Contacts of the strand formed by residues 140 - 146 (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 HIS 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS 2.9 7.9 + - - +
29B HIS* 3.4 21.7 + + + -
30B TRP* 2.8 27.8 + - - +
138B GLN 4.7 4.7 + - - -
139B ASP* 1.3 80.0 + - - +
141B VAL* 1.3 67.1 + - - +
180B ARG* 4.4 15.9 - - + -
181B LYS* 3.4 32.1 + - + +
278B MET* 4.8 6.8 - - - -
282B GLN* 3.3 48.2 - - + +
283B PHE* 3.9 16.4 - + + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 3.5 10.3 - - + +
32B VAL* 5.2 0.4 - - + -
133B LEU* 4.1 17.7 - - + -
135B SER* 3.8 23.6 - - - +
140B HIS* 1.3 79.9 - - - +
142B PHE* 1.3 62.3 + - - +
143B ILE* 3.9 22.9 - - + -
179B TYR* 3.8 14.8 - - + -
181B LYS 3.1 6.6 + - - +
182B MET* 3.3 37.0 - - + +
183B VAL 2.9 26.2 + - - -
283B PHE* 4.0 5.1 - - - -
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Residues in contact with PHE 142 (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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30B TRP 2.9 10.9 + - - +
31B VAL* 3.2 20.2 - - + +
32B VAL 2.9 24.9 + - - -
33B ILE* 6.0 0.7 - - + -
52B ALA* 6.1 0.9 - - + -
56B ILE* 4.2 9.9 - - + -
141B VAL* 1.3 74.5 - - - +
143B ILE* 1.3 65.8 + - - +
144B TYR* 4.3 15.9 - - + -
183B VAL* 3.5 17.0 - - + +
185B TYR* 3.7 50.0 - + + -
237B TRP* 4.1 17.0 - + - -
251B LEU* 6.2 0.4 - - + -
283B PHE* 3.3 37.2 - - + +
284B GLN* 4.0 21.3 - - + -
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Residues in contact with ILE 143 (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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32B VAL* 3.4 18.2 - - + +
34B VAL* 5.7 0.4 - - + -
113B PHE* 3.9 22.2 - - + -
117B LEU* 3.9 25.8 - - + -
141B VAL* 3.9 13.0 - - + -
142B PHE* 1.3 81.3 - - - +
144B TYR* 1.3 67.0 + - - +
145B PHE* 4.9 4.0 - - + +
182B MET* 4.0 15.9 - - - -
183B VAL 2.8 9.9 + - - +
184B PHE* 3.4 48.5 - - + +
185B TYR* 2.9 27.0 + - - +
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Residues in contact with TYR 144 (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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32B VAL 2.9 11.9 + - - +
33B ILE* 3.4 13.8 - - + -
34B VAL* 2.8 26.7 + - - +
48B ASP* 3.3 20.6 - - - +
49B ALA* 4.3 1.1 - - - -
52B ALA* 3.6 31.6 - - + -
142B PHE* 4.2 20.3 - - + -
143B ILE* 1.3 75.0 - - - +
145B PHE* 1.3 72.3 + - - +
146B THR* 3.4 18.7 - - + -
185B TYR* 3.3 23.8 - - + -
187B GLU* 4.6 3.1 - - + -
233B TYR* 4.9 1.3 - + - -
234B SER* 2.5 34.5 + - - -
237B TRP* 3.6 25.4 - + - -
238B MET* 3.9 1.6 - - + +
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.3 33.0 - - + -
36B GLY* 4.0 4.9 - - - -
113B PHE* 5.9 6.3 - + + -
143B ILE* 4.2 6.1 + - + +
144B TYR* 1.3 77.4 - - - +
146B THR* 1.3 62.0 + - - +
147B SNN 3.6 23.3 - - + -
148B HIS 3.8 13.7 - - - -
154B LEU* 3.8 38.8 - - + -
155B VAL 3.3 23.3 - - - -
156B PHE* 3.8 26.9 - + - -
185B TYR 3.0 9.4 + - - +
186B ILE* 3.6 12.8 - - + -
187B GLU 2.8 33.8 + - - -
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Residues in contact with THR 146 (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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34B VAL 2.9 18.7 + - - +
35B ALA* 3.4 3.8 - - - -
36B GLY 3.1 14.4 + - - -
45B HIS* 3.3 36.0 - - - +
48B ASP* 3.0 21.3 + - + -
49B ALA* 4.2 2.7 - - + +
144B TYR* 3.4 32.3 - - + +
145B PHE* 1.3 77.6 - - - +
147B SNN 1.3 69.1 + - - +
187B GLU* 3.5 12.9 - - - +
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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