Contacts of the strand formed by residues 387 - 392 (chain A) in PDB entry 4WXS
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 GLY 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A TYR* 3.8 22.2 - - - -
383A VAL* 3.3 8.6 - - - -
384A ASP* 3.0 32.2 + - - +
385A GLU 3.6 0.2 - - - -
386A ALA* 1.3 80.8 - - - +
388A LEU* 1.3 60.7 + - - -
389A TRP* 3.3 8.8 - - - -
405A LYS* 4.1 2.4 - - - +
606A P6G 3.7 1.7 - - - -
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Residues in contact with LEU 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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328A VAL* 3.9 25.8 - - + -
330A TYR* 4.5 13.9 - - + -
335A TYR* 3.5 42.4 - - + -
381A LEU* 4.7 3.8 - - + -
382A ALA 3.6 14.1 - - - +
383A VAL* 4.1 7.0 - - + -
387A GLY* 1.3 72.1 - - - -
389A TRP* 1.3 68.5 + - - +
405A LYS* 3.4 13.9 - - - +
406A LEU* 2.9 57.5 + - + +
408A PRO* 4.1 13.7 - - + +
411A LEU* 4.3 1.8 - - + -
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Residues in contact with TRP 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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381A LEU* 3.5 12.4 - - - +
382A ALA* 2.7 38.5 + - + +
384A ASP* 2.5 40.2 + - + -
386A ALA* 4.6 5.8 - - + -
387A GLY 3.3 15.0 + - - -
388A LEU* 1.3 75.6 - - - +
390A VAL* 1.3 62.2 + - - +
403A LEU* 3.9 16.4 - - + -
404A SER 3.3 8.1 - - - -
405A LYS* 3.5 38.5 - - + +
406A LEU* 4.4 3.6 - - - +
417A TRP* 3.4 36.6 - + - -
431A ILE* 3.4 34.1 - - + -
434A GLY* 4.4 8.5 - - - -
455A THR* 3.9 20.4 - - + -
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Residues in contact with VAL 390 (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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344A VAL* 4.8 0.2 - - + -
360A ILE* 4.4 16.2 - - + -
379A ILE* 3.6 30.5 - - + -
380A ASP 3.7 3.8 - - - +
381A LEU* 3.8 16.2 - - + -
389A TRP* 1.3 75.8 - - - +
391A ILE* 1.3 66.0 + - - +
392A TYR* 3.6 26.8 - - + -
403A LEU* 3.3 5.5 - - - +
404A SER* 3.0 40.6 + - - +
406A LEU* 3.9 19.3 - - + -
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Residues in contact with ILE 391 (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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371A TYR* 3.9 13.7 - - - +
378A ASP 3.7 0.9 - - - +
379A ILE* 3.5 2.4 - - - -
380A ASP* 2.7 63.2 + - + +
382A ALA* 4.2 18.2 - - + -
390A VAL* 1.3 76.3 - - - +
392A TYR* 1.3 68.0 + - - +
401A ILE* 3.8 27.8 - - + -
402A VAL 3.5 2.9 - - - +
403A LEU* 4.7 3.8 - - + -
423A LYS* 4.3 6.1 - - - -
429A ALA* 4.2 15.5 - - + -
431A ILE* 4.3 14.4 - - + -
436A LEU* 3.8 25.8 - - + -
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Residues in contact with TYR 392 (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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360A ILE* 3.7 16.4 - - + -
361A PRO 4.4 5.6 + - - -
363A ALA* 3.6 20.0 - - + -
364A GLY 5.3 0.7 - - - +
378A ASP 3.6 15.9 - - - +
379A ILE* 4.2 14.1 - - + -
390A VAL* 3.6 35.4 - - + -
391A ILE* 1.3 77.2 - - - +
393A SER* 1.3 73.8 + - - +
394A THR* 3.7 20.4 - - + -
401A ILE* 3.6 5.0 - - - +
402A VAL* 2.7 60.4 + - + +
404A SER* 2.7 28.6 + - - -
413A LEU* 3.8 11.1 - - - +
416A THR* 4.0 3.3 - - - +
423A LYS* 4.0 8.3 - - - +
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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