Contacts of the strand formed by residues 573 - 581 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A LEU* 3.6 5.8 - - - -
569A ASN* 3.6 1.9 - - - -
570A PHE* 2.8 44.9 + - + +
571A GLN* 3.5 31.5 + - + +
572A GLY* 1.3 81.4 - - - +
574A ALA* 1.3 65.3 + - - +
575A LYS* 3.7 10.3 + - - +
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Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ALA* 3.7 34.5 - - + -
541A VAL* 4.2 9.0 - - + -
542A LEU* 3.7 14.9 - - + +
567A THR* 4.9 0.2 - - + -
568A PHE 3.5 6.1 - - - -
573A LYS* 1.3 76.1 - - - +
575A LYS* 1.3 64.5 + - - +
576A HIS* 4.1 16.4 + - + +
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Residues in contact with LYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A LEU 3.7 0.2 - - - +
567A THR* 3.2 5.7 - - - +
568A PHE* 2.8 59.8 + - + +
570A PHE* 3.5 46.4 - - + -
573A LYS* 4.2 10.3 - - + +
574A ALA* 1.3 79.0 - - - +
576A HIS* 1.3 66.9 + - - +
611A LEU* 4.8 4.7 - - + -
613A SER* 3.0 31.6 + - - -
814G GLU* 2.9 26.0 + - + +
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Residues in contact with HIS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A ARG* 3.2 55.4 + - + +
538A ALA* 4.4 6.9 - - + +
555A ARG* 2.9 22.0 + - - +
565A VAL* 3.9 5.2 - - + -
566A LEU 3.6 3.1 - - - -
567A THR* 2.9 30.3 + - + -
568A PHE* 4.9 0.2 - - - -
574A ALA* 4.1 17.4 + - + +
575A LYS* 1.3 79.0 + - - +
577A LEU* 1.3 56.1 + - - +
578A ARG 4.1 0.4 - - - -
812G ASP 4.2 3.1 + - - +
813G PTR 3.4 24.1 - - + +
814G GLU* 2.8 37.7 + - - +
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A VAL* 3.3 4.6 - - - +
566A LEU* 2.7 63.7 + - + +
568A PHE* 4.3 9.2 - - + -
575A LYS 4.3 0.2 - - - -
576A HIS* 1.3 70.8 - - - +
578A ARG* 1.3 69.3 + - - +
579A LEU* 3.6 7.3 - - + +
589A VAL* 3.5 35.4 - - + -
590A GLN* 3.9 19.5 - - - +
604A PHE* 4.5 7.6 - - + -
609A ILE* 4.3 20.6 - - + -
611A LEU* 5.3 0.2 - - + -
814G GLU* 4.0 17.0 - - + +
816G LEU* 4.4 10.1 - - + -
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Residues in contact with ARG 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A ARG* 3.8 17.9 - - - +
563A GLU* 2.9 43.4 + - - +
564A CYS 3.6 5.6 - - - -
565A VAL* 4.5 3.6 - - + +
576A HIS 4.1 0.8 + - - -
577A LEU* 1.3 86.6 - - + +
579A LEU* 1.3 64.5 + - - +
588A ARG 4.4 0.2 - - - +
589A VAL* 3.9 10.4 - - - +
590A GLN* 5.2 3.8 + - - +
810G THR* 3.1 30.9 + - - +
813G PTR 3.5 46.5 - - + +
814G GLU 5.4 0.4 + - - -
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Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A VAL* 4.2 11.2 - - + -
563A GLU* 3.2 10.4 - - - +
564A CYS* 2.8 52.3 + - + +
565A VAL 4.0 5.8 - - - -
566A LEU* 3.9 22.9 - - + +
577A LEU* 3.6 14.8 - - + +
578A ARG* 1.3 83.9 - - - +
580A SER* 1.3 61.0 + - - +
581A LEU* 4.0 3.1 + - + -
587A CYS* 4.2 10.5 - - - -
588A ARG 3.8 3.1 - - - -
589A VAL* 3.8 20.0 - - + -
597A ILE* 4.3 6.7 - - + -
600A MET* 3.6 36.3 - - + -
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Residues in contact with SER 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A GLY 3.7 7.2 + - - -
563A GLU* 4.2 10.1 - - - +
579A LEU* 1.3 73.7 - - - +
581A LEU* 1.3 63.9 + - - +
582A ASN 4.2 0.2 + - - -
586A GLN 3.4 1.2 - - - +
587A CYS* 3.3 5.0 - - - -
588A ARG* 2.8 72.1 + - - +
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Residues in contact with LEU 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A LEU* 4.0 28.0 - - + -
562A GLY* 2.9 29.1 + - - +
564A CYS* 4.1 24.5 - - + -
579A LEU* 5.0 2.2 - - + +
580A SER* 1.3 77.3 + - - +
582A ASN* 1.3 65.4 + - - +
585A GLY* 4.5 8.5 - - - +
586A GLN 3.2 6.3 - - - +
587A CYS* 3.5 37.7 - - + -
597A ILE* 4.3 16.8 - - + -
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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