Contacts of the helix formed by residues 537 - 547 (chain B) in PDB entry 4OL0
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 HIS 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B LEU* 3.8 24.1 - - + +
500B ASP* 4.0 33.8 + - + +
503B LEU* 3.4 29.9 - - + +
507B MET* 5.3 4.7 - - + +
533B HIS 3.8 13.9 + - - -
534B MET* 3.0 14.9 + - + +
536B GLN* 1.3 91.9 - - + +
538B PHE* 1.3 64.2 + - - +
539B ASN 3.4 2.2 - - - -
540B GLY* 3.1 15.0 + - - +
541B LEU* 3.2 14.1 + - - +
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Residues in contact with PHE 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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534B MET 3.2 7.4 + - - +
535B ALA* 3.7 14.6 - - - +
536B GLN 3.2 3.0 + - - -
537B HIS* 1.3 74.2 - - - +
539B ASN* 1.3 66.3 + - - +
541B LEU* 2.6 33.7 + - + +
542B LEU* 2.9 32.8 + - + -
565B THR* 4.0 21.1 - - + -
568B VAL* 4.3 15.9 - - + -
569B LEU* 3.8 29.8 - - + -
572B LEU* 3.9 16.6 - - + -
580B CYS* 3.5 46.7 - - + -
584B LEU* 5.2 2.7 - - + -
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Residues in contact with ASN 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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536B GLN 4.6 4.8 + - - +
537B HIS 3.4 0.8 - - - -
538B PHE* 1.3 86.1 - - - +
540B GLY* 1.3 60.6 + - - +
542B LEU* 3.4 13.8 + - - +
543B GLU* 3.2 20.3 + - - +
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Residues in contact with GLY 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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507B MET* 4.7 12.2 - - - +
537B HIS* 3.1 10.2 + - - -
538B PHE 3.0 1.0 - - - -
539B ASN* 1.3 77.3 - - - +
541B LEU* 1.3 63.6 + - - +
543B GLU* 3.4 8.6 + - - +
544B ILE* 3.1 29.1 + - - +
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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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503B LEU* 5.5 0.2 - - + -
507B MET* 4.9 5.4 - - + -
523B ILE* 4.5 7.6 - - + -
527B CYS* 3.8 15.3 - - - -
534B MET* 3.6 31.4 - - + +
537B HIS 3.2 9.4 + - - +
538B PHE* 2.6 26.6 + - + +
540B GLY* 1.3 71.2 - - - -
542B LEU* 1.3 60.8 + - - +
544B ILE* 3.3 23.1 + - + +
545B ALA* 3.1 19.2 + - - +
561B LEU* 5.9 0.9 - - + -
565B THR* 4.1 30.3 + - + +
568B VAL* 4.1 33.2 - - + -
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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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538B PHE* 2.9 30.4 + - + +
539B ASN* 3.6 18.2 - - - +
540B GLY 3.2 0.2 - - - -
541B LEU* 1.3 75.4 - - - +
543B GLU* 1.3 56.2 + - - +
545B ALA* 2.7 30.4 + - + +
546B ARG* 2.8 40.5 + - + +
565B THR* 5.1 0.8 - - - +
580B CYS* 4.5 6.5 - - - +
583B GLU* 3.9 47.8 - - + +
584B LEU* 4.4 17.3 - - + -
587B VAL* 5.0 0.7 - - + -
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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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539B ASN 3.2 11.0 + - - +
540B GLY* 3.7 11.2 - - - +
541B LEU 3.4 0.2 - - - -
542B LEU* 1.3 78.1 - - - +
544B ILE* 1.3 58.8 + - + +
546B ARG* 3.3 24.1 + - - +
547B SER* 2.8 57.0 + - - +
551B PHE* 5.1 0.2 - - - -
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Residues in contact with ILE 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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507B MET* 3.9 36.1 - - + -
510B LEU* 4.0 21.5 - - + -
523B ILE* 4.3 9.9 - - + -
540B GLY 3.1 15.3 + - - +
541B LEU* 3.4 22.2 - - + +
542B LEU 3.1 0.4 - - - -
543B GLU* 1.3 77.1 - - + +
545B ALA* 1.3 60.4 + - - +
547B SER 3.7 1.2 - - - -
548B LEU* 3.2 24.4 + - + +
551B PHE* 3.7 10.0 - - + -
561B LEU* 3.8 36.8 - - + -
565B THR* 5.9 1.8 - - - +
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Residues in contact with ALA 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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541B LEU 3.1 11.2 + - - +
542B LEU* 2.7 15.0 + - + +
544B ILE* 1.3 77.1 - - - +
546B ARG* 1.3 62.6 + - - +
547B SER 3.2 0.6 + - - -
548B LEU* 3.5 22.1 + - - +
562B LEU* 4.0 15.3 - - + -
565B THR* 5.4 1.1 - - + +
584B LEU* 3.8 27.6 - - + -
587B VAL* 3.7 20.0 - - + +
588B GLN* 5.0 2.2 + - - +
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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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542B LEU* 2.8 37.5 + - + +
543B GLU* 3.5 29.7 + - - +
545B ALA* 1.3 77.2 - - - +
547B SER* 1.3 59.8 + - - +
548B LEU 3.8 0.5 + - - -
549B ASP* 5.1 1.9 + - - +
583B GLU* 3.3 43.5 + - - +
586B SER* 5.6 3.2 + - - -
587B VAL* 4.1 22.6 - - + +
590B MET* 5.2 10.1 - - - +
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Residues in contact with SER 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLU* 2.8 38.6 + - - +
545B ALA 3.2 0.2 - - - -
546B ARG* 1.3 77.6 - - - +
548B LEU* 1.3 63.9 + - - +
549B ASP 3.1 3.4 - - - -
550B SER* 2.6 38.8 + - - -
551B PHE* 3.2 23.7 - - - -
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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