Contacts of the strand formed by residues 501 - 508 (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 GLN 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A ALA* 3.3 6.8 - - - +
485A GLY 2.8 32.7 + - - +
486A TRP 2.9 20.1 + - - -
498A SER* 2.8 28.5 + - - -
499A PHE* 3.1 9.6 + - + +
500A LEU* 1.3 77.7 - - - +
502A GLU* 1.3 62.4 + - - +
541A GLN* 4.1 24.7 + - + +
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Residues in contact with GLU 502 (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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364A ALA* 5.2 4.1 - - - +
365A HIS* 2.9 33.3 + - + +
482A GLN* 3.3 23.4 + - + +
483A VAL 3.3 11.7 - - - +
501A GLN* 1.3 78.6 - - - +
503A ALA* 1.3 64.8 + - - +
541A GLN* 3.6 10.3 - - - +
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Residues in contact with ALA 503 (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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482A GLN* 3.2 9.4 - - - -
483A VAL* 2.7 50.2 + - + +
502A GLU* 1.3 80.4 - - - +
504A GLN* 1.3 67.7 + - - +
505A VAL* 3.6 5.3 + - + -
538A ASP 5.2 4.5 - - - +
541A GLN* 3.7 21.5 - - - +
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Residues in contact with GLN 504 (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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480A LEU* 3.9 31.4 - - - +
481A CYS 3.4 19.5 + - - +
482A GLN* 4.2 21.6 + - + +
503A ALA* 1.3 73.3 - - - +
505A VAL* 1.3 65.7 + - - +
506A PRO* 4.6 0.4 - - - -
532A PHE* 4.1 16.3 - - + -
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Residues in contact with VAL 505 (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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481A CYS* 2.9 39.9 + - + +
483A VAL* 4.7 17.0 - - + -
503A ALA* 3.6 4.2 + - + +
504A GLN* 1.3 80.8 - - - +
506A PRO* 1.3 66.5 - - + +
530A ALA* 3.7 19.7 - - + +
531A GLY* 4.1 13.0 - - - +
532A PHE* 4.9 6.7 - - + -
538A ASP 6.0 2.5 - - - +
548A LEU* 3.5 32.5 - - + -
580A TYR* 4.7 6.7 - - - +
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Residues in contact with PRO 506 (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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477A GLU 4.6 9.2 - - - +
479A THR 4.6 5.6 - - - +
480A LEU* 6.0 0.2 - - - -
504A GLN 4.6 0.2 - - - -
505A VAL* 1.3 88.2 - - + +
507A PHE* 1.3 66.0 + - - +
508A LEU* 5.1 1.8 - - + -
530A ALA* 3.0 6.5 - - - -
531A GLY 3.0 44.8 + - - +
532A PHE* 3.5 34.3 - - + -
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Residues in contact with PHE 507 (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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475A PRO* 3.3 37.9 - - + -
476A SER 3.3 29.6 - - - +
477A GLU* 3.7 22.5 + - + +
479A THR* 3.9 16.7 + - - +
481A CYS* 4.4 15.6 - - - -
505A VAL 3.8 1.8 + - - -
506A PRO* 1.3 77.9 - - - +
508A LEU* 1.3 82.7 + - - +
509A SER* 3.9 21.3 - - - -
510A LEU* 5.0 9.0 - - + -
528A LEU* 4.2 32.3 - - + -
529A CYS 3.8 13.0 - - - -
530A ALA* 4.1 4.7 - - + -
548A LEU* 5.7 0.9 - - + -
550A CYS* 5.7 1.3 - - - -
562A GLN* 6.3 2.2 - - + -
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Residues in contact with LEU 508 (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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477A GLU* 3.7 10.3 - - - +
506A PRO* 4.2 4.3 - - + +
507A PHE* 1.3 93.1 - - - +
509A SER* 1.3 69.0 + - - +
510A LEU* 3.5 4.0 + - - +
512A ARG* 5.0 7.0 - - + -
513A CYS* 4.3 18.3 - - + +
529A CYS* 2.8 41.2 + - + +
530A ALA 4.0 0.4 - - - +
531A GLY 3.6 24.5 - - - +
533A LEU* 4.0 32.3 - - + -
577A PRO* 4.2 23.1 - - + -
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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