Contacts of the strand formed by residues 563 - 570 (chain B) 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 GLU 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557B SER* 3.2 24.8 + - - -
560B ARG* 3.3 31.0 + - + +
561B ARG 3.1 7.3 - - - +
562B GLY* 1.3 82.1 - - - +
564B CYS* 1.3 68.3 + - - +
565B VAL* 6.1 0.3 - - - +
578B ARG* 2.8 52.0 + - - +
579B LEU 3.1 15.5 - - - +
580B SER* 3.9 15.7 + - - +
581B LEU* 5.9 0.4 - - - -
624E TYR* 4.0 6.1 + - - -
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Residues in contact with CYS 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B LEU* 4.7 5.2 - - - -
528B PHE* 4.6 6.7 - - - -
554B VAL* 4.1 17.3 - - + -
555B ARG 3.2 15.7 - - - +
556B GLN* 4.1 19.3 - - - -
557B SER 4.1 2.0 - - - +
563B GLU* 1.3 80.7 - - - +
565B VAL* 1.3 71.8 + - - +
578B ARG* 3.7 1.2 - - - +
579B LEU* 2.8 39.3 + - + +
581B LEU* 4.1 22.8 - - + +
597B ILE* 5.5 0.4 - - - -
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Residues in contact with VAL 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B VAL* 3.4 8.1 - - - +
555B ARG* 2.7 79.4 + - + +
557B SER* 4.9 11.4 - - - -
563B GLU* 6.1 0.4 - - + +
564B CYS* 1.3 80.8 - - - +
566B LEU* 1.3 66.7 + - - +
567B THR* 3.6 2.1 + - - +
576B HIS* 3.7 21.1 - - + -
577B LEU 3.4 12.8 - - - +
578B ARG* 4.8 4.9 - - + -
579B LEU* 4.5 1.8 - - - -
813H PTR 4.0 22.4 - - + +
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B PHE* 3.9 26.5 - - + -
553B LEU 3.8 3.6 - - - +
554B VAL* 3.9 21.5 - - + +
565B VAL* 1.3 70.5 - - - +
567B THR* 1.3 57.6 + - - +
568B PHE* 3.5 22.6 - - + -
576B HIS* 3.5 0.3 - - - -
577B LEU* 2.7 61.6 + - + +
579B LEU* 4.2 12.7 - - + +
600B MET* 4.3 18.4 - - + -
601B LEU* 3.9 11.7 - - + -
604B PHE* 4.5 9.4 - - + -
609B ILE* 4.7 1.8 - - + -
621B LEU* 4.5 11.2 - - + -
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Residues in contact with THR 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B ALA 3.6 24.9 - - - +
538B ALA* 4.2 0.4 - - - +
541B VAL* 3.8 14.0 - - + +
552B PHE* 3.2 4.0 - - - +
553B LEU* 3.0 46.1 + - - -
555B ARG* 2.8 29.8 + - - -
565B VAL* 3.6 1.1 + - - +
566B LEU* 1.3 72.6 - - - +
568B PHE* 1.3 64.6 + - - +
574B ALA* 5.0 0.7 - - + -
575B LYS 3.3 5.6 - - - +
576B HIS* 3.0 29.2 + - + -
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Residues in contact with PHE 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B VAL* 4.0 7.6 - - - +
550B GLY 5.3 1.3 - - - -
551B VAL 3.1 13.2 - - - +
552B PHE* 3.8 10.1 - - + -
566B LEU* 3.5 26.7 - - + -
567B THR* 1.3 75.8 - - - +
569B ASN* 1.3 72.7 + - - +
570B PHE* 4.4 1.8 - - + -
574B ALA* 3.5 3.5 - - - -
575B LYS* 2.8 61.8 + - + +
576B HIS 4.9 0.2 - - - -
577B LEU* 4.2 16.6 - - + -
609B ILE* 3.6 33.4 - - + -
611B LEU* 4.2 21.3 - - + -
619B VAL* 4.2 20.6 - - + -
621B LEU* 4.6 4.9 - - + -
814H GLU* 4.8 0.7 - - + -
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Residues in contact with ASN 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B VAL* 3.0 29.9 + - - +
542B LEU* 3.9 12.6 - - - +
545B GLY 3.0 24.9 + - - -
548B SER* 3.2 29.1 - - - +
549B HIS* 3.6 3.8 + - - -
550B GLY* 3.0 22.7 + - - -
551B VAL 2.8 10.6 + - - +
568B PHE* 1.3 78.2 - - - +
570B PHE* 1.3 64.1 + - - +
571B GLN 3.5 1.4 + - - -
572B GLY* 3.0 22.5 + - - -
573B LYS 3.6 5.8 - - - -
619B VAL* 4.1 1.7 - - - +
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Residues in contact with PHE 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B HIS* 3.7 10.8 - + - -
568B PHE* 3.7 3.8 + - + -
569B ASN* 1.3 73.4 + - - +
571B GLN* 1.3 79.8 + - + +
572B GLY 3.2 0.2 - - - -
573B LYS* 2.6 34.0 + - + +
575B LYS* 3.7 34.5 - - + -
611B LEU* 4.1 13.0 - - + -
613B SER* 5.4 12.3 - - - -
617B SER* 3.6 36.3 - - - -
619B VAL* 3.4 39.0 - - + -
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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