Contacts of the strand formed by residues 573 - 581 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542E LEU* 3.8 3.8 - - - -
568E PHE 3.6 0.5 - - - +
569E ASN* 3.6 1.2 + - - -
570E PHE* 2.7 46.4 + - + +
571E GLN 4.9 3.1 - - - +
572E GLY* 1.3 79.1 - - - +
574E ALA* 1.3 64.5 + - - +
575E LYS* 3.5 25.1 + - - +
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Residues in contact with ALA 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E ALA* 3.8 34.3 - - + +
541E VAL* 4.2 5.2 - - + -
542E LEU* 3.5 25.0 - - + +
568E PHE 3.6 5.6 - - - -
573E LYS* 1.3 73.3 - - - +
575E LYS* 1.3 65.2 + - - +
576E HIS* 4.2 12.7 + - + +
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Residues in contact with LYS 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567E THR* 3.3 6.9 - - - +
568E PHE* 2.8 58.6 + - + +
570E PHE* 3.5 46.6 - - + -
573E LYS* 3.8 25.0 - - - +
574E ALA* 1.3 76.9 - - - +
576E HIS* 1.3 70.7 + - - +
577E LEU 4.3 0.2 - - - -
611E LEU* 5.0 3.1 - - + -
613E SER* 4.0 18.7 + - - -
614E GLY* 5.5 1.5 - - - +
814K GLU* 3.6 24.8 + - + +
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Residues in contact with HIS 576 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534E ARG* 3.4 55.1 + - + +
538E ALA* 4.2 7.8 - - + +
555E ARG* 2.9 15.1 + - - -
565E VAL* 4.0 5.8 - - + -
566E LEU 3.8 2.5 - - - -
567E THR* 2.8 36.8 + - + -
574E ALA* 4.2 16.0 - - + +
575E LYS* 1.3 81.2 + - - +
577E LEU* 1.3 57.8 + - - +
578E ARG 4.1 0.2 - - - -
812K ASP 4.0 4.0 + - - +
813K PTR 3.3 23.0 - - + -
814K GLU* 2.7 38.3 + - - +
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Residues in contact with LEU 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565E VAL* 3.4 4.4 - - - +
566E LEU* 2.8 64.9 + - + +
568E PHE* 4.4 9.4 - - + -
576E HIS* 1.3 71.9 - - - +
578E ARG* 1.3 66.9 + - + +
579E LEU* 3.6 6.1 + - + +
589E VAL* 3.6 32.8 - - + -
590E GLN* 4.1 9.2 - - - +
604E PHE* 4.3 15.5 - - + -
609E ILE* 4.3 15.5 - - + -
814K GLU* 3.8 26.7 - - + +
816K LEU* 4.3 11.9 - - + -
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Residues in contact with ARG 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E ARG* 3.8 22.6 - - - +
563E GLU* 2.8 45.3 + - - +
564E CYS 3.8 4.7 - - - +
565E VAL* 4.6 4.7 - - + +
576E HIS 4.1 0.6 + - - -
577E LEU* 1.3 77.8 - - - +
579E LEU* 1.3 65.2 + - - +
588E ARG 4.4 0.2 - - - +
589E VAL* 3.7 19.8 - - - +
590E GLN* 5.2 0.6 + - - +
813K PTR 3.4 51.0 - - + +
814K GLU 5.3 0.8 + - - -
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Residues in contact with LEU 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554E VAL* 4.3 5.6 - - + -
563E GLU* 3.1 10.9 - - - +
564E CYS* 2.9 47.3 + - + +
566E LEU* 3.9 22.0 - - + +
577E LEU* 3.7 16.2 - - + +
578E ARG* 1.3 82.4 - - - +
580E SER* 1.3 60.5 + - - +
581E LEU* 3.9 3.3 + - + +
587E CYS* 4.2 9.2 - - - -
588E ARG 3.9 2.9 - - - -
589E VAL* 3.9 16.8 - - + -
597E ILE* 3.7 22.7 - - + -
600E MET* 3.4 36.3 - - + -
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Residues in contact with SER 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562E GLY 3.7 6.7 + - - -
563E GLU* 4.7 12.6 + - - +
578E ARG 4.3 0.2 - - - -
579E LEU* 1.3 74.0 - - - +
581E LEU* 1.3 62.6 + - - +
586E GLN 3.4 1.2 - - - +
587E CYS* 3.2 5.4 - - - -
588E ARG* 2.8 78.6 + - - +
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Residues in contact with LEU 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522E LEU* 4.1 18.8 - - + -
562E GLY* 2.9 31.6 + - - +
563E GLU 5.7 0.2 - - - -
564E CYS* 3.7 31.9 - - + -
579E LEU* 4.8 4.3 - - + +
580E SER* 1.3 76.8 + - - +
582E ASN* 1.3 63.8 + - - +
585E GLY* 4.3 9.9 - - - +
586E GLN 3.3 4.7 - - - +
587E CYS* 3.5 40.6 - - + +
597E ILE* 4.3 15.0 - - + -
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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