Contacts of the strand formed by residues 144 - 150 (chain A) in PDB entry 5JAU
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 TYR 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 4.1 5.2 - + - -
86A PRO* 3.7 23.1 - - + -
138A LEU* 4.0 16.6 - - + -
139A ARG* 2.9 54.2 + - - +
142A GLU* 3.5 45.8 - - + +
143A LYS* 1.3 72.5 - - - +
145A PRO* 1.4 68.4 - - - +
146A LEU 3.8 0.5 + - - -
171A GLY 3.2 21.1 - - - +
173A ILE* 3.9 31.6 - - + +
261A SER* 2.8 20.5 + - - +
262A ILE* 3.4 9.5 - - - +
263A ASP* 2.7 24.8 + - - -
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Residues in contact with PRO 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 5.5 2.2 - - - +
143A LYS 4.2 4.7 - - - +
144A TYR* 1.4 85.0 - - + +
146A LEU* 1.4 59.3 + - - +
171A GLY 3.4 15.3 - - - +
172A PHE* 3.6 35.9 - - + -
173A ILE* 3.0 26.2 + - - +
263A ASP* 4.0 6.7 - - + +
266A LYS* 3.4 31.6 - - + +
396A LEU* 4.6 1.6 - - + -
398A LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PRO* 1.4 72.4 - - - +
147A VAL* 1.3 76.7 + - - +
148A VAL* 4.5 4.5 - - + -
172A PHE* 4.8 0.4 - - - -
173A ILE* 3.4 33.9 - - + +
175A ALA* 4.4 2.2 - - + +
233A LEU* 3.7 29.2 - - + -
236A ILE* 3.7 45.3 - - + -
237A LEU* 5.3 1.1 - - + -
262A ILE* 4.3 21.1 - - + -
263A ASP 5.0 0.2 + - - -
266A LYS 2.9 12.3 + - - +
267A ILE* 3.4 8.9 - - + +
268A ALA* 2.9 26.7 + - - +
396A LEU* 5.2 0.7 - - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 1.3 78.1 - - - +
148A VAL* 1.3 76.7 + - - +
149A PHE* 4.0 4.0 + - + +
167A LEU* 4.3 14.1 - - + -
172A PHE* 3.8 28.7 - - + -
173A ILE 2.9 11.0 + - - +
174A VAL* 3.5 14.6 - - + -
175A ALA 2.8 26.9 + - - -
268A ALA* 3.4 12.8 - - + +
270A ILE* 3.7 39.7 - - + -
392A LEU* 4.5 2.9 - - + -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.5 14.1 - - + -
147A VAL* 1.3 74.8 - - - +
149A PHE* 1.3 55.7 + - - +
175A ALA* 3.4 11.0 - - + +
177A VAL* 3.8 26.2 - - + -
229A CYS* 4.0 33.9 - - + +
232A ALA* 4.7 1.1 - - + -
233A LEU* 4.5 14.4 - - + +
236A ILE* 4.9 1.1 - - + -
267A ILE* 5.0 0.2 - - + -
268A ALA 2.9 8.5 + - - +
269A VAL* 3.3 6.4 - - + +
270A ILE 2.9 30.8 + - - +
289A PHE* 3.7 29.2 - - + -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.0 3.3 + - + -
148A VAL* 1.3 72.2 - - - +
150A SER* 1.4 75.4 + - - +
151A HIS* 4.2 1.6 - - + -
160A TYR* 3.3 54.1 - + + -
163A ILE* 4.0 27.4 - - + -
164A GLY* 6.4 0.4 - - - -
167A LEU* 5.5 0.4 - - + -
174A VAL* 4.2 16.6 - - + -
175A ALA 2.8 10.2 + - - +
176A ALA* 3.6 21.9 - - + -
177A VAL* 3.0 32.9 + - - +
270A ILE* 3.2 35.9 - - + -
271A GLY* 4.2 1.8 - - - -
272A HIS 4.1 12.6 - - - -
295A LEU* 4.1 7.0 - - + -
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 1.4 77.8 - - - +
151A HIS* 1.4 58.6 + - - +
177A VAL* 4.3 0.2 - - - -
179A HIS* 2.8 28.0 + - - -
225A ARG* 3.1 14.6 + - - -
229A CYS* 4.3 7.2 - - - -
269A VAL* 5.5 1.6 - - - -
270A ILE 2.8 12.6 + - - -
271A GLY* 3.2 1.0 - - - -
272A HIS 3.1 26.3 + - - -
275A GLY* 3.3 16.1 - - - -
278A THR* 3.3 18.3 - - - -
279A VAL 5.2 0.7 - - - -
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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