Contacts of the strand formed by residues 573 - 581 (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 LYS 573 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542C LEU* 3.9 4.0 - - - -
568C PHE 3.5 1.2 - - - +
569C ASN* 3.5 0.9 - - - -
570C PHE* 2.7 48.6 + - + +
571C GLN* 3.8 11.7 - - - +
572C GLY* 1.3 84.6 - - - +
574C ALA* 1.3 62.4 + - - +
575C LYS* 3.6 23.2 + - - +
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Residues in contact with ALA 574 (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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538C ALA* 3.6 36.6 - - + +
541C VAL* 4.3 5.4 - - + -
542C LEU* 3.7 18.4 - - + +
567C THR* 5.1 0.2 - - + -
568C PHE 3.7 4.9 - - - -
573C LYS* 1.3 73.2 - - - +
575C LYS* 1.3 67.0 + - - +
576C HIS* 4.3 12.2 + - + +
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Residues in contact with LYS 575 (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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566C LEU 3.7 0.2 - - - +
567C THR* 3.2 5.4 - - - +
568C PHE* 2.8 57.1 + - + +
570C PHE* 3.7 37.9 - - + -
573C LYS* 4.0 28.3 - - - +
574C ALA* 1.3 78.7 + - - +
576C HIS* 1.3 67.2 + - - +
611C LEU* 4.8 7.9 - - + -
613C SER* 5.3 2.2 + - - -
614C GLY* 4.8 12.5 - - - +
814I GLU* 3.0 37.4 + - + +
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Residues in contact with HIS 576 (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 ARG* 3.4 54.2 + - + +
538C ALA* 4.3 7.0 - - + +
555C ARG* 2.7 25.8 + - - +
565C VAL* 3.7 12.6 - - + -
566C LEU 3.5 3.8 - - - -
567C THR* 2.9 27.8 + - + +
568C PHE* 4.9 0.2 - - - -
574C ALA* 4.3 15.4 + - - +
575C LYS* 1.3 80.8 - - - +
577C LEU* 1.3 59.9 - - - +
812I ASP 4.1 3.5 + - - +
813I PTR 3.4 17.7 - - + -
814I GLU* 2.9 32.5 + - - +
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Residues in contact with LEU 577 (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 VAL* 3.8 2.4 - - - +
566C LEU* 2.7 65.7 + - + +
568C PHE* 4.1 10.3 - - + -
576C HIS* 1.3 72.5 - - - +
578C ARG* 1.3 70.3 + - - +
579C LEU* 3.6 5.9 + - + +
589C VAL* 3.7 34.3 - - + -
590C GLN* 4.0 8.7 - - - +
604C PHE* 4.3 15.0 - - + -
609C ILE* 4.3 13.9 - - + -
814I GLU* 3.8 27.1 - - + +
816I LEU* 4.5 9.4 - - + -
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Residues in contact with ARG 578 (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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560C ARG* 4.3 13.9 - - - +
563C GLU* 2.5 39.5 + - + +
564C CYS 3.7 4.3 - - - -
565C VAL* 4.5 2.0 - - + +
576C HIS 4.1 0.6 + - - -
577C LEU* 1.3 86.5 - - + +
579C LEU* 1.3 66.6 + - - +
580C SER* 4.2 4.2 - - - -
588C ARG* 4.3 6.2 - - - +
589C VAL* 4.0 9.2 - - - +
590C GLN* 5.4 1.8 + - - +
813I PTR 3.3 52.5 - - + +
814I GLU 5.3 0.4 + - - -
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Residues in contact with LEU 579 (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 VAL* 4.3 12.6 - - + -
562C GLY 3.7 0.3 - - - +
563C GLU* 3.3 7.1 - - - +
564C CYS* 2.6 61.6 + - + +
565C VAL 4.2 2.0 - - - -
566C LEU* 4.0 21.5 - - + +
577C LEU* 3.7 16.2 - - + +
578C ARG* 1.3 84.8 - - - +
580C SER* 1.3 60.3 + - - +
581C LEU* 3.9 3.7 + - + +
587C CYS* 4.0 10.5 - - - -
588C ARG 3.9 2.9 - - - -
589C VAL* 3.9 16.4 - - + -
597C ILE* 4.4 7.6 - - + -
600C MET* 3.7 35.4 - - + -
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Residues in contact with SER 580 (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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562C GLY 3.6 5.2 + - - -
563C GLU* 4.8 1.8 - - - +
578C ARG* 4.2 4.2 - - - -
579C LEU* 1.3 71.8 - - - +
581C LEU* 1.3 66.4 + - - +
586C GLN 3.6 0.9 - - - +
587C CYS* 3.5 0.7 - - - -
588C ARG* 2.7 76.7 + - - +
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Residues in contact with LEU 581 (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* 4.4 8.5 - - + -
562C GLY* 2.7 35.0 + - - +
564C CYS* 4.1 17.7 - - + -
579C LEU* 4.7 5.4 - - + +
580C SER* 1.3 78.2 + - - +
582C ASN* 1.3 65.5 + - - +
585C GLY* 4.1 8.7 - - - +
586C GLN 3.3 6.7 - - - +
587C CYS* 3.4 37.9 - - + -
597C ILE* 3.5 35.0 - - + -
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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