Contacts of the helix formed by residues 156 - 171 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLU* 2.4 37.3 + - - +
162A ARG* 3.3 15.2 - - - +
180A ASP* 3.4 12.6 - - - +
147B ILE* 5.6 1.2 - - - +
149B TYR* 5.0 3.0 + - - +
155B ARG* 1.3 75.2 - - - +
157B PHE* 1.3 60.8 + - - +
158B ASP* 3.1 23.6 + - - +
159B GLU* 3.4 22.0 + - + +
160B ILE* 3.4 24.9 + - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.8 17.3 - - + -
180A ASP* 3.2 7.7 + - - +
35B ILE* 6.1 0.4 - - + -
37B PHE* 4.3 25.1 - + - -
50B GLU* 3.7 29.8 - - + -
53B ARG* 4.0 12.3 - - + -
54B ALA* 3.9 25.8 - - + -
57B LEU* 3.6 33.8 - - + +
61B PHE* 4.6 10.8 - + - -
68B LEU* 5.4 2.7 - - + -
155B ARG* 4.2 17.9 - - + -
156B ASN* 1.3 72.3 - - - +
158B ASP* 1.3 65.8 + - - +
159B GLU 3.1 2.2 - - - -
160B ILE* 3.5 29.7 + - + +
161B LEU* 3.4 17.7 + - - +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASP* 3.6 13.6 - - - +
53B ARG* 3.4 28.1 + - - -
57B LEU* 4.6 3.5 - - - +
156B ASN* 3.1 13.0 + - - +
157B PHE* 1.3 80.4 - - - +
159B GLU* 1.3 60.4 + - - +
161B LEU* 4.0 9.0 + - - +
162B ARG* 3.5 20.4 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 3.5 22.3 + - - +
156A ASN* 3.2 35.9 + - - +
159A GLU* 4.4 13.8 - - + +
149B TYR* 5.9 0.9 - - - +
156B ASN* 3.4 30.7 + - + +
157B PHE 3.1 0.2 - - - -
158B ASP* 1.3 79.2 - - - +
160B ILE* 1.3 64.9 + - + +
161B LEU 3.3 0.2 - - - -
162B ARG* 2.3 40.4 + - - +
163B VAL* 3.2 24.8 + - - +
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.7 28.7 - - + -
61B PHE* 3.9 8.3 - - + -
134B VAL* 3.9 37.7 - - + -
136B VAL* 5.6 3.4 - - + -
147B ILE* 4.8 11.2 - - + -
155B ARG* 5.2 2.9 - - + -
156B ASN 3.4 15.0 + - - +
157B PHE* 3.5 38.6 + - + +
158B ASP 3.5 0.2 - - - -
159B GLU* 1.3 79.6 - - + +
161B LEU* 1.3 60.0 + - - +
163B VAL* 3.6 9.1 - - + +
164B VAL* 3.3 23.1 + - + +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.7 13.9 - - + -
60B GLU* 3.9 38.8 - - + +
61B PHE* 3.8 31.8 - - + -
64B ARG* 4.8 9.4 - - - +
157B PHE 3.4 14.4 + - - +
158B ASP* 4.0 7.6 + - - +
159B GLU 3.3 0.2 - - - -
160B ILE* 1.3 79.4 - - - +
162B ARG* 1.3 62.7 + - - +
164B VAL* 3.4 3.6 + - + +
165B ILE* 3.2 37.0 + - + +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 4.5 1.6 - - - -
153A THR* 5.1 2.0 - - - +
154A GLY 3.5 25.7 + - - -
156A ASN* 3.9 20.6 - - - +
158B ASP 3.5 16.8 + - - +
159B GLU* 2.3 43.3 + - - +
160B ILE 3.2 0.2 - - - -
161B LEU* 1.3 80.7 - - - +
163B VAL* 1.3 75.7 + - - +
165B ILE* 3.5 7.2 + - - +
166B SER* 3.3 15.8 + - - -
177B THR* 5.1 1.4 + - - -
180B ASP 4.3 1.5 - - - +
181B TRP* 3.1 65.0 + - + +
182B LYS* 4.9 9.6 - - - +
183B ASP* 5.1 3.8 - - + +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 3.4 27.8 - - + +
153A THR* 3.9 12.8 - - + -
136B VAL* 5.2 3.4 - - + -
145B LEU* 3.7 26.9 - - + -
159B GLU* 3.2 15.9 - - - +
160B ILE* 3.6 15.3 - - + +
162B ARG* 1.3 91.5 - - - +
164B VAL* 1.3 65.4 + - + +
165B ILE 3.3 0.2 - - - -
166B SER* 3.6 8.3 - - - -
