Contacts of the helix formed by residues 156 - 172 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E TYR* 4.6 1.8 + - - -
154E GLY 3.8 1.2 + - - -
155E ARG* 1.3 70.4 - - - +
157E PHE* 1.3 58.1 + - - +
158E ASP* 3.1 13.1 + - - +
159E GLU* 3.0 38.5 + - + +
160E ILE* 3.4 9.5 + - - +
156F ASN* 5.1 3.4 + - - -
159F GLU* 2.9 40.3 + - - +
162F ARG* 4.4 9.4 - - - +
180F ASP* 2.8 28.1 - - - +
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Residues in contact with PHE 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ILE* 5.8 2.0 - - + -
37E PHE* 4.3 30.5 - + + -
50E GLU* 4.0 31.2 - - + -
53E ARG* 4.5 5.6 - - + -
54E ALA* 3.6 30.1 - - + -
57E LEU* 3.6 30.7 - - + +
61E PHE* 4.6 6.4 - + - -
68E LEU* 4.6 8.3 - - + -
134E VAL* 5.8 1.8 - - + -
155E ARG* 3.4 31.5 + - + -
156E ASN* 1.3 71.3 - - - +
158E ASP* 1.3 60.9 + - - +
159E GLU 3.4 0.2 - - - -
160E ILE* 3.6 29.5 - - + +
161E LEU* 3.6 5.7 + - - +
179F VAL* 4.3 13.5 - - + -
180F ASP* 3.1 11.3 + - - +
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Residues in contact with ASP 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ARG* 3.1 29.5 + - - -
57E LEU* 3.7 9.2 - - - +
156E ASN* 3.0 13.3 + - - +
157E PHE* 1.3 79.5 - - - +
159E GLU* 1.3 60.4 + - - +
160E ILE 3.2 0.4 - - - -
161E LEU* 3.5 10.2 + - - +
162E ARG* 3.1 23.7 + - - +
180F ASP* 4.0 13.8 - - - +
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Residues in contact with GLU 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ASN* 3.0 30.4 + - + +
158E ASP* 1.3 75.8 - - - +
160E ILE* 1.3 69.7 + - + +
162E ARG* 2.9 56.7 + - - +
163E VAL* 3.2 10.2 + - - +
149F TYR* 2.9 29.1 + - - +
156F ASN* 3.2 28.8 + - + +
159F GLU* 4.8 10.8 - - + -
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Residues in contact with ILE 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ILE* 3.4 31.9 - - + -
61E PHE* 4.2 10.8 - - + -
134E VAL* 4.2 29.8 - - + -
136E VAL* 5.3 2.2 - - + -
145E LEU* 5.2 4.3 - - + -
147E ILE* 4.7 17.5 - - + -
155E ARG* 5.7 2.9 - - + -
156E ASN 3.8 12.3 - - - +
157E PHE* 3.6 25.4 - - + +
159E GLU* 1.3 82.3 - - + +
161E LEU* 1.3 61.1 + - - +
163E VAL* 3.2 13.5 - - + +
164E VAL* 3.2 24.2 + - + +
149F TYR* 5.8 1.3 - - - +
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Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LEU* 4.4 16.2 - - + -
60E GLU* 4.0 36.1 - - + +
61E PHE* 3.6 33.4 - - + -
64E ARG* 5.0 5.6 - - + +
157E PHE 3.6 6.1 + - - +
158E ASP* 3.5 11.1 + - - +
160E ILE* 1.3 77.2 - - - +
162E ARG* 1.3 65.4 + - - +
164E VAL* 4.2 6.1 - - + -
165E ILE* 3.1 48.0 + - + +
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Residues in contact with ARG 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E ASP 3.1 15.2 + - - +
159E GLU* 2.9 45.0 + - - +
161E LEU* 1.3 78.4 - - - +
163E VAL* 1.3 62.2 + - - +
165E ILE* 3.7 7.1 + - - +
166E SER* 3.3 23.5 + - - -
177E THR* 4.2 8.3 + - - -
178E PRO 3.9 0.8 + - - -
181E TRP* 2.9 61.3 + - + +
182E LYS* 4.9 9.4 - - + -
183E ASP 5.6 1.6 - - - +
149F TYR* 4.1 4.4 - - - -
153F THR* 5.0 1.8 - - - +
154F GLY 2.8 30.5 + - - -
155F ARG* 3.6 1.4 - - - +
156F ASN* 3.2 21.0 - - - +
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Residues in contact with VAL 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E VAL* 5.4 2.5 - - + -
145E LEU* 3.8 33.4 - - + -
159E GLU* 3.2 20.2 + - - +
160E ILE* 3.2 20.9 - - + +
162E ARG* 1.3 81.0 - - - +
164E VAL* 1.3 61.5 + - + +
166E SER* 3.7 8.6 - - - -
167E LEU* 3.1 34.4 + - + +
149F TYR* 3.4 32.3 - - + +
153F THR* 4.0 11.7 - - + -
