Contacts of the helix formed by residues 541 - 546 (chain M) in PDB entry 2PPB
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408M ARG* 6.4 0.2 - - - -
439M CYS* 3.2 14.5 - - - -
442M GLU* 2.5 33.4 + - - -
455M LEU 3.5 22.9 - - - -
456M ALA* 4.0 1.8 - - - +
457M ALA* 4.6 0.9 - - - -
540M PHE* 1.3 77.6 - - - +
542M VAL* 1.3 63.5 - - - +
543M ASN 3.4 1.0 + - - -
544M THR* 2.9 19.1 + - - -
545M ASN* 2.9 21.7 + - - +
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Residues in contact with VAL 542 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LEU* 5.5 3.4 - - + -
18M LEU* 3.8 16.8 - - + -
401M LEU* 5.1 2.9 - - + -
404M LEU* 4.6 6.5 - - + -
408M ARG* 3.1 44.4 - - - +
457M ALA* 4.6 9.0 - - - +
541M SER* 1.3 72.7 - - - +
543M ASN* 1.3 67.9 + - + +
545M ASN* 3.1 22.4 + - - +
546M LEU* 3.3 15.4 - - + +
583M LEU* 4.3 15.4 - - + +
587M VAL* 3.7 30.1 - - + -
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Residues in contact with ASN 543 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401M LEU* 4.4 13.8 - - + +
405M ARG* 3.4 33.4 - - + +
442M GLU* 3.2 24.1 + - - +
541M SER* 4.0 0.2 - - - -
542M VAL* 1.3 81.9 - - - +
544M THR* 1.3 58.8 + - - +
546M LEU* 3.5 21.5 - - - +
547M ILE* 5.3 1.4 - - - +
562M SER* 2.8 48.1 + - - +
565M GLN* 3.8 16.5 - - - +
566M THR* 4.4 1.5 + - - -
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Residues in contact with THR 544 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439M CYS* 4.1 1.8 - - - -
441M VAL* 4.1 18.2 - - + +
442M GLU* 4.1 1.2 + - - -
540M PHE* 3.9 20.2 - - + -
541M SER* 2.9 20.4 + - - -
543M ASN* 1.3 71.9 - - - +
545M ASN* 1.3 68.7 + - - +
546M LEU 2.9 2.9 - - - -
547M ILE* 2.7 26.4 + - + +
550M LEU* 3.3 39.2 - - + +
562M SER* 3.7 22.0 + - - -
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Residues in contact with ASN 545 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LEU* 5.3 1.6 - - - +
457M ALA* 4.6 9.1 - - - +
537M LYS* 3.2 41.6 + - - +
540M PHE* 4.2 5.7 - - - +
541M SER 2.9 14.9 + - - +
542M VAL 3.3 11.0 - - - +
544M THR* 1.3 76.7 - - - +
546M LEU* 1.3 56.1 + - - +
547M ILE 3.0 4.2 + - - +
550M LEU* 5.9 0.2 - - - -
581M THR* 2.9 26.3 - - - +
583M LEU* 2.9 32.1 - - + +
905M ILE* 3.1 34.6 - - + +
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Residues in contact with LEU 546 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401M LEU* 4.2 22.7 - - + -
542M VAL* 3.3 26.7 - - + +
543M ASN* 3.5 18.4 - - - +
544M THR 2.8 1.0 + - - -
545M ASN* 1.3 71.4 - - - +
547M ILE* 1.3 56.2 + - - -
548M PRO* 3.3 0.3 - - - +
565M GLN* 3.1 20.4 - - - +
581M THR* 3.1 18.9 - - - +
583M LEU* 4.5 3.8 - - + -
584M GLU* 3.3 40.4 - - - +
587M VAL* 4.4 6.5 - - + -
666M LEU* 3.8 21.8 - - + -
842M ARG* 2.9 31.8 + - - +
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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