Contacts of the strand formed by residues 384 - 389 (chain A) in PDB entry 1L8A
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 THR 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A LEU 3.3 7.6 + - - -
254A VAL* 3.3 8.5 - - + +
255A PHE 2.9 23.6 + - - +
287A TRP* 3.6 5.0 - - - -
288A ASN* 3.0 31.3 + - - +
290A ILE* 3.6 31.2 - - + -
376A ALA* 3.9 23.6 + - + -
379A THR* 3.9 13.3 - - - +
382A LYS 4.0 1.1 + - - -
383A ALA* 1.3 75.0 - - - +
385A VAL* 1.3 68.3 + - - +
386A ILE* 4.2 4.0 - - + -
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Residues in contact with VAL 385 (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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255A PHE* 3.2 15.5 - - + +
257A ILE* 3.7 31.0 - - + -
282A PHE* 3.8 24.9 - - + -
287A TRP* 3.7 14.1 - - + -
288A ASN 2.9 15.3 + - - +
289A VAL* 3.8 24.0 - - + +
290A ILE 2.9 25.5 + - - +
384A THR* 1.3 75.0 - - - +
386A ILE* 1.3 64.0 + - - +
387A LEU* 3.9 12.2 + - + -
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Residues in contact with ILE 386 (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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254A VAL* 3.9 13.9 - - + -
255A PHE 2.7 11.9 + - - +
256A VAL* 3.6 9.7 - - + +
257A ILE* 2.9 28.9 + - - +
290A ILE* 3.4 7.9 - - + +
292A VAL* 3.9 25.1 - - + -
372A ALA* 3.9 27.8 - - + +
373A PHE* 3.8 44.2 - - + -
376A ALA* 4.2 2.0 - - + -
384A THR* 4.3 11.0 - - + -
385A VAL* 1.3 75.6 - - - +
387A LEU* 1.3 61.1 + - - +
388A ALA* 3.5 13.4 + - + +
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Residues in contact with LEU 387 (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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257A ILE* 3.6 37.9 - - + -
259A CYS* 3.9 13.9 - - - -
275A ILE* 3.6 30.9 - - + +
278A LEU* 3.9 14.1 - - + -
279A GLU* 3.9 12.8 - - - +
282A PHE* 5.7 0.4 - - + -
289A VAL* 4.0 21.1 - - + -
290A ILE 2.9 12.4 + - - +
291A LYS* 3.7 15.3 - - + +
292A VAL 2.9 26.0 + - - +
293A MET* 4.9 2.3 - - - +
385A VAL* 3.9 12.8 - - + -
386A ILE* 1.3 71.0 - - - +
388A ALA* 1.3 61.0 + - - +
389A HIS 3.7 1.2 + - - -
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Residues in contact with ALA 388 (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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116A ILE* 3.5 33.4 - - + -
256A VAL* 5.1 3.1 - - + -
257A ILE 3.0 14.4 + - - +
258A ASN* 3.7 1.8 - - - -
259A CYS* 2.6 31.2 + - - -
292A VAL* 4.0 9.4 - - + -
363A GLY* 4.5 7.2 - - - -
369A ILE* 6.1 1.1 - - + -
373A PHE* 6.5 0.2 - - + -
386A ILE* 3.5 12.9 + - + +
387A LEU* 1.3 70.9 - - - +
389A HIS* 1.3 61.4 + - - +
390A THR* 3.5 3.5 + - - +
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Residues in contact with HIS 389 (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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59A TYR* 4.2 7.1 + + - -
259A CYS* 3.5 17.0 - - - -
261A LEU* 3.9 13.8 - - + +
275A ILE* 3.7 13.5 - - + -
292A VAL 2.9 21.4 + - - +
293A MET* 3.0 41.9 + - + +
294A TRP* 3.9 22.6 - + - -
322A TYR* 5.4 5.1 - + - -
361A ARG* 3.2 48.4 + - + +
363A GLY* 2.7 27.6 + - - +
387A LEU 3.7 1.6 + - - -
388A ALA* 1.3 69.6 - - - +
390A THR* 1.3 58.4 + - - +
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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