Contacts of the strand formed by residues 538 - 546 (chain B) in PDB entry 1HKB
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 PHE 538 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531B LEU* 4.4 17.0 - - + -
532B ASP 3.2 17.0 - - - +
533B LEU* 3.8 22.0 - - + +
534B GLY 5.7 0.4 - - - +
536B THR 4.3 0.8 + - - -
537B ASN* 1.3 72.1 - - - +
539B ARG* 1.3 71.1 + - - +
540B VAL* 4.2 8.3 - - + -
559B ILE* 3.6 2.8 - - - +
560B TYR* 2.9 53.3 + + + +
562B ILE* 3.3 36.6 - - + -
577B HIS* 4.8 0.2 - - - -
578B ILE* 4.2 25.6 - - + -
581B CYS* 3.5 39.0 - - + -
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Residues in contact with ARG 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PRO* 5.0 8.7 - - - +
530B ALA 4.3 0.2 - - - +
531B LEU* 3.9 1.6 - - - -
532B ASP* 3.1 55.2 + - + +
537B ASN* 4.2 21.5 + - - +
538B PHE* 1.3 80.5 - - - +
540B VAL* 1.3 68.0 + - - +
541B LEU* 4.0 25.2 - - + +
557B ASN* 3.4 24.1 + - - +
558B LYS 3.3 14.1 - - - +
559B ILE* 3.4 39.1 - - + +
560B TYR 4.5 0.2 - - - +
921B G6P 5.3 4.4 + - - -
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Residues in contact with VAL 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LEU* 4.8 4.9 - - + -
530B ALA 3.7 9.4 - - - +
531B LEU* 3.9 14.8 - - + -
538B PHE* 4.2 16.8 - - + -
539B ARG* 1.3 76.3 - - - +
541B LEU* 1.3 66.3 + - - +
557B ASN* 3.1 3.3 - - - +
558B LYS 3.0 29.2 + - - -
560B TYR* 3.4 33.0 - - + -
581B CYS* 4.4 11.2 - - + +
582B ILE* 4.6 10.1 - - + +
585B PHE* 3.4 31.3 - - + -
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Residues in contact with LEU 541 (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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529B LEU* 3.2 12.1 - - - +
530B ALA* 2.8 66.3 + - + +
531B LEU 4.4 1.8 - - - +
532B ASP* 4.6 17.7 - - + +
539B ARG* 4.0 14.4 - - - -
540B VAL* 1.3 78.2 - - - +
542B LEU* 1.3 59.9 + - - +
543B VAL* 4.2 8.1 - - + -
555B MET* 3.7 26.7 - - + -
556B HIS 3.2 7.6 - - - +
557B ASN* 3.3 24.5 - - + +
585B PHE* 3.6 5.4 - - - -
895B ASP 5.5 1.1 - - - +
898B GLY* 3.9 16.4 - - - +
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Residues in contact with LEU 542 (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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527B ASP* 5.2 1.6 - - + -
528B PHE 3.3 22.9 - - - +
529B LEU* 4.5 1.8 - - + -
541B LEU* 1.3 72.3 - - - +
543B VAL* 1.3 62.7 + - - +
544B LYS* 3.6 34.3 - - + -
555B MET* 3.0 4.9 - - - +
556B HIS* 2.7 56.2 + - + +
585B PHE* 3.5 18.6 - - + -
589B MET* 4.1 12.3 - - + -
591B ILE* 4.0 31.6 - - + -
596B MET* 4.3 11.0 - - + -
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ASP* 3.5 0.7 - - - -
528B PHE* 2.8 44.6 + - - +
530B ALA* 5.1 4.3 - - + -
541B LEU* 4.4 8.5 - - + -
542B LEU* 1.3 82.6 - - - +
544B LYS* 1.3 64.1 + - - +
545B ILE* 4.2 7.0 - - + -
553B VAL* 3.9 26.7 - - + -
554B GLU 3.4 2.2 - - - -
555B MET* 3.4 31.2 - - + -
898B GLY 4.6 8.7 - - - +
899B LYS* 4.9 4.3 - - - -
902B ALA* 4.0 28.5 - - + -
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Residues in contact with LYS 544 (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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526B GLY 3.4 4.7 - - - -
527B ASP* 3.5 31.8 + - + +
542B LEU* 3.6 26.9 - - + -
543B VAL* 1.3 76.3 - - - +
545B ILE* 1.3 63.1 + - - +
546B ARG* 4.0 15.1 + - + +
552B THR* 3.8 1.2 + - - +
553B VAL* 3.2 6.4 - - - +
554B GLU* 2.8 67.2 + - + +
556B HIS* 5.2 0.9 - - - -
591B ILE* 5.9 5.6 - - - +
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Residues in contact with ILE 545 (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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524B GLU* 3.0 30.1 - - + +
525B ASN* 3.2 8.9 - - - -
526B GLY 2.7 39.3 + - - +
528B PHE* 4.4 9.0 - - + -
543B VAL* 4.2 11.7 - - + -
544B LYS* 1.3 77.9 - - - +
546B ARG* 1.3 68.0 + - - +
547B SER* 5.0 1.3 - - - -
551B ARG* 6.5 0.2 - - + -
552B THR 3.5 7.4 - - - +
553B VAL* 4.3 15.3 - - + -
667B TYR* 5.1 5.8 - - + +
899B LYS 4.8 0.4 - - - +
902B ALA* 4.2 13.7 - - + +
903B LEU* 3.8 47.1 - - + +
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Residues in contact with ARG 546 (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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525B ASN* 3.9 11.4 - - - +
526B GLY* 3.3 15.4 + - - +
527B ASP* 2.7 35.1 + - - -
544B LYS* 4.0 15.7 + - + +
545B ILE* 1.3 94.0 + - - +
547B SER* 1.3 61.1 + - - +
550B LYS 4.9 2.5 - - - +
551B ARG* 3.1 4.9 - - - +
552B THR* 2.7 59.9 + - + +
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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