Contacts of the strand formed by residues 383 - 388 (chain A) in PDB entry 1UWV
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 ARG 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A GLU 5.0 1.0 + - - -
281A TRP* 2.9 30.1 + - - +
282A LEU* 3.8 19.6 + - + +
283A ASP* 3.7 27.1 + - - +
358A ASP 3.6 1.6 + - - -
359A LYS* 3.4 25.2 - - + +
360A VAL 3.2 21.8 + - - -
381A PRO* 3.3 1.9 - - - +
382A ILE* 1.3 89.6 - - + +
384A ILE* 1.3 68.0 + - - +
428A LEU* 3.8 19.8 - - + +
429A PHE 3.5 6.3 - - - +
430A SER* 4.1 13.7 - - - +
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Residues in contact with ILE 384 (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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282A LEU* 4.3 0.2 - - - -
360A VAL* 3.1 14.4 - - + +
362A LEU* 3.9 23.8 - - + -
376A ILE* 3.5 25.6 - - + -
381A PRO* 3.5 13.2 - - + -
383A ARG* 1.3 80.5 - - - +
385A VAL* 1.3 66.7 - - - +
386A TYR* 4.9 0.4 - - + -
401A LEU* 3.8 25.1 - - + -
406A TYR* 3.7 32.3 - - + -
427A VAL 3.6 1.0 - - - +
428A LEU* 3.5 3.5 - - - +
429A PHE* 2.9 47.2 + - + +
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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
----------------------------------------------------------
278A ALA* 4.3 4.5 - - + +
281A TRP* 4.1 16.2 - - + -
282A LEU* 3.6 26.9 - - + -
360A VAL 2.9 7.1 + - - -
361A LEU* 3.2 26.5 - - + -
362A LEU* 2.9 29.1 + - - +
384A ILE* 1.3 74.5 - - - +
386A TYR* 1.3 63.3 + - - +
387A VAL* 4.4 2.7 - - + -
426A MSE 3.8 32.8 - - + -
427A VAL 3.3 5.2 - - - +
428A LEU* 3.8 16.4 - - + -
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Residues in contact with TYR 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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362A LEU* 3.4 31.0 - - + -
364A PRO* 3.9 15.2 - - + +
368A GLY* 3.8 14.7 - - - -
369A ALA 3.9 1.0 + - - -
373A MSE 4.1 10.1 - - - -
384A ILE* 4.9 0.4 - - + -
385A VAL* 1.3 75.5 - - - +
387A VAL* 1.3 78.0 + - - +
388A SER* 3.7 15.5 + - - -
393A THR* 4.3 2.3 + - - -
394A LEU* 3.9 27.7 - - + +
397A ASP* 2.5 44.4 + - + -
401A LEU* 5.3 1.1 - - + -
425A SER 3.9 0.3 - - - +
426A MSE 3.3 3.5 - - - -
427A VAL* 3.0 31.6 + - + +
429A PHE* 4.1 23.6 - + + -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MSE 3.8 21.3 - - - -
300A PHE* 3.7 27.6 - - + -
361A LEU* 4.9 2.2 - - + -
362A LEU 2.8 15.3 + - - +
363A ASP* 3.5 27.0 - - - +
364A PRO* 3.4 24.9 - - - +
385A VAL* 4.4 7.0 - - + -
386A TYR* 1.3 76.1 - - - +
388A SER* 1.3 65.5 + - - +
414A LEU* 4.3 4.3 - - + -
424A GLU* 6.0 2.9 - - + -
425A SER 3.4 10.1 - - - +
426A MSE 4.0 20.4 - - + -
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Residues in contact with SER 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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363A ASP* 5.3 0.9 - - - -
364A PRO* 5.4 2.2 - - - -
386A TYR* 3.7 19.6 + - - -
387A VAL* 1.3 79.7 - - - +
389A CYS* 1.3 57.8 + - - +
390A ASN* 3.1 31.2 + - - +
393A THR* 4.7 1.7 + - - -
394A LEU* 3.5 19.0 + - - +
423A LEU 4.3 0.3 - - - +
424A GLU* 3.3 6.6 - - - +
425A SER* 2.9 42.5 + - - +
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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