Contacts of the strand formed by residues 464 - 473 (chain D) in PDB entry 6PI7
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 464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418D GLU* 5.3 3.0 + - - -
460D GLN* 3.5 2.9 - - - +
461D THR* 2.6 43.8 + - - +
463D ILE* 1.4 74.2 + - - +
465D THR* 1.3 67.6 + - - +
466D TRP* 4.0 22.2 - - - -
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Residues in contact with THR 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D TYR* 4.8 16.6 - - + -
459D VAL 3.3 7.9 - - - -
460D GLN* 3.4 30.5 - - + +
463D ILE 5.6 1.1 - - - +
464D SER* 1.3 77.7 - - - +
466D TRP* 1.3 65.5 + - - +
467D PRO* 4.0 5.4 - - - +
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Residues in contact with TRP 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASN 3.5 25.4 - - - -
320D HIS* 3.4 37.7 - + + -
418D GLU* 3.2 48.5 + - + +
419D CYS* 4.2 7.6 - - - -
458D TYR* 3.4 4.4 - - - -
459D VAL* 2.9 53.9 + - + +
461D THR* 3.5 31.6 - - + +
464D SER* 4.0 14.9 - - - -
465D THR* 1.3 77.6 - - - +
467D PRO* 1.3 67.4 - - - +
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Residues in contact with PRO 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D ILE* 4.3 19.5 - - + -
418D GLU 3.4 15.0 - - - +
419D CYS* 3.4 12.2 - - + +
420D SER 3.2 21.8 + - - -
455D ILE* 4.3 22.9 - - + -
457D SER 3.9 0.9 - - - +
458D TYR* 3.7 27.8 - - + -
465D THR 4.0 5.8 - - - +
466D TRP* 1.3 84.2 - - - +
468D LYS* 1.3 60.2 + - - +
469D ILE* 5.4 3.1 - - + +
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Residues in contact with LYS 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D SER* 3.2 19.7 - - - +
421D LEU 5.0 1.3 - - - +
422D ALA* 4.0 18.4 - - - +
423D ARG 5.7 2.5 - - - +
455D ILE* 3.7 3.7 - - - -
456D SER* 3.1 24.4 + - - -
457D SER* 2.9 40.9 + - - +
458D TYR 4.1 5.0 + - - -
459D VAL* 3.6 45.2 - - + +
466D TRP 3.5 0.2 + - - -
467D PRO* 1.3 71.2 - - - +
469D ILE* 1.3 58.3 - - - +
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Residues in contact with ILE 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PHE* 4.1 22.7 - - + -
323D ILE* 6.0 1.6 - - + -
419D CYS* 4.6 8.3 - - + -
420D SER 2.9 15.3 + - - +
421D LEU* 3.5 10.4 - - + +
422D ALA* 2.7 30.8 + - - +
453D ALA* 4.8 6.3 - - + -
454D LYS 3.0 17.9 - - - +
455D ILE* 4.9 4.7 - - + -
467D PRO* 5.1 4.0 - - + +
468D LYS* 1.3 73.7 - - - +
470D TYR* 1.3 67.0 + - - +
471D LEU* 4.7 9.0 - - + -
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Residues in contact with TYR 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 5.2 0.9 - - - -
422D ALA* 4.0 21.8 - - + -
423D ARG* 3.4 34.7 + - + +
452D VAL 3.9 0.5 - - - +
453D ALA* 3.4 5.9 - - - -
454D LYS* 2.9 49.7 + - + +
456D SER* 3.6 27.3 - - - -
469D ILE* 1.3 73.8 - - - +
471D LEU* 1.3 58.9 + - - +
472D TYR* 3.5 33.5 - - + +
481D ASP* 4.9 12.6 - - - +
494D GLU* 5.4 2.7 - - - -
497D GLU* 4.9 4.7 - - - +
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Residues in contact with LEU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D VAL* 4.1 17.0 - - + -
312D VAL* 4.1 9.6 - - + -
321D PHE* 4.4 17.3 - - + -
323D ILE* 5.6 0.9 - - + -
421D LEU* 4.0 20.1 - - + +
439D PHE* 4.7 1.6 - - + -
443D THR* 3.9 19.7 - - + -
451D LEU* 3.8 28.3 - - + -
452D VAL 3.6 13.5 - - - +
453D ALA* 4.0 17.5 - - + -
469D ILE* 4.2 8.5 + - + -
470D TYR* 1.3 73.2 - - - +
472D TYR* 1.3 62.2 + - - +
481D ASP* 3.6 7.6 + - - +
482D ILE* 2.9 35.0 + - + +
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Residues in contact with TYR 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D LEU* 3.5 8.8 - - - +
452D VAL* 2.9 51.4 + - + +
453D ALA 5.7 0.2 - - - -
454D LYS* 4.9 10.6 - - + +
470D TYR* 3.5 39.4 - - + +
471D LEU* 1.3 73.5 - - - +
473D ASP* 1.3 60.4 + - - +
474D THR* 4.0 3.8 + - - -
479D LYS* 5.0 15.0 - - + -
480D LEU 3.2 11.2 - - - +
481D ASP* 3.9 37.0 + - + -
482D ILE* 6.1 0.4 - - - -
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Residues in contact with ASP 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D LEU 3.8 10.3 - - - +
444D HIS* 2.9 31.2 + - - -
450D PRO 4.6 4.2 - - - +
451D LEU* 3.9 20.3 - - + +
472D TYR* 1.3 71.9 - - - +
474D THR* 1.3 54.1 + - - +
475D SER* 3.2 24.9 + - - -
478D LYS 2.9 24.1 - - - +
480D LEU* 3.0 29.1 + - + +
482D ILE* 6.1 1.5 - - + +
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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