Contacts of the strand formed by residues 566 - 573 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564C ALA 4.0 1.9 + - - +
565C TRP* 1.3 76.5 - - - +
567C ILE* 1.3 62.0 + - - +
592C ASP 4.1 0.3 - - - +
593C VAL* 3.4 2.6 - - - +
594C GLU* 2.5 57.0 + - + +
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Residues in contact with ILE 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C TRP* 4.2 0.6 + - + -
566C LYS* 1.3 82.4 - - - +
568C SER* 1.3 72.8 + - - +
569C ILE* 4.3 1.6 - - + -
591C ILE* 4.2 11.0 - - + -
592C ASP 3.4 7.2 - - - +
593C VAL* 3.6 22.4 - - + -
661C GLN* 4.0 15.0 - - + +
664C LEU* 3.5 42.0 - - + -
665C GLN* 3.0 36.9 + - + +
668C LEU* 3.6 24.1 - - + +
683C LEU* 4.2 12.8 - - + -
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Residues in contact with SER 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C ILE* 1.3 77.5 - - - +
569C ILE* 1.3 62.6 + - - +
570C PRO* 3.2 12.9 - - - +
591C ILE* 3.6 4.5 - - - +
592C ASP* 2.7 45.3 + - - +
661C GLN* 3.5 17.0 - - - -
665C GLN* 5.1 0.7 - - - -
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Residues in contact with ILE 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C ILE* 4.3 5.2 - - + -
568C SER* 1.3 76.8 - - - +
570C PRO* 1.3 65.9 - - - +
571C TYR 3.2 5.6 - - - +
589C PHE* 3.9 28.3 - - + -
590C CYS 3.7 14.1 - - - +
591C ILE* 4.5 5.6 - - + +
620C PHE* 4.2 16.2 - - + -
657C ARG* 3.0 37.0 + - + +
660C PHE* 3.7 19.1 - - + +
661C GLN* 3.0 45.4 + - + +
664C LEU* 4.3 7.0 - - + -
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Residues in contact with PRO 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C SER* 3.2 23.3 - - - +
569C ILE* 1.3 84.9 - - - +
571C TYR* 1.3 81.5 + - + +
590C CYS 3.3 11.7 - - - +
592C ASP* 3.4 26.7 - - - +
654C LYS* 5.5 0.2 + - - -
657C ARG* 3.5 18.4 + - - +
661C GLN* 5.3 0.4 - - - +
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Residues in contact with TYR 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C ILE* 3.2 5.6 + - - +
570C PRO* 1.3 100.0 - - + +
572C VAL* 1.3 77.7 + - - +
573C ASP* 3.2 27.5 + - + -
590C CYS* 3.2 53.0 + - + +
592C ASP* 5.0 2.7 - - - -
614C TYR* 4.1 6.4 + - - -
654C LYS* 4.8 6.3 - - - +
657C ARG* 3.7 9.2 - - - +
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Residues in contact with VAL 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C TYR* 1.3 85.0 - - - +
573C ASP* 1.3 66.1 + - - +
587C PRO* 5.0 1.3 - - + -
588C VAL 3.6 14.1 - - - +
589C PHE* 4.5 6.1 - - + -
590C CYS 4.4 0.4 - - - +
650C TYR* 3.6 40.4 + - + -
653C LEU* 4.0 26.5 - - + +
654C LYS* 3.4 45.7 + - + +
657C ARG* 4.3 8.5 - - + -
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Residues in contact with ASP 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C TYR* 3.2 31.0 + - + -
572C VAL* 1.3 78.5 - - - +
574C PHE* 1.3 94.9 + - - +
587C PRO* 3.6 5.9 - - - +
588C VAL* 3.0 39.7 + - + +
590C CYS* 4.3 5.6 - - + -
614C TYR* 4.1 11.5 + - + -
650C TYR* 5.3 0.2 - - - -
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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