167B LEU* 3.0 36.4 + - + +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 6.1 2.6 - - + -
35B ILE* 4.1 15.7 - - + -
61B PHE* 4.1 20.4 - - + -
64B ARG* 4.9 6.7 - - - -
66B VAL* 4.2 14.6 - - + -
136B VAL* 4.9 13.5 - - + -
160B ILE* 3.3 20.3 + - + +
161B LEU* 3.5 9.4 - - + +
162B ARG 3.2 0.4 - - - -
163B VAL* 1.3 84.1 - - + +
165B ILE* 1.3 65.2 + - + +
167B LEU* 3.5 5.9 + - - +
168B GLN* 3.0 49.1 + - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.5 47.6 - - - +
161B LEU* 3.2 26.8 + - + +
162B ARG* 3.8 9.0 - - - +
164B VAL* 1.3 74.5 - - + +
166B SER* 1.3 57.3 + - - +
168B GLN* 3.3 7.9 + - + +
169B LEU* 2.7 36.4 + - + +
181B TRP* 3.9 12.6 - - + -
183B ASP* 3.8 35.2 - - + +
223B GLN* 5.2 2.0 - - - +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A THR* 2.2 32.9 + - - -
162B ARG* 3.3 12.3 + - - -
163B VAL* 3.6 8.7 - - - -
164B VAL 3.2 0.2 - - - -
165B ILE* 1.3 78.2 - - - +
167B LEU* 1.3 50.9 + - - +
169B LEU* 2.6 9.2 + - - -
170B THR* 2.5 41.3 + - - +
177B THR* 3.2 27.9 - - - +
181B TRP* 4.0 9.6 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PRO* 3.6 31.9 - - + -
152A THR* 4.3 5.6 - - - +
153A THR* 3.6 11.0 - - - +
33B TRP* 3.8 20.2 - - + -
136B VAL* 3.8 28.9 - - + -
144B LYS* 3.9 22.2 - - + +
145B LEU* 4.3 10.8 - - + -
163B VAL* 3.0 26.1 + - + +
164B VAL* 3.9 5.6 - - - +
166B SER* 1.3 74.7 - - - +
168B GLN* 1.3 56.7 + - - +
170B THR* 3.5 5.5 + - - +
171B ALA* 3.2 27.4 + - - +
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TRP* 3.7 33.5 - - + +
64B ARG* 2.5 47.9 + - - +
66B VAL* 3.5 17.2 - - - +
164B VAL* 3.0 27.1 + - + +
165B ILE* 3.4 6.8 - - - +
166B SER 3.0 0.6 - - - -
167B LEU* 1.3 76.9 - - - +
169B LEU* 1.3 57.9 + - - +
171B ALA* 4.3 2.5 - - - +
172B GLU* 3.4 22.3 + - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ILE* 2.7 18.8 + - + +
166B SER 2.6 10.5 + - - +
168B GLN* 1.3 71.3 - - - +
170B THR* 1.3 56.7 + - - +
171B ALA 3.1 4.7 - - - -
172B GLU* 3.1 6.5 + - + +
173B LYS* 2.9 37.4 + - + +
175B VAL* 4.3 9.4 - - + -
177B THR* 4.6 5.8 - - + -
181B TRP* 3.9 29.4 - - + -
187B VAL* 4.0 19.5 - - + -
223B GLN* 4.1 15.7 - - + +
224B PRO* 4.7 18.4 - - + +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 3.5 50.8 + - - +
166B SER* 2.5 35.3 + - - +
167B LEU* 3.5 8.5 + - - +
169B LEU* 1.3 73.0 - - + +
171B ALA* 1.3 57.1 + - - +
173B LYS 2.7 19.2 - - - +
174B ARG* 4.9 0.5 - - - -
175B VAL* 3.5 25.6 - - + +
176B ALA* 3.8 6.5 - - - -
177B THR* 3.9 7.6 - - + -
190B LEU* 6.0 0.5 - - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TRP* 5.2 8.3 - - + -
167B LEU 3.2 19.2 + - - +
168B GLN* 4.7 2.7 - - - +
169B LEU 3.1 0.4 - - - -
170B THR* 1.3 78.5 + - - +
172B GLU* 1.3 64.3 - - - +
173B LYS 4.3 0.8 - - - -
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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
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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