Contacts of the strand formed by residues 181 - 186 (chain B) in PDB entry 5LUA
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 LYS 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP 3.5 3.0 + - - +
140B HIS* 3.4 26.5 - - + +
141B VAL 3.1 21.7 + - - -
179B TYR* 3.6 5.8 - - - +
180B ARG* 1.3 99.3 - - + +
182B MET* 1.3 61.9 + - - +
203B ASN* 3.5 22.6 + - + +
275B ILE* 4.0 18.7 - - + +
278B MET* 3.8 26.5 - - + -
283B PHE* 3.8 17.6 - - + -
1E NAG 2.7 33.5 + - - -
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Residues in contact with MET 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 3.3 31.2 - - + +
143B ILE* 4.0 14.6 - - + -
170B ILE* 5.5 2.7 - - - -
173B MET* 3.2 38.1 - - + +
179B TYR* 3.3 36.8 - - + -
181B LYS* 1.3 74.6 - - - +
183B VAL* 1.3 72.3 + - - +
184B PHE* 3.8 28.0 - - + -
203B ASN 3.0 7.1 + - - +
204B VAL* 3.3 11.6 - - + +
205B TYR* 2.9 26.2 + - - +
275B ILE* 4.8 0.9 - - - +
283B PHE* 4.4 0.2 - - - -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL 2.9 9.7 + - - +
142B PHE* 3.5 12.0 - - + -
143B ILE* 2.8 28.6 + - - +
182B MET* 1.3 79.8 - - - +
184B PHE* 1.3 65.9 + - - +
185B TYR* 3.7 32.5 - - + -
205B TYR* 3.1 18.4 - - + +
206B ALA* 5.3 0.2 - - - -
251B LEU* 3.9 19.3 - - + -
275B ILE* 4.3 9.2 - - + -
283B PHE* 3.6 34.5 - - + -
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Residues in contact with PHE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 5.2 2.0 - + - -
117B LEU* 4.8 2.9 - - + -
143B ILE* 3.4 49.1 - - + -
166B LEU* 4.5 14.1 - - + -
170B ILE* 4.0 28.9 - - + -
173B MET* 5.9 0.2 - - - -
182B MET* 3.8 21.5 - - + -
183B VAL* 1.3 73.7 - - - +
185B TYR* 1.3 61.4 + - - +
186B ILE* 4.2 17.5 - - + -
195B MET* 3.8 18.6 - - + -
204B VAL* 3.8 25.8 - - + -
205B TYR 3.0 7.1 + - - -
206B ALA* 3.3 13.8 - - + -
207B THR 2.8 32.5 + - - +
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Residues in contact with TYR 185 (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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142B PHE* 3.7 17.5 - + + -
143B ILE 2.9 7.7 + - - +
144B TYR* 3.3 18.9 - - + -
145B PHE 3.0 24.4 + - - -
183B VAL* 3.7 18.4 - - + -
184B PHE* 1.3 79.3 - - - +
186B ILE* 1.3 62.6 + - - +
205B TYR* 5.4 2.0 - + - -
207B THR* 4.2 16.8 - - + -
233B TYR* 3.3 16.4 - + + +
237B TRP* 3.5 43.5 - + + -
251B LEU* 3.3 23.6 + - + +
254B GLN* 2.7 36.5 + - + +
255B TYR* 5.3 1.1 + - - -
284B GLN* 3.9 8.3 - - - -
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Residues in contact with ILE 186 (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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145B PHE* 3.6 12.8 - - + -
154B LEU* 3.8 35.7 - - + -
166B LEU* 5.2 1.1 - - + -
184B PHE* 4.2 18.6 - - + -
185B TYR* 1.3 78.4 - - - +
187B GLU* 1.3 59.4 + - - +
191B SER* 2.8 33.5 + - - +
194B MET* 4.4 10.1 - - + -
195B MET* 3.8 41.5 - - + -
207B THR 3.1 11.5 + - - +
208B THR* 3.5 4.2 - - + -
209B ALA 3.0 20.1 + - - -
233B TYR* 3.5 5.6 + - - -
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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
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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