4.8 0.4 - - - -
256F SER* 3.7 19.1 - - - -
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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