Contacts of the strand formed by residues 156 - 163 (chain B) in PDB entry 5AOL
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 ARG 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY 3.5 12.1 - - - +
155B THR* 1.3 79.1 - - - +
157B VAL* 1.3 69.4 + - - +
158B ARG* 3.9 19.6 - - - +
202B ARG 5.6 1.0 + - - -
204B GLU* 2.9 35.4 + - - +
217B VAL* 3.6 31.1 + - + +
218B VAL 3.2 17.5 - - - +
219B PRO* 4.2 10.5 - - + +
220B CYS 3.9 0.9 - - - +
257B LEU* 3.6 3.8 - - - +
258B GLU* 2.8 44.5 + - + +
259B ASP 5.0 5.4 + - - +
260B SER* 5.3 10.7 + - - +
262B GLY* 6.0 2.4 - - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 4.7 2.2 - - + -
145B LEU* 3.5 26.9 - - + -
156B ARG* 1.3 80.2 - - - +
158B ARG* 1.3 62.7 + - - +
216B VAL 3.9 0.9 - - - +
217B VAL* 3.3 3.4 - - - -
218B VAL* 2.8 37.0 + - - +
219B PRO 5.1 0.4 - - - -
220B CYS* 3.7 15.9 - - + -
232B ILE* 3.9 24.0 - - + -
234B TYR* 4.4 3.9 + - - +
255B ILE* 3.5 28.9 - - + -
256B THR 3.3 7.0 - - - +
257B LEU* 3.7 16.2 - - + -
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.9 20.8 - - - +
157B VAL* 1.3 74.1 - - - +
159B ALA* 1.3 66.5 + - - +
160B MET* 4.8 10.5 - - + -
206B LEU* 3.7 24.7 - - - +
215B SER* 2.9 38.7 + - - -
216B VAL 3.4 6.5 - - - +
217B VAL* 3.8 23.0 - - + +
234B TYR* 4.6 2.5 - - - -
254B ILE 3.5 0.9 - - - +
255B ILE* 3.3 6.9 - - - +
256B THR* 2.8 46.3 + - - +
258B GLU* 2.7 42.4 + - - +
262B GLY* 5.4 2.4 - - - -
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Residues in contact with ALA 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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158B ARG* 1.3 74.8 - - - +
160B MET* 1.3 60.6 + - - +
195B ILE* 4.3 11.0 - - + +
215B SER* 3.2 8.5 - - - -
216B VAL* 2.9 38.9 + - + +
234B TYR* 3.5 35.4 - - + +
253B THR* 4.3 5.2 - - + -
254B ILE 3.5 4.3 - - - -
255B ILE* 3.6 10.8 - - + -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.5 36.1 - - + -
158B ARG* 4.8 9.2 - - + -
159B ALA* 1.3 76.5 - - - +
161B ALA* 1.3 71.3 + - - +
162B ILE* 4.6 2.9 - - + -
195B ILE* 4.0 6.7 - - - +
206B LEU* 6.3 1.1 - - + -
208B ASP* 6.1 3.1 - - + +
211B THR* 5.9 0.4 - - - +
213B ARG* 4.0 22.2 - - + -
214B HIS 3.5 17.7 - - - +
215B SER* 4.1 19.7 - - - +
252B LEU 3.8 0.3 - - - +
253B THR* 3.4 1.4 - - - -
254B ILE* 2.8 42.4 + - + +
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Residues in contact with ALA 161 (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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160B MET* 1.3 80.6 - - - +
162B ILE* 1.3 67.2 - - - +
173B VAL* 3.7 35.1 + - + +
194B LEU* 4.2 5.4 - - + -
195B ILE* 3.8 19.3 - - + +
213B ARG* 4.3 5.5 + - - +
214B HIS 4.7 2.7 + - - +
251B ILE* 4.1 14.8 - - + -
252B LEU 3.2 9.9 - - - +
253B THR* 4.9 0.2 - - - +
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Residues in contact with ILE 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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97B VAL* 4.5 11.4 - - + -
98B PRO* 4.0 28.5 - - + +
100B GLN* 3.9 21.5 - - + +
160B MET* 4.1 4.0 + - - -
161B ALA* 1.3 78.7 - - - +
163B TYR* 1.3 72.0 + - - +
169B MET* 4.9 6.3 - - + +
173B VAL* 3.6 9.6 - - - -
213B ARG* 3.8 20.2 - - - +
251B ILE* 3.3 3.6 - - - -
252B LEU* 2.8 45.9 + - + +
254B ILE* 3.9 32.3 - - + -
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Residues in contact with TYR 163 (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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162B ILE* 1.3 82.6 - - - +
164B LYS* 1.3 64.9 + - - +
165B GLN 4.6 0.7 - - - +
168B HIS* 3.4 45.1 - - + +
169B MET* 3.6 21.4 + - - +
171B GLU* 3.5 22.0 + - + -
172B VAL 4.0 4.6 + - - -
173B VAL* 3.6 30.1 - - + +
174B ARG* 4.6 2.6 + - - +
245B GLY 3.5 3.5 + - - -
246B MET* 3.2 25.7 + - + +
249B ARG* 3.1 53.6 + - + -
250B PRO 3.7 8.5 - - - +
251B ILE* 3.6 23.8 - - + -
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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
------------------------------------------------------------
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