Contacts of the helix formed by residues 730 - 734 (chain N) 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 PRO 730 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684M PHE* 4.6 10.3 - - + -
633N VAL* 4.5 8.5 - - + -
634N GLY 4.2 15.3 - - - +
635N PRO* 4.5 1.6 - - + -
728N LEU 3.8 5.6 - - - +
729N HIS* 1.3 99.6 - - + +
731N LEU* 1.3 64.0 + - - +
733N CYS* 3.0 30.8 + - - +
734N GLU 4.5 0.2 + - - -
782N SER* 5.0 4.2 - - - -
785N ILE* 4.9 4.3 - - + -
935N LYS* 3.4 25.6 - - + -
939N PHE* 3.3 33.9 - - + -
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Residues in contact with LEU 731 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639N LEU* 5.7 5.6 - - + -
729N HIS* 2.9 22.5 + - + +
730N PRO* 1.3 77.3 - - - +
732N VAL* 1.3 60.2 + - + +
733N CYS 3.2 3.8 + - - -
734N GLU* 3.5 11.6 + - - +
778N LEU 3.7 14.6 - - - +
779N ALA* 3.7 29.3 - - + +
780N LYS 4.1 2.8 - - - +
781N PRO* 4.0 23.8 - - + -
782N SER* 4.7 0.7 - - - +
785N ILE* 4.4 11.2 - - + -
931N LEU* 3.2 50.5 - - + +
932N ASP* 4.0 2.2 - - - +
935N LYS* 3.8 16.6 - - + -
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Residues in contact with VAL 732 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639N LEU* 5.9 5.4 - - + -
714N GLN* 3.1 32.3 - - - +
716N PHE* 3.8 12.6 - - + -
728N LEU* 3.4 14.4 - - + -
729N HIS* 3.2 33.9 - - + +
731N LEU* 1.3 72.0 - - + +
733N CYS* 1.3 57.7 + - - +
734N GLU 2.9 10.2 + - - -
735N ALA* 3.1 16.3 + - + +
736N PHE* 3.2 22.5 - - + -
765N SER* 4.1 11.7 - - - -
778N LEU 5.3 0.9 - - - -
779N ALA* 6.0 0.4 - - - +
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Residues in contact with CYS 733 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684M PHE* 3.5 24.2 - - + -
685M GLU* 4.8 3.5 - - - +
728N LEU* 3.4 19.3 - - - -
729N HIS 3.5 5.6 + - - -
730N PRO* 3.0 28.0 + - - +
732N VAL* 1.3 77.2 - - - +
734N GLU* 1.3 57.3 + - - +
736N PHE* 2.6 21.2 - - - +
737N ASN* 4.4 1.0 - - - -
738N ALA* 3.6 16.6 + - - +
740N PHE* 3.4 33.4 - - - -
782N SER* 5.3 0.4 - - - +
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Residues in contact with GLU 734 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709N HIS* 5.1 1.4 - - - -
731N LEU 3.5 4.7 + - - +
732N VAL 2.9 0.2 - - - -
733N CYS* 1.3 81.2 - - - +
735N ALA* 1.3 66.4 + - - +
736N PHE 4.1 2.3 - - - +
737N ASN* 4.4 3.1 + - - +
778N LEU* 3.4 23.4 - - - +
780N LYS* 3.3 46.2 + - - +
781N PRO 5.7 0.3 - - - +
782N SER* 3.0 32.9 + - - +
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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