Contacts of the helix formed by residues 524 - 531 (chain B) in PDB entry 5JHQ
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 THR 524 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494B LEU* 3.6 0.9 - - - -
514B ILE 3.7 14.0 + - - -
515B ASN* 3.8 12.8 + - - +
516B PHE 3.5 12.3 - - - -
517B LYS* 4.4 2.7 - - - +
522B HIS 3.5 4.8 + - - -
523B GLU* 1.3 77.5 - - - +
525B ALA* 1.3 73.0 + - - +
526B LEU* 3.7 14.7 + - + +
527B HIS* 3.1 47.5 + - + +
528B CYS* 3.5 9.9 + - - -
549B ALA* 5.4 2.1 - - - +
550B ASN 4.9 1.6 - - - +
553B GLU* 3.6 30.5 - - + -
561B PRO* 5.1 0.7 - - + -
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Residues in contact with ALA 525 (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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493B LEU* 4.0 22.9 - - + -
494B LEU* 3.2 22.5 - - + +
497B ALA* 3.4 16.2 - - + +
514B ILE 4.0 15.3 - - - +
516B PHE 4.0 1.8 + - - -
524B THR* 1.3 76.9 + - - +
526B LEU* 1.3 55.3 + - - +
528B CYS* 3.4 2.4 + - - -
529B ALA 3.0 22.2 + - - -
544B LEU* 3.6 19.1 - - + +
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Residues in contact with LEU 526 (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 THR* 3.2 14.7 + - + +
525B ALA* 1.3 75.8 - - - +
527B HIS* 1.3 64.8 + - - +
529B ALA* 3.3 1.3 + - + +
530B VAL* 3.1 25.9 + - - +
541B THR* 3.8 39.5 - - + +
544B LEU* 3.9 17.8 - - + +
545B LEU* 3.7 28.7 - - + -
549B ALA* 4.5 8.1 - - + -
550B ASN 3.9 5.4 - - - +
551B VAL* 3.8 15.3 - - - -
561B PRO* 3.7 24.9 - - + -
577B LEU* 4.0 9.2 - - + -
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Residues in contact with HIS 527 (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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523B GLU* 3.5 29.4 - - + +
524B THR* 3.1 40.8 + - + +
526B LEU* 1.3 77.5 - - - +
528B CYS* 1.3 61.4 + - - +
530B VAL* 3.6 7.7 - - - +
531B ALA* 3.4 24.1 + - - +
553B GLU* 3.1 31.1 + - + -
554B LYS 3.9 2.5 - - - -
555B ASN* 3.8 19.7 - - + +
559B MET 3.1 13.1 + - - -
560B THR 3.8 2.2 - - - -
561B PRO* 3.5 25.5 - - + +
564B VAL* 3.9 17.8 - - + +
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Residues in contact with CYS 528 (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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494B LEU* 3.8 31.9 - - - +
497B ALA* 4.1 0.4 - - + -
498B ARG* 2.8 54.9 - - + +
523B GLU* 4.3 17.5 - - - -
524B THR 3.5 12.3 + - - -
525B ALA 3.4 7.8 + - - +
526B LEU 3.2 0.4 - - - -
527B HIS* 1.3 78.8 - - - +
529B ALA* 1.3 64.1 + - - +
531B ALA* 3.6 5.1 + - - +
532B SER 3.4 14.6 + - - -
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Residues in contact with ALA 529 (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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497B ALA* 3.5 12.1 + - + +
525B ALA 3.0 16.1 + - - +
526B LEU* 3.3 5.8 + - - +
528B CYS* 1.3 71.9 - - - +
530B VAL* 1.3 64.8 + - - +
531B ALA 3.1 1.6 - - - -
532B SER* 3.1 18.5 + - - -
537B ARG* 3.5 13.2 - - - +
540B VAL* 3.7 29.6 - - + -
541B THR* 3.8 15.5 - - - +
544B LEU* 4.1 6.7 - - + -
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Residues in contact with VAL 530 (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 LEU* 3.1 13.8 + - + +
527B HIS* 3.6 14.8 - - - +
529B ALA* 1.3 75.9 - - - +
531B ALA* 1.3 59.0 + - - +
532B SER 3.4 0.4 - - - -
537B ARG* 4.3 1.5 - - - -
541B THR* 3.8 26.9 - - + +
561B PRO* 3.6 26.5 - - + +
564B VAL* 3.9 12.8 - - + -
565B ALA* 4.1 6.6 - - + +
570B HIS* 2.9 27.6 + - - +
573B VAL* 3.8 26.7 - - + -
577B LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 531 (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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523B GLU* 5.7 1.8 - - - +
527B HIS 3.4 16.2 + - - +
528B CYS* 3.6 5.4 + - - +
529B ALA 3.1 1.0 - - - -
530B VAL* 1.3 80.5 - - - +
532B SER* 1.3 62.5 + - - +
533B LEU* 3.6 9.5 + - - +
564B VAL* 3.7 17.3 - - + -
568B ARG* 3.7 25.5 + - - +
570B HIS* 3.4 12.3 - - - -
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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