Contacts of the helix formed by residues 537 - 544 (chain B) in PDB entry 5KCU
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 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B THR* 4.1 7.2 - - - +
351B ASP* 2.6 40.7 + - - +
536B LEU* 1.3 76.3 - - - +
538B ASP* 1.3 61.2 + - - +
539B LEU 4.2 0.4 - - - -
540B LEU* 3.3 20.8 + - - +
541B LEU* 2.8 28.3 + - - +
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Residues in contact with ASP 538 (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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536B LEU 4.9 1.0 - - - +
537B SER* 1.3 75.9 - - - +
539B LEU* 1.3 61.1 + - - +
541B LEU* 4.0 16.5 - - - +
542B GLU* 3.4 27.2 + - - +
689D ILE* 3.9 16.0 - - + +
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Residues in contact with LEU 539 (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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351B ASP* 3.7 20.6 - - - +
354B LEU* 3.7 34.3 - - + -
355B VAL* 4.4 12.6 - - + -
358B ILE* 4.3 15.5 - - + -
537B SER* 3.2 1.4 + - - -
538B ASP* 1.3 76.8 - - - +
540B LEU* 1.3 64.2 + - - +
542B GLU* 3.3 6.3 + - - +
543B MET* 3.2 42.0 + - + +
689D ILE* 3.8 32.0 - - + +
690D LEU* 4.3 9.4 - - + +
693D LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 540 (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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347B THR* 3.6 26.9 - - + +
350B ALA* 4.6 4.9 - - + -
351B ASP* 4.4 5.6 - - + +
354B LEU* 3.6 22.7 - - + -
383B TRP* 3.5 36.3 - - + -
525B LEU* 6.1 0.2 - - + -
536B LEU* 4.4 10.3 - - + -
537B SER* 3.3 24.9 + - - +
539B LEU* 1.3 77.7 - - - +
541B LEU* 1.3 66.3 + - - +
543B MET* 3.0 5.8 + - - +
544B LEU* 3.0 33.2 + - + +
601B OB8 3.6 25.8 - - + +
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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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536B LEU* 3.7 41.3 - - + +
537B SER 2.8 23.5 + - - +
538B ASP* 4.0 18.8 - - - +
539B LEU 3.4 0.2 - - - -
540B LEU* 1.3 75.5 - - - +
542B GLU* 1.3 60.4 + - + +
544B LEU* 3.3 23.2 - - + +
545B ASP* 5.2 0.2 - - - -
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Residues in contact with GLU 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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380B GLU* 4.4 7.4 - - - +
538B ASP 3.4 12.0 + - - +
539B LEU* 3.3 11.0 + - + +
540B LEU 3.1 0.6 - - - -
541B LEU* 1.3 77.2 - - + +
543B MET* 1.3 66.4 + - + +
544B LEU 3.2 0.7 + - - -
545B ASP* 3.6 14.9 + - - +
688D LYS* 3.2 18.8 + - - +
689D ILE* 2.8 50.6 + - + +
690D LEU* 3.6 12.5 + - + +
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Residues in contact with MET 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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354B LEU* 4.1 31.9 - - + -
357B MET* 6.4 0.2 - - - -
358B ILE* 4.4 7.0 - - + -
379B LEU* 4.5 5.2 - - + +
380B GLU* 4.3 22.8 - - - +
383B TRP* 3.4 45.1 + - + +
522B MET* 5.7 0.9 - - - +
539B LEU* 3.2 30.7 - - + +
540B LEU* 3.0 8.6 + - - +
542B GLU* 1.3 76.6 - - - +
544B LEU* 1.3 58.1 + - - +
545B ASP* 3.0 14.2 + - - +
690D LEU* 3.7 44.0 - - + -
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Residues in contact with LEU 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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383B TRP* 3.6 30.1 - - + +
522B MET* 5.0 3.4 - - - -
525B LEU* 3.6 44.6 - - + +
526B TYR* 3.2 27.4 + - + +
536B LEU* 3.7 24.7 - - + -
540B LEU* 3.0 33.0 + - + +
541B LEU* 3.3 18.7 - - + +
542B GLU 3.1 0.4 - - - -
543B MET* 1.3 72.3 - - - +
545B ASP* 1.3 66.9 + - - +
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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