Contacts of the strand formed by residues 566 - 574 (chain D) in PDB entry 4PQP
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 LYS 566 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636B ASP* 5.4 6.3 + - - -
669B GLN* 5.7 7.9 - - - +
670B HIS* 5.5 7.3 + - - -
564D ALA 4.0 2.1 + - - +
565D TRP* 1.3 75.3 - - - +
567D ILE* 1.3 62.4 + - - +
593D VAL* 3.3 3.5 - - - -
594D GLU* 2.4 61.1 + - + +
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Residues in contact with ILE 567 (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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565D TRP* 4.7 0.7 - - + -
566D LYS* 1.3 83.7 - - - +
568D SER* 1.3 74.2 + - - +
569D ILE* 4.3 3.1 - - + -
591D ILE* 4.2 5.6 - - + -
592D ASP 3.2 8.7 - - - +
593D VAL* 4.0 20.0 - - + -
661D GLN* 4.0 15.0 - - + +
664D LEU* 3.5 42.6 - - + -
665D GLN* 3.0 36.6 + - + +
668D LEU* 3.6 24.8 - - + +
683D LEU* 4.2 13.0 - - + -
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Residues in contact with SER 568 (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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567D ILE* 1.3 78.3 - - - +
569D ILE* 1.3 64.2 + - - +
570D PRO* 3.2 13.3 - - - +
591D ILE* 3.3 4.9 - - - +
592D ASP* 2.8 42.4 + - - +
661D GLN* 3.4 16.6 - - - -
665D GLN* 5.1 0.9 - - - -
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Residues in contact with ILE 569 (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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567D ILE* 4.3 5.2 - - + -
568D SER* 1.3 76.9 - - - +
570D PRO* 1.3 66.1 - - - +
571D TYR 3.3 4.5 - - - +
589D PHE* 3.8 25.1 - - + -
590D CYS 3.6 12.8 - - - +
591D ILE* 4.5 6.5 - - + +
620D PHE* 4.2 15.7 - - + -
657D ARG* 2.9 42.7 + - + +
660D PHE* 3.7 18.4 - - + +
661D GLN* 3.0 47.3 + - + +
664D LEU* 4.3 6.5 - - + -
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Residues in contact with PRO 570 (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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638C GLN* 5.6 0.3 + - - -
568D SER* 3.2 17.9 - - - +
569D ILE* 1.3 85.0 - - - +
571D TYR* 1.3 82.1 + - + +
590D CYS 3.1 13.0 - - - +
592D ASP* 3.0 32.3 - - - +
654D LYS* 5.5 0.3 + - - -
657D ARG* 3.5 17.6 + - - +
661D GLN* 5.4 0.4 - - - +
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633C ALA* 4.0 22.2 + - + -
635C PRO* 4.6 23.7 - - + +
638C GLN* 4.4 19.1 - - - +
569D ILE* 3.3 6.7 - - - +
570D PRO* 1.3 100.4 - - + +
572D VAL* 1.3 77.7 + - - +
573D ASP* 3.2 32.3 + - + -
589D PHE* 4.0 0.2 - - - -
590D CYS* 3.2 48.6 + - + +
592D ASP* 5.4 0.7 - - - -
614D TYR* 4.1 5.7 + - - -
654D LYS* 4.8 6.1 - - - +
657D ARG* 3.7 9.0 - - - +
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Residues in contact with VAL 572 (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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633C ALA* 4.0 7.3 - - - +
571D TYR* 1.3 85.3 - - - +
573D ASP* 1.3 66.7 + - - +
587D PRO* 4.5 5.6 - - + -
588D VAL 3.2 12.8 - - - +
589D PHE* 4.5 5.6 - - + -
650D TYR* 3.6 39.0 + - + -
653D LEU* 4.0 24.5 - - + +
654D LYS* 3.4 45.7 + - + +
657D ARG* 4.3 8.1 - - + -
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Residues in contact with ASP 573 (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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632C GLY* 3.6 20.1 - - - -
633C ALA* 3.8 12.1 + - - +
571D TYR* 3.2 32.5 + - + -
572D VAL* 1.3 76.5 - - - +
574D PHE* 1.3 89.0 + - - +
587D PRO* 3.0 8.3 - - - +
588D VAL* 2.5 45.1 + - + +
590D CYS* 4.7 1.6 - - + -
614D TYR* 3.9 19.1 + - + -
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Residues in contact with PHE 574 (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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625C SER 5.4 0.9 - - - -
628C THR* 3.7 27.1 - - - +
629C GLU* 4.0 25.8 - - + -
632C GLY* 5.2 2.1 - - - -
573D ASP* 1.3 100.4 + - - +
575D PHE* 1.3 59.7 + - - +
576D GLU* 3.3 30.8 - - + +
586D ILE 3.2 24.7 - - - -
587D PRO* 3.5 24.5 - - + -
588D VAL* 4.2 4.0 - - - -
614D TYR* 5.9 1.0 - - - -
650D TYR* 3.7 44.9 - + + -
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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