Contacts of the strand formed by residues 384 - 388 (chain A) in PDB entry 5TQW
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 VAL 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A VAL* 3.7 26.2 - - + -
314A HIS 3.1 5.3 + - - -
315A ILE* 3.3 19.6 - - + +
316A LEU* 3.0 27.4 + - - +
354A LEU* 3.7 41.1 - - + -
355A LEU 3.6 8.7 - - - +
356A SER* 5.8 2.7 - - - -
383A MET* 1.3 77.5 - - - +
385A TYR* 1.3 63.6 + - - +
386A LEU 3.8 0.4 - - - -
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.6 13.0 - - + -
318A MET* 3.7 26.5 - - + -
353A GLU 2.9 13.9 - - - +
354A LEU* 4.4 1.3 - - - -
355A LEU* 2.8 51.0 + - + +
356A SER 3.5 11.9 - - - -
357A GLU* 3.0 35.2 + - - -
383A MET* 3.2 28.9 - - + +
384A VAL* 1.3 73.0 - - - +
386A LEU* 1.3 63.7 + - - +
387A PHE* 3.4 5.9 + - + -
443A ARG* 3.7 23.5 + - + +
446A GLN* 3.3 24.2 + - - +
447A GLY* 4.1 18.8 - - - -
450A ALA* 4.7 1.3 - - + -
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Residues in contact with LEU 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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315A ILE* 4.1 13.8 - - + +
316A LEU 3.2 7.8 + - - +
317A ASN* 3.4 41.6 - - + +
318A MET* 3.4 17.3 + - - +
319A THR* 4.3 1.3 + - - +
341A ILE* 4.3 17.3 - - + -
345A THR* 4.4 6.7 - - + +
347A ILE* 4.2 20.4 - - + -
352A GLN* 3.8 24.0 - - + -
353A GLU 3.2 2.2 - - - +
354A LEU* 3.8 20.6 - - + +
384A VAL 3.6 2.0 + - - -
385A TYR* 1.3 71.1 - - - +
387A PHE* 1.3 89.4 + - - +
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Residues in contact with PHE 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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318A MET* 3.5 34.3 - - + -
319A THR* 4.6 2.2 - - + -
351A SER 3.0 2.1 - - - +
353A GLU* 2.6 75.9 + - + +
355A LEU* 3.6 20.9 - - + -
385A TYR* 4.5 4.9 - - + -
386A LEU* 1.3 94.5 - - - +
388A ASP* 1.3 60.5 + - - +
394A TYR* 4.5 15.3 - + - +
447A GLY 4.3 9.4 - - - -
451A ALA* 3.9 20.6 - - + -
608A LEU* 3.8 27.4 - - + -
612A LEU* 5.6 8.3 - - + -
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Residues in contact with ASP 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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319A THR* 4.1 14.9 - - + +
347A ILE* 3.3 37.4 - - + +
348A ASN 5.0 0.2 + - - -
351A SER* 2.8 29.2 + - - -
387A PHE* 1.3 73.5 - - - +
389A LYS* 1.3 64.7 + - - +
390A SER* 3.1 14.7 + - - -
391A LYS* 3.3 32.8 + - + +
394A TYR* 2.5 29.6 + - - +
612A LEU* 4.7 1.9 - - - +
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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
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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