Contacts of the helix formed by residues 541 - 552 (chain B) in PDB entry 4UN5
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 SER 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539B PHE 3.8 1.6 + - - -
540B LEU* 1.3 73.5 - - - +
542B GLY* 1.3 58.5 + - - +
543B GLU* 3.5 15.3 + - - +
544B GLN* 3.0 36.9 + - - +
545B LYS* 2.9 33.7 + - - +
687B GLY 5.6 6.3 - - - -
690B ASN* 5.6 0.2 - - - -
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Residues in contact with GLY 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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541B SER* 1.3 73.6 - - - +
543B GLU* 1.3 61.0 + - - +
545B LYS* 3.3 5.8 + - - +
546B LYS* 2.9 43.9 + - - +
684B LYS 3.4 22.9 - - - -
685B SER* 4.0 16.0 + - - +
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Residues in contact with GLU 543 (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 SER* 3.5 15.7 + - - +
542B GLY* 1.3 78.3 + - - +
544B GLN* 1.3 58.7 + - + +
546B LYS* 3.4 13.6 + - + +
547B ALA* 2.9 30.4 + - - +
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Residues in contact with GLN 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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529B TYR* 3.3 31.4 + - - -
539B PHE 4.0 2.1 - - - +
540B LEU* 3.5 17.0 - - + -
541B SER* 3.0 35.9 + - - +
542B GLY 3.3 0.4 - - - -
543B GLU* 1.3 80.5 - - + +
545B LYS* 1.3 56.9 + - - +
547B ALA* 3.3 2.5 + - - +
548B ILE* 2.9 36.5 + - - +
568B TYR* 3.3 24.2 + - + +
569B PHE* 4.9 0.8 - - - -
573B GLU* 3.0 25.3 + - - +
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Residues in contact with LYS 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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521B TYR* 4.2 12.6 - - + -
524B LEU* 4.0 23.0 - - + +
525B THR* 3.6 29.8 - - + +
540B LEU* 3.6 30.7 + - + -
541B SER 2.9 21.8 + - - +
542B GLY* 3.5 10.4 - - - +
544B GLN* 1.3 76.0 - - - +
546B LYS* 1.3 58.1 + - - +
548B ILE* 3.3 4.9 + - - +
549B VAL* 2.9 35.0 + - - +
683B LEU 3.8 8.5 - - - +
684B LYS 2.7 33.4 + - - +
685B SER* 4.0 4.6 - - - +
686B ASP 5.0 0.8 - - - +
690B ASN* 3.6 17.4 + - - +
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Residues in contact with LYS 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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521B TYR* 4.0 21.3 - - + +
542B GLY* 2.9 30.8 + - - +
543B GLU* 3.8 11.5 + - + +
545B LYS* 1.3 72.3 - - - +
547B ALA* 1.3 60.0 + - - +
549B VAL* 3.3 1.2 + - - +
550B ASP* 2.9 41.7 + - - +
684B LYS* 4.5 25.1 - - + +
685B SER* 5.0 7.9 + - - -
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Residues in contact with ALA 547 (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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543B GLU 2.9 18.5 + - - +
544B GLN* 3.6 5.8 - - - +
546B LYS* 1.3 75.6 - - - +
548B ILE* 1.3 58.7 + - - +
550B ASP* 4.1 3.9 - - - +
551B LEU* 2.9 36.2 + - + +
568B TYR* 4.0 19.3 - - + +
572B ILE* 5.1 6.7 - - + -
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Residues in contact with ILE 548 (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 LEU* 4.4 9.6 - - + -
540B LEU* 3.9 31.9 - - + -
544B GLN 2.9 21.7 + - - +
545B LYS* 3.7 4.5 - - - +
547B ALA* 1.3 73.5 - - - +
549B VAL* 1.3 61.0 + - - +
551B LEU* 4.9 1.3 - - - -
552B LEU* 2.9 45.0 + - + +
553B PHE* 3.4 22.7 + - + -
559B VAL* 5.7 0.2 - - + -
564B LEU* 3.8 22.9 - - + -
568B TYR* 3.9 34.8 - - + -
569B PHE* 5.4 0.9 - - + -
587B PHE* 5.8 0.7 - - + -
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Residues in contact with VAL 549 (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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517B TYR* 5.0 3.1 - - + -
520B VAL* 4.7 6.5 - - + -
521B TYR* 3.5 40.4 - - + +
524B LEU* 4.2 12.6 - - + -
545B LYS 2.9 21.2 + - - +
546B LYS 3.7 3.8 - - - +
548B ILE* 1.3 76.3 - - - +
550B ASP* 1.3 63.4 + - - +
553B PHE* 2.9 23.6 + - + -
554B LYS* 2.9 51.2 + - + +
591B LEU* 4.6 6.5 - - + -
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Residues in contact with ASP 550 (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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546B LYS* 2.9 25.1 + - - +
547B ALA* 4.1 4.7 - - - +
549B VAL* 1.3 81.2 - - - +
551B LEU* 1.3 63.7 + - + +
554B LYS* 3.7 40.3 + - - +
555B THR* 3.9 9.2 - - - +
604B LYS* 4.9 4.0 + - - -
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Residues in contact with LEU 551 (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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547B ALA* 2.9 19.4 + - + +
548B ILE* 4.5 1.1 - - - +
550B ASP* 1.3 81.0 - - + +
552B LEU* 1.3 67.5 + - + +
555B THR* 2.7 26.3 + - - +
567B ASP 3.9 18.2 - - - +
568B TYR* 5.0 3.4 - - + -
571B LYS* 5.5 6.7 - - - +
572B ILE* 3.6 31.0 - - + -
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Residues in contact with LEU 552 (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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548B ILE* 2.9 30.2 + - + +
551B LEU* 1.3 93.6 - - + +
553B PHE* 1.3 61.2 + - + +
554B LYS 3.2 2.2 - - - -
555B THR* 3.4 1.1 + - - -
556B ASN* 2.9 46.6 + - - +
559B VAL* 3.8 24.6 - - + +
563B GLN* 3.9 20.6 - - + +
564B LEU* 3.9 17.9 - - + -
567B ASP* 3.7 31.2 - - + +
568B TYR* 4.3 9.6 - - + -
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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