Contacts of the helix formed by residues 808 - 818 (chain D) in PDB entry 4OIR
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 808 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS* 5.8 3.6 - - + +
806D PHE* 4.4 0.5 - - - +
807D ALA* 1.3 87.3 - - + +
809D PRO* 1.3 65.6 - - + +
810D GLU* 3.3 28.0 - - + +
811D GLU* 2.9 44.5 + - - +
812D ALA 3.6 2.4 + - - -
829D VAL* 4.3 5.9 - - - +
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Residues in contact with PRO 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS* 5.5 2.0 - - + -
65B PHE* 3.6 44.0 - - + -
807D ALA 4.4 2.7 - - - +
808D THR* 1.3 87.8 - - + +
810D GLU* 1.3 63.4 + - - +
812D ALA* 3.0 4.9 + - + +
813D LEU* 2.9 35.0 + - + +
829D VAL* 4.2 27.1 - - + -
830D ALA* 6.3 0.2 - - + -
839D LEU* 4.5 17.3 - - + -
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Residues in contact with GLU 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS* 3.6 42.7 + - - +
65B PHE* 4.2 11.4 - - - -
808D THR* 3.3 31.9 - - - +
809D PRO* 1.3 78.0 - - - +
811D GLU* 1.3 55.2 + - + +
813D LEU* 3.4 11.9 + - + +
814D ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D PHE* 3.7 16.3 - - + -
807D ALA* 3.0 37.6 + - - +
808D THR* 2.9 24.4 + - - +
810D GLU* 1.3 79.3 - - + +
812D ALA* 1.3 57.7 + - - +
814D ALA* 3.4 6.4 + - - +
815D ALA* 2.9 28.4 + - - +
818D ARG* 4.8 2.3 + - - -
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Residues in contact with ALA 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D PHE* 3.6 25.5 - - + -
808D THR 3.6 1.6 + - - -
809D PRO 3.0 10.9 + - - +
811D GLU* 1.3 77.5 - - - +
813D LEU* 1.3 60.2 + - + +
815D ALA* 3.1 3.4 + - - +
816D HIS* 2.9 30.5 + - - +
821D VAL* 6.3 0.2 - - - -
827D ILE* 4.2 22.2 - - + -
829D VAL* 4.3 10.3 - - + -
836D VAL* 4.5 7.4 - - + +
839D LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU* 5.9 2.0 - - - +
65B PHE* 5.2 11.0 - - + -
154B GLU* 4.7 14.8 - - - +
809D PRO* 2.9 27.3 + - + +
810D GLU* 3.7 12.3 - - - +
812D ALA* 1.3 76.4 - - + +
814D ALA* 1.3 57.5 + - - +
816D HIS* 3.5 9.6 + - - +
817D GLU* 2.9 29.0 + - - +
836D VAL* 4.8 6.1 - - + -
839D LEU* 4.0 30.1 - - + -
840D LYS* 4.4 26.9 - - + +
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Residues in contact with ALA 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810D GLU 2.9 19.6 + - - +
811D GLU* 3.6 7.2 - - - +
813D LEU* 1.3 76.2 - - - +
815D ALA* 1.3 58.6 + - - +
817D GLU* 3.1 9.2 + - - +
818D ARG* 2.9 48.5 + - - +
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Residues in contact with ALA 815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D PHE* 3.5 27.8 - - + -
811D GLU 2.9 18.8 + - - +
812D ALA 3.1 5.4 + - - +
814D ALA* 1.3 75.5 - - - +
816D HIS* 1.3 62.5 + - - +
818D ARG* 3.1 28.4 + - - +
820D GLU* 3.0 30.2 + - - +
821D VAL* 4.1 11.2 - - + -
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Residues in contact with HIS 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812D ALA 2.9 11.3 + - - +
813D LEU* 3.8 5.6 - - - +
815D ALA* 1.3 75.8 - - - +
817D GLU* 1.3 64.1 + - + +
819D GLY* 2.8 20.8 + - - -
821D VAL* 3.0 31.9 + - - +
822D ALA* 5.3 0.2 - - - -
823D LEU* 4.1 30.6 + - + +
836D VAL* 3.6 33.2 - - + -
840D LYS* 4.1 28.3 + - + +
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Residues in contact with GLU 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813D LEU 2.9 15.3 + - - +
814D ALA* 3.1 13.2 + - - +
816D HIS* 1.3 82.8 + - + +
818D ARG* 1.3 60.7 + - + +
819D GLY* 3.3 1.2 + - - -
840D LYS* 4.4 15.2 + - - -
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Residues in contact with ARG 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D PHE* 5.3 3.0 - - - -
811D GLU 4.8 1.8 + - - -
814D ALA* 2.9 38.7 + - + +
815D ALA* 3.1 25.3 + - - +
817D GLU* 1.3 77.0 - - + +
819D GLY* 1.3 60.6 + - - +
820D GLU* 2.7 47.7 + - + +
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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