Contacts of the helix formed by residues 896 - 907 (chain C) in PDB entry 6PB4
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 THR 896 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895C LEU* 1.3 81.7 - - - +
897C PRO* 1.3 68.1 - - - +
898C GLU* 2.6 30.4 + - + +
899C GLU* 3.5 22.9 - - + +
900C LYS* 2.9 23.4 + - - -
537F THR* 5.3 12.8 - - + -
540F LEU* 5.9 0.2 - - + -
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Residues in contact with PRO 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C LEU 4.4 1.8 - - - +
896C THR* 1.3 92.3 - - - +
898C GLU* 1.3 59.2 + - - +
900C LYS* 3.3 11.0 - - + +
901C LEU* 2.9 26.7 + - - +
563F PHE* 3.0 33.0 - - + +
564F GLY* 4.0 12.3 - - - +
565F ILE* 3.3 26.6 - - + +
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Residues in contact with GLU 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C THR* 2.6 34.4 + - + +
897C PRO* 1.3 76.9 - - - +
899C GLU* 1.3 61.0 + - - +
901C LEU* 3.0 11.9 + - + +
902C LEU* 2.9 23.7 + - - +
537F THR* 6.0 1.8 - - + -
540F LEU* 4.5 22.2 - - + +
541F ARG* 3.5 46.4 - - + +
544F THR* 4.5 11.9 - - + +
565F ILE* 3.7 27.1 - - + +
566F ASP 4.7 2.6 + - - -
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Residues in contact with GLU 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C LEU* 3.7 30.1 - - + -
896C THR* 3.4 14.6 + - + +
898C GLU* 1.3 75.5 - - - +
900C LYS* 1.3 60.1 + - - +
902C LEU* 3.0 37.4 + - - +
903C ARG* 2.9 34.3 + - - +
908C GLU* 4.6 8.1 - - - +
540F LEU* 4.3 13.8 - - + +
613F ASP* 4.2 17.4 - - - +
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Residues in contact with LYS 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C LEU* 3.1 17.1 - - + +
896C THR 2.9 15.0 + - - +
897C PRO* 3.3 15.3 - - + +
899C GLU* 1.3 77.9 - - - +
901C LEU* 1.3 56.5 + - - +
903C ARG* 3.3 24.7 + - - +
904C ALA* 2.9 35.5 + - - +
563F PHE* 3.5 35.2 - - + -
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Residues in contact with LEU 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897C PRO 2.9 14.6 + - - +
898C GLU* 3.0 13.4 + - + +
900C LYS* 1.3 76.1 - - - +
902C LEU* 1.3 61.6 + - - +
904C ALA* 3.6 12.7 + - + +
905C ILE* 3.7 15.8 + - + +
544F THR* 4.3 22.4 - - + -
548F LEU* 4.1 35.2 - - + -
559F LEU* 5.3 11.0 - - + +
563F PHE* 5.1 15.9 - - + -
565F ILE* 4.2 16.4 - - + -
607F LEU* 5.5 2.9 - - + +
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Residues in contact with LEU 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C GLU 2.9 11.1 + - - +
899C GLU* 3.0 39.9 + - - +
901C LEU* 1.3 79.5 - - - +
903C ARG* 1.3 63.2 + - - +
904C ALA 3.2 0.5 + - - -
905C ILE* 3.6 1.9 + - - +
906C PHE* 3.3 63.8 + - + -
908C GLU* 6.0 1.8 - - + -
540F LEU* 5.0 6.1 - - + -
607F LEU* 3.8 28.5 - - + +
610F PHE* 3.1 37.9 - - + +
611F LEU* 4.2 5.6 - - + +
613F ASP* 4.7 0.2 - - + -
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Residues in contact with ARG 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C LEU* 4.8 9.2 - - + -
899C GLU* 2.9 19.7 + - - +
900C LYS* 3.3 37.7 - - + +
902C LEU* 1.3 78.5 - - - +
904C ALA* 1.3 64.2 + - - +
905C ILE 3.3 0.2 - - - -
907C GLY 3.1 7.4 + - - -
908C GLU* 2.3 86.3 + - + +
909C LYS* 3.9 16.0 - - - +
910C ALA 5.2 0.4 - - - +
26G LYS* 3.1 32.3 - - - +
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Residues in contact with ALA 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900C LYS* 2.9 21.4 + - + +
901C LEU* 3.9 10.1 - - + +
902C LEU 3.1 0.8 - - - -
903C ARG* 1.3 91.2 - - - +
905C ILE* 1.3 57.6 + - - +
907C GLY* 4.1 2.3 + - - -
563F PHE* 4.8 17.0 - - + -
591F GLU* 4.6 6.2 - - - +
595F LEU* 4.2 12.4 - - + +
26G LYS* 4.6 8.1 + - - +
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Residues in contact with ILE 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901C LEU* 3.7 10.8 - - + +
902C LEU 3.6 10.5 - - - +
904C ALA* 1.3 78.3 - - - +
906C PHE* 1.3 79.9 + - + +
907C GLY* 3.0 4.9 + - - -
595F LEU* 3.4 50.1 - - + +
598F LEU* 4.4 10.8 - - + -
599F ARG* 3.4 45.7 + - + +
607F LEU* 4.2 12.8 - - + -
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Residues in contact with PHE 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902C LEU* 3.3 39.2 + - + +
905C ILE* 1.3 80.1 - - + +
907C GLY* 1.3 62.3 + - - +
908C GLU* 3.4 8.5 + - + +
599F ARG* 3.4 20.2 - - - +
604F SER* 3.2 30.1 - - - -
607F LEU* 3.3 44.4 - - + -
608F ARG* 3.2 28.7 - - - -
611F LEU* 4.0 25.6 - - + -
28G THR* 4.1 12.0 + - - -
31G HIS* 4.3 15.1 + + + -
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Residues in contact with GLY 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903C ARG 3.1 10.3 + - - -
904C ALA 4.7 1.6 - - - -
905C ILE 3.0 6.8 - - - -
906C PHE* 1.3 78.9 - - - +
908C GLU* 1.3 64.8 + - - +
909C LYS* 3.1 9.5 + - - +
26G LYS* 3.3 43.6 - - - +
28G THR* 4.7 6.3 + - - -
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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