Contacts of the strand formed by residues 567 - 573 (chain C) in PDB entry 4OQB
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 ASN 567 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP* 3.0 15.3 + - - +
559C LEU 3.5 4.4 - - - +
560C VAL* 4.1 12.1 - - + +
565C GLY 4.0 3.1 - - - +
566C THR* 1.3 74.8 - - - +
568C SER* 1.3 59.9 + - - +
591C ARG* 3.2 20.4 - - - +
592C VAL* 3.1 45.8 + - - +
737C TYR* 4.6 10.7 - - - +
741C PRO* 5.7 0.3 - - - +
742C HIS 3.5 16.2 + - - +
744C PHE* 4.0 19.6 - - - +
745C GLY 5.8 0.6 + - - -
749C PRO* 4.2 16.6 - - + -
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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
----------------------------------------------------------
45A ASP* 2.7 27.6 + - - +
558C GLY* 3.5 4.2 - - - -
559C LEU* 2.8 34.0 + - - +
566C THR* 3.0 15.6 + - - -
567C ASN* 1.3 74.5 + - - +
569C TYR* 1.3 65.2 + - - +
590C GLY 3.3 14.1 - - - -
592C VAL* 4.3 6.1 - - - +
638C PHE* 4.6 14.4 - - - -
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Residues in contact with TYR 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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536C ASP* 5.8 0.2 + - - -
556C THR* 5.5 5.4 - - + -
557C LEU 3.5 11.0 - - - +
558C GLY* 4.5 0.4 - - - -
568C SER* 1.3 77.2 - - - +
570C TYR* 1.3 68.4 + - - +
571C LYS* 4.4 7.2 - - + +
588C SER* 3.8 14.2 + - - -
589C TRP* 3.2 36.0 + - - +
590C GLY* 2.9 51.1 + - - +
591C ARG 3.7 10.5 - - - -
592C VAL* 3.4 22.0 - - + -
593C GLY 5.1 1.3 - - - -
594C THR 5.1 4.6 + - - -
596C ILE 4.3 5.0 + - - -
597C GLY* 4.7 1.7 - - - -
598C SER 5.0 0.3 + - - -
638C PHE* 4.1 6.3 - - - -
695C LYS* 4.6 18.8 - - - +
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Residues in contact with TYR 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C THR* 4.6 0.9 - - - -
557C LEU* 2.8 50.8 + - + +
569C TYR* 1.3 78.1 - - - +
571C LYS* 1.3 60.0 + - - +
572C LEU* 3.8 25.2 + - + +
587C ARG* 3.2 33.2 - - + +
588C SER 3.3 17.7 - - - -
589C TRP* 3.6 26.5 - + + -
617C LEU* 4.2 6.3 - - - +
621C LYS* 3.8 42.0 - - + -
638C PHE* 3.7 23.6 - + + -
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Residues in contact with LYS 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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534C ASP* 3.4 44.9 + - + +
554C SER* 5.5 1.8 - - - +
555C ALA 3.5 4.9 - - - +
556C THR* 3.6 32.7 - - + +
569C TYR* 4.4 6.0 - - + -
570C TYR* 1.3 73.6 - - - +
572C LEU* 1.3 65.0 + - - +
573C GLN* 3.9 18.5 + - + +
586C PHE* 3.8 3.6 - - + +
587C ARG* 3.7 2.1 - - - -
588C SER* 2.8 46.9 + - - +
643C ILE* 5.9 0.4 - - + -
695C LYS* 5.4 14.4 - - - +
698C LEU* 5.9 4.2 - - - +
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Residues in contact with LEU 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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554C SER* 3.4 0.9 + - - -
555C ALA* 2.8 38.8 + - + +
557C LEU* 5.9 3.1 - - + -
570C TYR* 3.8 16.5 + - + +
571C LYS* 1.3 75.5 - - - +
573C GLN* 1.3 68.7 - - - +
585C ILE* 4.3 16.4 - - + -
586C PHE 3.5 6.7 - - - +
587C ARG* 3.6 29.2 - - + -
614C PHE* 3.6 43.5 - - + +
617C LEU* 4.4 9.9 - - + -
618C TYR* 4.0 24.9 - - + +
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Residues in contact with GLN 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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532C ALA 3.8 9.0 + - - +
533C VAL* 3.7 6.3 - - - +
534C ASP* 3.4 39.2 + - - +
545C VAL* 4.5 6.0 - - + +
553C PHE 3.9 5.4 - - - -
554C SER* 3.5 21.5 + - - +
571C LYS* 3.9 19.2 + - + +
572C LEU* 1.3 80.7 - - - +
574C LEU* 1.3 61.6 + - - +
575C LEU* 3.4 27.4 - - + +
585C ILE* 3.3 11.8 - - - +
586C PHE* 3.0 43.2 + - + +
614C PHE* 4.1 4.2 - - - -
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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