Contacts of the helix formed by residues 537 - 542 (chain O) in PDB entry 6CNC
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 LEU 537 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ILE* 5.3 6.7 - - + -
507O LEU* 4.3 21.8 - - + -
511O ILE* 5.3 4.9 - - + -
519O GLU* 5.5 0.9 - - + -
522O ILE* 5.2 9.9 - - + -
533O ILE* 2.7 34.2 + - + +
534O ARG* 6.1 3.8 - - - +
536O THR* 1.3 78.3 - - - +
538O ALA* 1.3 65.2 + - + +
539O SER 3.2 1.1 - - - -
540O LEU* 2.7 26.6 + - - +
541O ILE* 3.0 13.6 + - + +
546O VAL* 5.1 15.1 - - + +
566O PHE* 3.4 49.8 - - + -
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Residues in contact with ALA 538 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU* 4.1 16.0 - - + +
309A ILE* 6.2 3.1 - - + -
312A MET* 4.0 27.1 - - + -
533O ILE 3.8 2.2 + - - -
534O ARG* 3.2 26.4 - - - +
535O SER 3.1 1.0 + - - -
537O LEU* 1.3 84.2 - - + +
539O SER* 1.3 63.3 + - - +
541O ILE* 3.0 28.9 + - + +
542O ARG 3.7 2.4 + - - -
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Residues in contact with SER 539 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU* 4.0 19.0 + - - -
304A ASP* 5.6 2.0 - - - -
500O LEU* 3.7 19.6 - - - +
535O SER* 2.6 28.1 + - - -
536O THR* 4.7 2.7 - - - -
538O ALA* 1.3 73.1 - - - +
540O LEU* 1.3 59.1 + - - +
542O ARG* 3.9 4.7 + - - +
543O TYR* 3.2 25.5 - - - -
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Residues in contact with LEU 540 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496O ILE* 4.4 15.0 - - + -
500O LEU* 3.5 26.1 - - + +
504O ALA* 5.1 2.2 - - + +
507O LEU* 4.6 8.5 - - + -
508O SER* 4.2 22.9 - - - +
536O THR 3.7 16.2 + - - +
537O LEU* 2.7 20.3 + - - +
539O SER* 1.3 70.3 - - - +
541O ILE* 1.3 54.0 + - - +
542O ARG 3.1 2.7 - - - -
543O TYR* 2.7 37.4 + - + -
544O ASN 3.4 8.4 - - - +
545O SER* 4.0 19.1 - - - +
546O VAL* 3.6 27.6 - - + -
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Residues in contact with ILE 541 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 6.4 2.0 - - + -
223A ASN* 5.7 0.9 - - - +
225A LEU* 3.6 21.1 - - + +
303A LEU* 5.2 8.1 - - + -
309A ILE* 5.3 8.7 - - + -
312A MET* 5.6 5.2 - - - -
537O LEU* 3.0 11.6 + - + +
538O ALA* 3.0 27.6 - - + +
540O LEU* 1.3 76.2 - - - +
542O ARG* 1.3 59.2 + - + +
544O ASN* 2.9 24.7 + - - -
546O VAL* 3.7 18.2 - - + -
547O GLU* 3.2 29.4 - - - +
548O ILE* 3.5 25.1 - - + -
566O PHE* 5.3 3.4 - - + -
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Residues in contact with ARG 542 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 4.5 20.1 - - - +
88A LEU* 4.6 14.4 - - + +
225A LEU* 4.2 19.2 - - + +
229A ASN* 4.5 10.7 + - - -
299A ILE 5.3 1.6 + - - -
300A LYS* 4.8 17.0 + - - +
303A LEU* 3.2 35.9 - - + +
538O ALA 3.7 4.4 + - - +
539O SER 4.1 10.1 - - - +
540O LEU 3.0 0.8 + - - -
541O ILE* 1.3 81.8 - - + +
543O TYR* 1.3 77.8 + - + +
544O ASN 3.1 3.2 + - - -
316P THR* 5.6 16.1 - - - -
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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