Contacts of the strand formed by residues 573 - 581 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542F LEU* 3.6 5.2 - - - -
568F PHE 3.6 0.2 - - - +
569F ASN* 3.6 0.9 - - - -
570F PHE* 2.7 43.5 + - + +
571F GLN 4.8 3.4 - - - +
572F GLY* 1.3 84.4 - - - +
574F ALA* 1.3 67.5 + - - +
575F LYS* 3.6 12.4 + - - +
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Residues in contact with ALA 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538F ALA* 3.7 36.3 - - + +
541F VAL* 4.4 4.5 - - + -
542F LEU* 3.6 20.0 - - + +
567F THR* 4.9 0.2 - - + -
568F PHE 3.6 5.6 - - - -
573F LYS* 1.3 75.4 - - - +
575F LYS* 1.3 64.6 + - - +
576F HIS* 4.2 14.6 - - + +
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Residues in contact with LYS 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566F LEU 3.6 0.7 - - - +
567F THR* 3.2 5.4 - - - +
568F PHE* 2.8 60.4 + - + -
570F PHE* 3.5 44.4 - - + -
573F LYS* 4.2 11.1 - - + +
574F ALA* 1.3 76.7 - - - +
576F HIS* 1.3 65.8 + - - +
577F LEU 4.2 0.4 - - - -
611F LEU* 4.8 2.7 - - + -
613F SER* 3.1 31.2 + - - -
814L GLU* 2.9 28.4 + - + +
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Residues in contact with HIS 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ARG* 3.2 53.4 + - + +
538F ALA* 4.3 8.5 - - + +
555F ARG* 3.1 15.9 + - - +
565F VAL* 3.9 10.8 - - + -
566F LEU 3.6 2.7 - - - -
567F THR* 3.0 39.8 + - + -
574F ALA* 4.2 18.5 + - + +
575F LYS* 1.3 78.5 + - - +
577F LEU* 1.3 59.7 + - - +
578F ARG 4.1 0.2 - - - -
812L ASP 4.2 3.1 + - - +
813L PTR 3.4 18.6 - - + +
814L GLU* 2.8 34.0 + - - +
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Residues in contact with LEU 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F VAL* 3.9 2.4 - - - +
566F LEU* 2.7 65.9 + - + +
568F PHE* 4.1 9.6 - - + -
576F HIS* 1.3 71.0 - - - +
578F ARG* 1.3 69.1 + - - +
579F LEU* 3.6 3.4 + - + +
589F VAL* 3.5 32.5 - - + -
590F GLN* 4.3 9.6 - - - +
604F PHE* 4.5 8.3 - - + -
609F ILE* 4.0 26.2 - - + -
814L GLU* 4.1 26.2 - - + +
816L LEU* 4.4 9.4 - - + -
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Residues in contact with ARG 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560F ARG* 3.6 21.1 - - - +
563F GLU* 2.8 46.3 + - - +
564F CYS 3.7 5.8 - - - +
565F VAL* 4.6 2.9 - - + +
576F HIS 4.0 1.0 + - - -
577F LEU* 1.3 77.7 - - + +
579F LEU* 1.3 65.8 + - - +
588F ARG 4.6 0.2 - - - +
589F VAL* 3.7 18.4 - - - +
590F GLN* 5.3 0.7 + - - +
810L THR* 3.3 27.6 + - - +
813L PTR 3.3 46.6 - - + +
814L GLU 5.3 1.0 + - - -
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Residues in contact with LEU 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F VAL* 4.2 12.8 - - + -
563F GLU* 3.2 10.5 - - - +
564F CYS* 2.7 52.5 + - + +
565F VAL 4.1 5.4 - - - -
566F LEU* 4.0 22.9 - - + +
577F LEU* 3.7 13.5 - - + +
578F ARG* 1.3 81.4 - - - +
580F SER* 1.3 60.1 + - - +
581F LEU* 4.8 2.6 - - + +
587F CYS* 4.1 9.6 - - - -
588F ARG 3.9 2.9 - - - -
589F VAL* 3.7 18.6 - - + -
597F ILE* 4.7 6.7 - - + -
600F MET* 3.4 37.5 - - + -
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Residues in contact with SER 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562F GLY 3.9 4.9 + - - -
563F GLU* 4.0 12.6 + - - +
579F LEU* 1.3 73.4 - - - +
581F LEU* 1.3 65.9 + - - +
586F GLN 3.4 1.0 - - - +
587F CYS* 3.3 5.0 - - - -
588F ARG* 2.7 81.9 + - - +
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Residues in contact with LEU 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F LEU* 4.1 9.6 - - + -
562F GLY* 2.8 31.0 + - - +
563F GLU 5.5 0.2 - - - -
564F CYS* 3.8 29.2 - - + -
579F LEU* 4.8 3.8 - - + +
580F SER* 1.3 86.9 + - - +
582F ASN* 1.3 67.5 + - - +
585F GLY* 4.2 10.8 - - - +
586F GLN 3.5 4.5 - - - +
587F CYS* 3.8 17.0 - - + -
597F ILE* 3.6 35.7 - - + -
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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