Contacts of the strand formed by residues 573 - 581 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542D LEU* 3.7 6.7 - - - -
569D ASN* 3.4 3.3 - - - -
570D PHE* 2.7 47.1 + - + +
571D GLN 4.8 3.6 - - - +
572D GLY* 1.3 78.2 - - - +
574D ALA* 1.3 64.3 + - - +
575D LYS* 3.6 10.9 + - - -
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Residues in contact with ALA 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D ALA* 3.6 36.3 - - + +
541D VAL* 4.4 4.3 - - + -
542D LEU* 3.8 19.2 - - + +
568D PHE 3.6 5.6 - - - -
573D LYS* 1.3 74.4 - - - +
575D LYS* 1.3 63.6 + - - +
576D HIS* 4.2 13.9 - - + +
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Residues in contact with LYS 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D LEU 3.8 0.2 - - - +
567D THR* 3.4 4.7 - - - +
568D PHE* 2.8 57.8 + - + +
570D PHE* 3.5 45.7 - - + -
573D LYS* 4.2 9.6 - - - +
574D ALA* 1.3 77.2 - - - +
576D HIS* 1.3 67.7 + - - +
611D LEU* 4.6 3.4 - - + -
613D SER* 2.9 30.5 + - - -
814J GLU* 3.1 33.6 + - + +
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Residues in contact with HIS 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ARG* 3.3 69.1 + - + +
538D ALA* 4.3 8.7 - - + +
555D ARG* 3.1 14.0 + - - -
565D VAL* 3.9 11.0 - - + -
566D LEU 3.7 4.0 - - - -
567D THR* 3.2 32.1 + - + +
574D ALA* 4.2 17.6 + - + +
575D LYS* 1.3 77.2 - - - +
577D LEU* 1.3 56.0 + - - +
812J ASP 4.2 3.2 + - - +
813J PTR 3.4 9.7 - - + -
814J GLU* 2.7 38.2 + - - +
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Residues in contact with LEU 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D VAL* 4.0 3.1 - - - +
566D LEU* 2.8 64.8 + - + +
568D PHE* 4.2 11.0 - - + -
575D LYS 4.3 0.2 - - - -
576D HIS* 1.3 73.2 - - - +
578D ARG* 1.3 69.9 + - - +
579D LEU* 3.7 4.5 - - + +
589D VAL* 3.8 33.4 - - + -
590D GLN* 4.0 8.1 - - - +
604D PHE* 4.2 14.8 - - + -
609D ILE* 4.3 13.9 - - + -
814J GLU* 3.7 28.3 - - + +
816J LEU* 4.3 10.3 - - + -
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Residues in contact with ARG 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D ARG* 2.9 32.3 - - - +
563D GLU* 2.5 36.2 + - + +
564D CYS 3.8 6.1 - - - +
565D VAL* 4.5 1.8 - - - +
576D HIS 4.1 0.2 - - - -
577D LEU* 1.3 85.7 - - + +
579D LEU* 1.3 66.7 + - - +
580D SER 4.2 0.6 + - - +
589D VAL* 4.0 12.1 - - - +
590D GLN* 5.4 5.0 + - - +
813J PTR 2.9 65.5 - - + +
814J GLU 5.2 1.3 + - - +
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Residues in contact with LEU 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D VAL* 4.2 12.6 - - + -
563D GLU* 3.4 7.5 - - - +
564D CYS* 2.7 55.5 + - + +
565D VAL 4.0 5.4 - - - -
566D LEU* 3.9 21.1 - - + +
577D LEU* 3.7 15.0 - - + +
578D ARG* 1.3 83.8 - - - +
580D SER* 1.3 61.3 + - - +
581D LEU* 3.8 2.0 + - + +
587D CYS* 4.1 10.1 - - - -
588D ARG 4.0 3.1 - - - -
589D VAL* 4.0 15.0 - - + -
597D ILE* 4.5 10.1 - - + -
600D MET* 3.6 36.6 - - + -
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Residues in contact with SER 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D GLY 3.6 5.6 + - - -
563D GLU* 4.9 1.3 - - - +
578D ARG 4.1 0.6 - - - -
579D LEU* 1.3 72.9 - - - +
581D LEU* 1.3 67.0 + - - +
586D GLN 3.6 0.7 - - - +
587D CYS* 3.4 2.8 - - - -
588D ARG* 2.7 76.1 + - - +
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Residues in contact with LEU 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D LEU* 4.7 7.2 - - + -
562D GLY* 2.7 36.2 + - - +
564D CYS* 3.9 20.0 - - + -
579D LEU* 4.6 6.1 - - + +
580D SER* 1.3 81.6 + - - +
582D ASN* 1.3 67.2 + - - +
585D GLY* 4.2 9.6 - - - +
586D GLN 3.3 16.6 - - - +
587D CYS* 3.7 13.5 - - + -
597D ILE* 3.5 41.5 - - + -
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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