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Residues in contact with VAL 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TRP* 5.5 8.0 - - + -
35E ILE* 5.3 5.2 - - + -
61E PHE* 3.8 23.3 - - + -
64E ARG* 5.1 3.6 - - + -
66E VAL* 4.1 16.8 - - + -
136E VAL* 5.3 10.8 - - + -
160E ILE* 3.2 21.5 + - + +
161E LEU* 3.3 13.7 + - + +
163E VAL* 1.3 76.9 - - + +
165E ILE* 1.3 68.4 + - + +
166E SER 3.0 1.3 - - - -
167E LEU* 3.4 4.8 + - + +
168E GLN* 2.9 52.9 + - + +
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Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ARG* 3.6 40.2 - - + +
161E LEU* 3.1 36.5 + - + +
162E ARG* 3.9 4.5 - - - +
164E VAL* 1.3 79.9 - - - +
166E SER* 1.3 60.2 + - - +
168E GLN* 3.8 7.7 - - - +
169E LEU* 3.2 25.6 + - + +
181E TRP* 3.6 20.4 - - + -
183E ASP* 3.6 33.7 - - + +
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Residues in contact with SER 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ARG* 3.3 16.1 + - - -
163E VAL* 3.7 10.5 - - - -
164E VAL 3.0 0.8 - - - -
165E ILE* 1.3 76.9 - - - +
167E LEU* 1.3 53.3 + - - +
169E LEU* 2.9 6.4 + - - +
170E THR* 2.7 36.8 + - - +
177E THR* 3.3 33.6 + - - +
181E TRP* 4.1 5.8 - - - -
152F THR 3.3 4.9 + - - -
153F THR* 3.0 22.3 + - - -
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Residues in contact with LEU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TRP* 3.5 21.1 - - + -
136E VAL* 4.2 13.5 - - + -
144E LYS* 3.5 30.7 - - + -
145E LEU* 4.3 12.1 - - + -
163E VAL* 3.1 20.5 + - + +
164E VAL* 4.0 3.8 - - + +
166E SER* 1.3 78.9 - - - +
168E GLN* 1.3 62.3 + - - +
170E THR* 3.3 10.5 + - - +
171E ALA* 3.1 27.4 + - - +
150F PRO* 3.9 18.6 - - + -
152F THR* 4.5 2.7 - - - +
153F THR* 3.4 22.4 - - - +
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Residues in contact with GLN 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TRP* 3.6 36.4 - - + +
64E ARG* 2.5 47.7 + - - +
65E ASN* 4.9 0.2 - - - +
66E VAL* 3.8 15.4 - - - +
164E VAL* 2.9 31.9 + - + +
165E ILE* 3.8 9.1 - - - +
167E LEU* 1.3 77.5 - - - +
169E LEU* 1.3 61.5 + - - +
171E ALA* 3.9 9.1 - - - +
172E GLU* 4.0 8.8 + - - +
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Residues in contact with LEU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ILE* 3.2 15.8 + - + +
166E SER* 2.9 10.1 + - - +
168E GLN* 1.3 77.2 - - - +
170E THR* 1.3 64.0 + - + +
171E ALA 3.0 5.4 + - - -
172E GLU* 3.2 3.8 + - - +
173E LYS* 3.1 44.7 + - + +
175E VAL* 3.5 27.4 - - + -
177E THR* 5.2 1.6 - - + -
181E TRP* 4.2 16.6 - - + -
187E VAL* 5.1 4.3 - - + -
223E GLN* 3.2 34.8 - - + +
224E PRO* 5.1 7.2 - - + +
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Residues in contact with THR 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E SER* 2.7 26.4 + - - +
167E LEU* 3.3 13.9 + - - +
169E LEU* 1.3 72.7 - - + +
171E ALA* 1.3 62.2 + - - +
173E LYS 2.8 22.4 - - - +
175E VAL* 3.9 17.1 - - + +
176E ALA* 4.3 1.8 - - - -
177E THR* 4.2 11.0 - - + -
152F THR* 3.2 52.5 + - - +
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Residues in contact with ALA 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E TRP* 4.8 9.4 - - + +
144E LYS* 6.3 0.2 - - - +
167E LEU 3.1 18.4 + - - +
168E GLN* 3.9 9.0 - - - +
169E LEU 3.0 0.2 - - - -
170E THR* 1.3 82.1 + - - +
172E GLU* 1.3 69.0 + - + +
173E LYS 3.4 1.6 + - - -
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Residues in contact with GLU 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLN 4.0 6.7 + - - +
169E LEU 3.2 6.2 + - - +
171E ALA* 1.3 87.0 - - + +
173E LYS* 1.3 73.8 + - - +
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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