Contacts of the strand formed by residues 376 - 384 (chain A) in PDB entry 4XE4
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 SER 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A TYR* 3.5 8.1 - - - +
373A TRP* 2.5 73.9 + - - -
374A GLY 3.3 0.7 - - - +
375A HIS* 1.3 79.1 + - - +
377A PHE* 1.3 61.7 + - - +
1B NAG 5.8 1.0 - - - -
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Residues in contact with PHE 377 (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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370A ALA* 3.9 9.2 - - + -
371A LEU 3.2 10.8 - - - -
372A TYR* 3.2 43.1 - + + -
373A TRP* 4.0 3.6 - - - -
376A SER* 1.3 79.0 - - - +
378A CYS* 1.3 83.9 + - - +
413A ARG* 3.7 45.8 - - - +
486A TRP* 3.7 27.4 - + - -
543A ASP* 3.9 28.7 - - + -
544A SER* 5.5 0.9 - - - -
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Residues in contact with CYS 378 (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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370A ALA* 3.6 1.0 - - - -
371A LEU* 2.6 50.4 + - + +
373A TRP* 3.8 11.8 - - + -
377A PHE* 1.3 88.9 - - - +
379A ALA* 1.3 61.0 + - - +
390A THR* 4.5 0.4 - - + -
394A CYS* 2.0 55.9 - - + -
544A SER* 3.5 18.8 - - - +
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Residues in contact with ALA 379 (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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368A ILE* 4.6 10.5 - - + -
369A ALA 3.4 10.5 - - - +
370A ALA* 4.7 1.1 - - - +
371A LEU* 5.1 2.1 - - - +
377A PHE* 4.1 1.8 - - - -
378A CYS* 1.3 75.3 - - - +
380A GLY* 1.3 50.8 + - - +
390A THR* 2.8 31.7 - - - +
486A TRP* 4.7 2.7 - - + -
543A ASP* 3.7 31.3 - - + +
544A SER 2.9 6.1 + - - -
545A GLY* 3.3 7.4 - - - -
546A GLY* 3.6 22.7 - - - +
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Residues in contact with GLY 380 (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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368A ILE* 3.6 9.5 - - - +
369A ALA* 2.9 31.1 + - - -
379A ALA* 1.3 76.6 - - - +
381A SER* 1.3 66.5 + - - -
388A VAL* 4.1 9.0 - - - -
389A LEU 3.5 11.4 - - - -
390A THR* 4.1 3.8 - - - -
545A GLY 3.7 7.5 + - - -
547A PRO* 4.2 2.3 - - - +
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Residues in contact with SER 381 (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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367A TYR* 3.5 6.3 - - - -
380A GLY* 1.3 75.5 + - - -
382A LEU* 1.3 63.7 - - - +
383A ILE* 3.4 4.7 + - - +
388A VAL* 3.4 5.4 - - - +
389A LEU 2.9 35.8 + - - -
466A VAL* 4.4 8.1 - - - -
545A GLY 4.7 0.7 + - - -
546A GLY 4.7 0.5 - - - -
547A PRO* 3.3 31.2 - - - +
561A LEU* 3.8 25.3 - - - +
564A ILE* 6.0 1.5 - - - +
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Residues in contact with LEU 382 (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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366A PRO 5.1 0.4 - - - +
367A TYR* 2.8 22.3 + - - +
369A ALA* 4.8 1.0 - - - +
380A GLY 4.3 0.2 - - - -
381A SER* 1.3 69.3 - - - +
383A ILE* 1.3 58.6 + - - +
384A ALA 3.2 23.6 - - - +
385A PRO* 4.4 3.6 - - + +
387A TRP 3.5 8.3 - - - +
388A VAL* 3.8 16.9 - - + +
408A LEU* 4.2 17.5 - - + -
448A LEU* 4.0 15.0 - - + -
457A ALA* 4.5 6.3 - - + -
459A LEU* 5.6 1.1 - - + -
463A VAL* 4.1 21.8 - - + -
464A GLN 3.8 6.7 - - - +
465A PRO* 3.2 27.7 - - + +
466A VAL* 3.0 29.8 + - - +
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Residues in contact with ILE 383 (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 SER 3.7 11.2 - - - +
382A LEU* 1.3 78.4 - - - +
384A ALA* 1.3 65.3 + - + +
387A TRP* 3.1 23.9 + - + +
388A VAL 4.6 0.2 - - - +
389A LEU* 4.2 14.1 - - + -
445A LEU* 3.9 28.7 - - + -
465A PRO* 3.5 12.1 - - - +
466A VAL* 3.9 23.4 - - + +
468A LEU* 3.9 29.5 - - + +
561A LEU* 4.4 4.9 - - + -
590A ILE* 4.3 16.4 - - + -
594A THR* 4.3 5.6 - - + -
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Residues in contact with ALA 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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382A LEU* 3.2 11.7 - - - +
383A ILE* 1.3 81.7 - - + +
385A PRO* 1.3 77.1 - - + +
386A CYS 2.9 4.3 + - - -
387A TRP* 3.1 38.9 - - + +
465A PRO* 4.0 6.7 - - - -
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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