Contacts of the helix formed by residues 156 - 173 (chain F) in PDB entry 5B6N
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 156 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ASN* 5.1 3.5 + - - -
159E GLU* 3.2 36.4 + - - +
162E ARG* 3.2 10.2 - - - +
180E ASP* 3.3 32.2 + - - +
181E TRP 5.3 0.2 + - - -
147F ILE* 5.9 0.2 - - - +
149F TYR* 4.6 1.2 - - - -
155F ARG* 1.3 72.3 - - - +
157F PHE* 1.3 61.2 - - - +
158F ASP* 3.5 11.4 + - - +
159F GLU* 3.2 31.3 + - + +
160F ILE* 3.4 23.9 + - - +
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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
----------------------------------------------------------
179E VAL* 4.5 4.0 - - + -
180E ASP* 3.3 10.2 + - - +
35F ILE* 5.9 0.7 - - + -
37F PHE* 4.3 35.4 - + + -
50F GLU* 3.8 29.4 - - + -
53F ARG* 4.7 11.7 - - + +
54F ALA* 3.9 30.1 - - + -
57F LEU* 4.0 17.1 - - + +
61F PHE* 5.0 10.2 - + - -
68F LEU* 5.2 6.5 - - + -
134F VAL* 5.6 2.0 - - + -
155F ARG* 3.9 30.1 - - + -
156F ASN* 1.3 73.6 - - - +
158F ASP* 1.3 65.3 + - - +
159F GLU 3.1 1.6 - - - -
160F ILE* 3.6 25.1 - - + +
161F LEU* 3.3 21.7 + - - +
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Residues in contact with ASP 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASP* 3.9 18.9 + - - +
182E LYS* 5.8 1.9 + - - -
53F ARG* 3.9 20.5 + - - -
57F LEU* 4.7 4.1 - - - +
156F ASN* 3.5 14.5 + - - +
157F PHE* 1.3 80.0 - - - +
159F GLU* 1.3 58.7 + - - +
161F LEU* 3.8 4.1 + - - +
162F ARG* 3.0 26.6 + - - +
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Residues in contact with GLU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 2.7 28.6 + - - +
156E ASN* 2.9 34.0 + - - +
159E GLU* 4.8 10.5 - - + -
149F TYR* 6.0 0.4 - - - +
156F ASN* 3.2 26.1 + - + +
157F PHE 3.1 0.2 - - - -
158F ASP* 1.3 79.7 - - - +
160F ILE* 1.3 61.4 + - + +
161F LEU 3.3 0.2 - - - -
162F ARG* 2.8 45.3 + - - -
163F VAL* 2.8 37.4 + - + +
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Residues in contact with ILE 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ILE* 4.2 22.9 - - + -
61F PHE* 4.1 15.9 - - + -
134F VAL* 4.0 34.5 - - + -
136F VAL* 5.2 1.6 - - + -
145F LEU* 5.6 2.5 - - + -
147F ILE* 4.4 19.1 - - + -
155F ARG* 5.5 0.9 - - + -
156F ASN 3.4 16.8 + - - +
157F PHE* 3.5 28.9 + - + +
158F ASP 3.4 0.4 - - - -
159F GLU* 1.3 80.9 - - + +
161F LEU* 1.3 57.5 + - - +
163F VAL* 3.1 14.4 - - + +
164F VAL* 3.0 29.3 + - + +
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LEU* 4.1 21.8 - - + -
60F GLU* 3.8 34.5 - - + +
61F PHE* 4.1 19.7 - - + -
64F ARG* 4.0 14.1 - - - +
157F PHE 3.3 12.7 + - - +
158F ASP* 4.1 4.5 - - - +
160F ILE* 1.3 77.2 - - - +
162F ARG* 1.3 61.2 + - - +
164F VAL* 2.9 9.6 + - + +
165F ILE* 2.8 52.0 + - + +
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Residues in contact with ARG 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E THR* 4.5 4.2 - - - +
154E GLY 2.8 28.1 + - - -
155E ARG 4.5 0.4 - - - -
156E ASN* 4.2 13.1 - - - +
158F ASP 3.0 21.6 + - - +
159F GLU* 2.8 43.4 + - - +
161F LEU* 1.3 78.3 - - - +
163F VAL* 1.3 67.3 + - - +
165F ILE* 3.8 8.9 + - + +
166F SER* 3.4 21.4 + - - -
177F THR* 5.3 1.4 + - - -
180F ASP 4.8 2.2 - - - -
181F TRP* 2.3 73.0 + - + +
182F LYS* 4.8 11.4 - - + +
183F ASP 5.5 2.0 - - - +
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Residues in contact with VAL 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 3.2 36.6 - - + +
153E THR* 4.5 3.5 - - + +
136F VAL* 5.3 3.4 - - + -
145F LEU* 4.1 30.3 - - + -
159F GLU* 2.8 30.3 + - + +
160F ILE* 3.1 24.5 - - + +
162F ARG* 1.3 80.6 - - - +
164F VAL* 1.3 63.9 + - + +
166F SER* 3.9 7.6 - - - -
167F LEU* 3.0 35.3 + - + +
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Residues in contact with VAL 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F TRP* 6.0 5.3 - - + -
35F ILE* 3.7 30.1 - - + -
61F PHE* 3.9 13.9 - - + -
64F ARG* 4.8 5.4 - - + -
66F VAL* 4.3 11.2 - - + -
136F VAL* 5.0 5.8 - - + -
160F ILE 3.0 20.9 + - - +
