Contacts of the strand formed by residues 467 - 476 (chain A) in PDB entry 4X61
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 GLU 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A PRO 3.5 0.4 - - - -
466A GLY* 1.3 79.4 - - - +
468A TYR* 1.3 63.9 + - - +
469A THR* 5.2 3.6 - - - +
520A THR* 3.8 18.7 - - - +
521A PHE 3.2 16.4 - - - +
522A SER* 4.3 10.7 + - - +
523A HIS 4.8 0.2 - - - +
557A THR* 2.7 24.1 + - - -
558A VAL* 2.8 43.7 + - + +
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Residues in contact with TYR 468 (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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437A LEU* 3.5 22.7 - - + -
441A ALA* 3.8 20.2 - - + -
442A ASP* 4.1 12.3 - - + -
446A SER* 2.8 25.9 + - - -
447A PRO* 3.1 12.2 - - + +
450A LEU* 5.0 0.2 - - + -
465A PRO* 4.0 13.2 - - + -
467A GLU* 1.3 82.1 - - - +
469A THR* 1.3 65.5 + - - +
519A PHE 3.9 0.6 - - - +
520A THR* 3.4 2.3 - - - +
521A PHE* 3.2 52.2 + + + -
523A HIS* 2.7 40.1 + + - -
555A PHE* 5.1 0.4 - - + -
556A GLU 3.2 14.1 - - - +
557A THR* 3.4 13.0 - - - +
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Residues in contact with THR 469 (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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441A ALA* 4.3 4.0 - - - -
467A GLU* 4.9 4.9 + - - +
468A TYR* 1.3 75.7 + - - +
470A SER* 1.3 73.4 + - - +
471A PHE* 3.7 19.9 - - + -
517A PRO* 3.9 16.8 - - + -
519A PHE 3.2 5.2 - - - +
520A THR* 2.8 32.6 + - - +
555A PHE* 3.2 4.4 - - - +
556A GLU* 2.8 43.1 + - - -
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Residues in contact with SER 470 (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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440A PHE* 3.6 44.2 - - - -
441A ALA* 4.3 1.0 - - - +
442A ASP* 4.5 3.6 - - - -
469A THR* 1.3 75.3 - - - +
471A PHE* 1.3 56.2 + - - +
517A PRO* 3.3 5.9 - - - +
518A CYS* 2.6 36.1 + - - +
519A PHE* 2.8 43.4 + - - +
554A TYR 3.4 4.5 - - - -
555A PHE* 4.3 1.6 - - - +
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Residues in contact with PHE 471 (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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440A PHE* 3.5 3.3 - - - -
469A THR* 3.7 29.6 - - + -
470A SER* 1.3 76.9 - - - +
472A LEU* 1.3 63.5 + - - +
515A PRO* 4.1 13.2 - - + -
516A GLN* 3.4 13.5 - - - -
517A PRO* 3.4 36.8 - - + -
552A ALA 3.5 0.7 - - - +
553A GLY* 3.3 6.2 - - - -
554A TYR* 2.7 45.8 + - + +
555A PHE* 4.5 2.2 - - - -
556A GLU* 3.4 41.1 - - + -
568A ARG* 3.6 37.7 - - + -
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Residues in contact with LEU 472 (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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440A PHE* 3.6 28.9 - - + -
471A PHE* 1.3 74.1 - - - +
473A ALA* 1.3 60.7 + - - +
515A PRO* 3.1 4.2 - - - +
516A GLN 3.0 29.0 + - - -
518A CYS* 3.7 22.4 - - + -
538A LEU* 3.9 21.8 - - + -
540A PHE* 3.2 12.0 - - + -
551A PHE* 3.9 20.9 - - + -
552A ALA 3.2 12.8 - - - +
554A TYR* 5.4 0.2 - - - -
584A PHE* 4.1 7.2 - - + -
600A VAL* 4.7 3.6 - - + -
602A PHE* 3.5 39.3 - - + -
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Residues in contact with ALA 473 (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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472A LEU* 1.3 75.3 - - - +
474A PRO* 1.3 68.8 - - - +
475A ILE* 3.7 2.1 - - - +
511A GLN* 3.9 23.8 - - + +
513A SER 3.7 20.0 - - - +
515A PRO* 3.9 13.0 - - + -
540A PHE* 4.1 0.4 - - - -
551A PHE* 3.3 4.2 - - - -
552A ALA* 2.8 38.8 + - + +
554A TYR* 4.6 4.3 - - + -
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Residues in contact with PRO 474 (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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473A ALA* 1.3 86.9 - - + +
475A ILE* 1.3 59.3 + - - +
511A GLN* 3.8 1.9 - - - +
512A LEU* 2.9 31.7 + - + -
513A SER* 3.8 19.7 + - - +
540A PHE* 3.4 42.4 - - + -
542A VAL* 5.0 0.2 - - + -
548A LEU* 3.7 18.4 - - + -
550A GLY 3.6 7.2 - - - +
551A PHE* 3.7 13.6 - - + -
598A ILE* 3.9 13.7 - - + -
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Residues in contact with ILE 475 (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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473A ALA 3.7 9.9 - - - +
474A PRO* 1.3 80.6 - - - +
476A SER* 1.3 60.1 + - - +
477A SER* 4.4 20.4 - - - +
480A LEU* 4.5 11.4 - - + -
506A LEU* 4.5 6.3 - - + -
509A PHE* 3.7 28.0 - - + -
510A HIS 3.2 8.1 - - - +
511A GLN* 4.3 5.6 - - + -
512A LEU* 3.6 5.5 - - - +
548A LEU* 3.6 4.0 - - - +
549A HIS* 3.1 25.3 + - + -
550A GLY* 2.9 27.7 + - - +
551A PHE 4.3 0.9 - - - +
552A ALA* 3.9 16.6 - - + +
583A LEU* 3.7 24.5 - - + -
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Residues in contact with SER 476 (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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186A TRP* 6.1 0.3 - - - -
222A LEU 5.0 4.6 + - - -
223A GLY* 4.1 2.1 - - - -
224A GLU* 5.7 1.0 + - - -
475A ILE* 1.3 74.3 - - - +
477A SER* 1.3 63.7 + - - +
478A SER 5.1 0.3 + - - -
509A PHE* 3.5 1.6 - - - +
510A HIS* 2.8 40.6 + - - +
512A LEU* 3.7 10.5 - - - +
546A THR* 3.3 22.1 + - - -
547A VAL* 2.6 27.6 + - - +
549A HIS* 3.8 5.3 + - - -
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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