Contacts of the strand formed by residues 563 - 570 (chain C) in PDB entry 2HDX
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 563 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A TYR* 4.2 4.3 + - - -
557C SER* 3.2 29.9 + - - -
560C ARG* 3.1 57.6 + - + +
561C ARG 3.1 4.1 - - - +
562C GLY* 1.3 80.1 - - - +
564C CYS* 1.3 77.4 + - - +
565C VAL* 4.1 7.8 - - - +
578C ARG* 2.5 48.9 + - + +
579C LEU 3.3 9.0 - - - +
580C SER* 4.8 1.8 - - - +
813I PTR 5.1 0.2 + - - -
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Residues in contact with CYS 564 (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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522C LEU* 4.6 2.5 - - - -
528C PHE* 4.3 16.6 - - - -
554C VAL* 4.3 3.6 - - + -
555C ARG 3.3 13.5 - - - +
556C GLN* 4.3 11.9 - - - -
557C SER 4.4 0.9 - - - +
562C GLY 4.2 0.2 + - - -
563C GLU* 1.3 77.9 - - - +
565C VAL* 1.3 65.1 + - - +
579C LEU* 2.6 54.3 + - + +
581C LEU* 4.1 22.4 - - + +
597C ILE* 4.3 11.0 - - + -
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Residues in contact with VAL 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C LEU 3.7 0.2 - - - +
554C VAL* 3.5 4.9 - - - +
555C ARG* 2.8 77.3 + - + +
557C SER* 5.3 5.2 - - - -
563C GLU* 4.1 14.1 - - + +
564C CYS* 1.3 81.8 - - - +
566C LEU* 1.3 67.2 + - - +
567C THR 3.6 1.6 + - - -
576C HIS* 3.7 20.2 - - + -
577C LEU 3.4 11.2 - - - +
578C ARG* 4.5 3.1 - - - -
579C LEU* 4.2 4.7 - - - -
813I PTR 3.9 22.2 - - + +
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Residues in contact with LEU 566 (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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552C PHE* 3.7 35.0 - - + -
553C LEU 3.7 6.1 - - - +
554C VAL* 4.3 5.4 - - + +
565C VAL* 1.3 71.7 - - - +
567C THR* 1.3 59.1 + - - +
568C PHE* 3.6 20.9 - - + -
576C HIS* 3.5 1.4 - - - -
577C LEU* 2.7 60.0 + - + +
579C LEU* 4.0 13.4 - - + +
600C MET* 4.4 12.6 - - + -
601C LEU* 4.2 14.6 - - + -
604C PHE* 4.7 1.6 - - + -
609C ILE* 4.3 5.6 - - + -
621C LEU* 4.3 19.7 - - + -
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Residues in contact with THR 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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537C ALA* 3.8 14.0 - - - +
538C ALA* 4.3 0.7 - - - +
541C VAL* 3.8 24.9 - - + +
552C PHE* 3.1 4.9 - - - +
553C LEU* 3.0 46.7 + - - -
555C ARG* 2.9 29.6 + - - -
565C VAL 3.6 1.0 + - - -
566C LEU* 1.3 73.7 - - - +
568C PHE* 1.3 62.9 + - - +
575C LYS 3.2 12.8 - - - +
576C HIS* 2.9 23.8 + - + +
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Residues in contact with PHE 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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541C VAL* 4.1 6.9 - - - +
550C GLY* 5.3 1.6 - - - -
551C VAL 3.1 12.3 - - - +
552C PHE* 3.8 10.3 - - + -
566C LEU* 3.6 25.1 - - + -
567C THR* 1.3 76.4 - - - +
569C ASN* 1.3 72.9 + - - +
570C PHE* 4.0 9.4 - - + -
573C LYS 3.5 0.3 - - - +
574C ALA* 3.7 1.9 - - - -
575C LYS* 2.8 64.2 + - + -
577C LEU* 4.1 17.0 - - + -
609C ILE* 3.9 28.3 - - + -
611C LEU* 4.1 22.2 - - + -
619C VAL* 4.3 17.7 - - + -
621C LEU* 4.7 6.3 - - + -
814I GLU* 4.5 1.1 - - + -
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Residues in contact with ASN 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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541C VAL* 2.9 34.4 + - - +
542C LEU* 4.0 8.3 - - - +
545C GLY 3.2 21.6 + - - -
548C SER* 3.2 25.4 - - - +
549C HIS* 3.3 11.1 + - - -
550C GLY* 2.9 27.9 + - - -
551C VAL 2.7 12.2 + - - +
568C PHE* 1.3 77.1 - - - +
570C PHE* 1.3 57.3 + - - +
572C GLY* 3.0 26.9 + - - -
573C LYS 3.5 4.7 - - - -
619C VAL* 4.2 1.6 - - - +
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Residues in contact with PHE 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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549C HIS* 3.8 7.6 - + - -
568C PHE* 3.6 5.3 + + + -
569C ASN* 1.3 72.4 + - - +
571C GLN* 1.3 78.5 + - + +
572C GLY 3.2 0.2 - - - -
573C LYS* 2.7 31.0 + - + +
575C LYS* 3.7 38.6 - - + -
611C LEU* 3.8 13.5 - - + -
614C GLY* 3.9 33.4 - - - -
615C GLY 4.5 0.7 - - - -
617C SER* 3.5 37.9 - - - -
619C VAL* 3.5 37.9 - - + -
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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