161F LEU* 2.9 14.2 + - + +
163F VAL* 1.3 77.2 - - + +
165F ILE* 1.3 73.6 + - + +
167F LEU* 3.1 17.6 + - + +
168F GLN* 3.3 35.2 + - - +
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Residues in contact with ILE 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ARG* 3.2 49.6 - - + +
161F LEU* 2.8 32.5 + - + +
162F ARG* 3.8 8.3 - - + +
164F VAL* 1.3 78.3 - - + +
166F SER* 1.3 62.3 + - - +
168F GLN* 3.5 7.2 + - - +
169F LEU* 3.3 22.5 + - + +
181F TRP* 3.6 24.9 - - + -
183F ASP* 3.6 27.4 - - + +
223F GLN* 6.0 0.4 - - - +
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Residues in contact with SER 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E THR* 3.3 24.8 + - - -
162F ARG* 3.4 14.3 + - - -
163F VAL 3.9 1.3 - - - -
164F VAL 3.2 0.4 - - - -
165F ILE* 1.3 78.6 - - - +
167F LEU* 1.3 55.7 + - - +
169F LEU* 3.3 1.1 + - - +
170F THR* 2.7 39.3 + - - +
177F THR* 2.4 35.5 + - - +
181F TRP* 3.8 18.2 - - - -
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Residues in contact with LEU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E PRO* 4.2 10.8 - - + -
152E THR* 4.6 4.0 - - - +
153E THR* 3.7 15.9 - - - +
33F TRP* 3.9 21.9 - - + -
136F VAL* 3.7 31.0 - - + -
144F LYS* 4.0 30.3 - - + +
145F LEU* 4.5 7.9 - - + -
163F VAL* 3.0 28.3 + - + +
164F VAL* 3.1 10.9 + - + +
166F SER* 1.3 78.4 - - - +
168F GLN* 1.3 61.1 + - - +
170F THR* 2.5 17.4 + - - +
171F ALA* 3.3 12.1 + - - +
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Residues in contact with GLN 168 (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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33F TRP* 3.8 33.3 - - + +
64F ARG* 3.2 40.7 + - - +
66F VAL* 3.7 17.0 - - - +
164F VAL* 3.3 22.8 + - - +
165F ILE* 4.0 6.5 - - - +
166F SER 3.2 0.6 - - - -
167F LEU* 1.3 73.9 - - - +
169F LEU* 1.3 63.0 + - - +
170F THR 3.1 1.6 - - - -
171F ALA* 3.2 17.4 + - - +
172F GLU* 3.3 17.8 + - - +
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Residues in contact with LEU 169 (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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165F ILE* 3.3 15.8 + - + +
166F SER 3.9 1.3 - - - +
168F GLN* 1.3 78.7 - - - +
170F THR* 1.3 57.9 + - - +
172F GLU* 3.8 13.9 + - - +
173F LYS* 3.2 41.5 + - + +
175F VAL* 4.2 12.3 - - + +
177F THR* 4.2 6.7 - - + -
181F TRP* 3.5 36.3 - - + -
187F VAL* 4.1 11.9 - - + -
223F GLN* 3.8 34.5 - - + +
224F PRO* 4.6 7.2 - - + +
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Residues in contact with THR 170 (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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152E THR* 3.9 43.7 + - - +
153E THR* 4.4 0.2 - - - +
166F SER* 2.7 27.0 + - - +
167F LEU* 2.5 29.5 + - - +
169F LEU* 1.3 77.8 - - + +
171F ALA* 1.3 59.4 + - - +
173F LYS 3.2 16.7 - - - +
175F VAL* 3.7 19.1 - - - +
176F ALA* 4.4 0.2 - - - -
177F THR* 4.3 11.0 - - + -
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Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F TRP* 5.2 7.9 - - + -
167F LEU 3.3 11.6 + - - +
168F GLN* 3.2 13.8 + - - +
170F THR* 1.3 81.0 - - - +
172F GLU* 1.3 63.3 + - + +
173F LYS 3.7 1.2 + - - +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F GLN 3.3 15.2 - - - +
169F LEU* 3.8 19.0 - - - +
171F ALA* 1.3 80.4 - - + +
173F LYS* 1.3 90.7 + - - +
174F ARG* 5.4 1.6 - - - +
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Residues in contact with LYS 173 (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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169F LEU* 3.2 17.6 + - + +
170F THR 3.2 22.5 - - - +
171F ALA 4.5 0.8 - - - +
172F GLU* 1.3 111.8 - - + +
174F ARG* 1.3 59.7 + - - +
175F VAL* 2.9 23.2 + - + +
202F PHE* 5.5 1.8 - - + -
224F PRO* 4.0 38.6 + - + +
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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
------------------------------------------------------------
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