Contacts of the helix formed by residues 805 - 816 (chain A) in PDB entry 5LOH
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 805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 2.7 34.1 + - - -
803A LYS 3.9 1.4 + - - -
804A LEU* 1.3 76.3 - - - +
806A ASP* 1.3 61.4 + - - +
807A ASN* 3.8 4.9 + - - +
808A ALA* 3.2 17.1 + - - +
809A GLN* 2.8 27.4 + - - +
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Residues in contact with ASP 806 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A LYS* 5.9 2.6 - - - +
804A LEU 4.5 2.9 - - - +
805A SER* 1.3 75.9 - - - +
807A ASN* 1.3 62.5 + - - +
809A GLN* 3.8 10.0 - - - +
810A SER* 2.9 29.1 + - - -
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Residues in contact with ASN 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 5.8 0.2 - - - +
805A SER* 3.3 4.8 + - - +
806A ASP* 1.3 80.2 - - - +
808A ALA* 1.3 59.5 + - - +
810A SER* 3.3 5.3 + - - -
811A ALA* 2.9 26.2 + - - +
832A HIS* 3.3 11.1 - - - -
833A PRO* 3.7 40.9 + - - +
834A LEU* 3.9 24.1 - - + +
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Residues in contact with ALA 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.7 11.4 - - - +
768A LEU* 5.8 0.2 - - - -
772A LEU* 3.8 25.1 - - + -
804A LEU* 4.5 6.3 - - + -
805A SER* 3.2 27.3 + - - +
807A ASN* 1.3 74.3 - - - +
809A GLN* 1.3 64.6 + - - +
811A ALA* 3.2 2.3 + - - +
812A VAL* 2.9 31.1 + - - +
834A LEU* 4.0 16.3 - - + +
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Residues in contact with GLN 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A TRP* 3.9 38.6 - - + +
803A LYS* 5.9 2.1 - - - +
804A LEU* 4.6 13.7 - - + +
805A SER 2.8 19.7 + - - +
806A ASP* 3.8 9.5 - - - +
808A ALA* 1.3 72.4 - - - +
810A SER* 1.3 57.3 + - - +
812A VAL 3.5 0.9 + - - -
813A GLU* 2.9 55.3 + - - +
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Residues in contact with SER 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ASP 2.9 19.6 + - - -
807A ASN* 3.5 7.4 - - - -
809A GLN* 1.3 77.5 - - - +
811A ALA* 1.3 57.7 + - - +
813A GLU* 3.3 11.5 + - - +
814A ILE* 2.9 38.4 + - - +
832A HIS* 2.8 20.7 + - - -
833A PRO* 5.4 1.8 - - - +
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Residues in contact with ALA 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A LEU* 3.7 11.2 - - + -
807A ASN 2.9 16.2 + - - +
808A ALA 3.2 3.1 + - - +
810A SER* 1.3 77.0 + - - +
812A VAL* 1.3 56.8 + - - +
814A ILE* 3.3 11.5 - - + +
815A LEU* 2.9 38.5 + - + +
829A LEU* 5.4 0.9 - - + -
832A HIS* 3.6 12.1 - - + +
834A LEU* 3.7 24.2 - - + -
835A PHE* 4.5 6.3 - - + -
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Residues in contact with VAL 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A GLY 3.9 6.7 - - - +
768A LEU* 3.9 26.2 - - + -
769A PHE* 3.6 36.8 - - + +
772A LEU* 4.8 5.6 - - + -
795A ILE* 4.6 1.5 - - + +
797A TRP* 3.9 18.8 - - + -
804A LEU* 5.0 1.8 - - + -
808A ALA 2.9 18.6 + - - +
811A ALA* 1.3 76.0 - - - +
813A GLU* 1.3 57.3 + - - +
815A LEU* 4.7 3.1 - - - -
816A LEU* 3.0 48.2 + - + +
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Residues in contact with GLU 813 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A ARG* 3.9 23.1 + - - +
795A ILE* 5.4 0.2 - - - -
797A TRP* 3.7 21.5 + - + -
809A GLN* 2.9 49.8 + - - +
810A SER* 3.6 12.8 - - - +
812A VAL* 1.3 75.4 - - - +
814A ILE* 1.3 67.0 + - + +
816A LEU* 3.3 13.3 + - - +
817A THR* 3.1 16.6 - - - +
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Residues in contact with ILE 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A SER* 2.9 29.7 + - - +
811A ALA* 3.3 8.7 - - - +
813A GLU* 1.3 79.7 - - + +
815A LEU* 1.3 64.2 + - + +
817A THR* 3.2 18.0 - - - +
822A LYS 6.0 0.4 - - - +
823A ARG* 3.6 1.3 - - - +
824A ALA* 3.1 41.4 + - + -
828A GLU* 4.5 11.2 - - + +
829A LEU* 4.5 9.2 - - + -
832A HIS* 3.5 29.2 - - + +
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Residues in contact with LEU 815 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ILE* 5.6 1.3 - - + -
761A TRP* 3.6 30.5 - - + +
762A TRP* 3.7 10.4 + - - -
764A LEU* 4.2 18.6 - - + -
765A GLY* 3.5 29.4 - - - +
768A LEU* 3.9 18.8 - - + -
811A ALA* 2.9 21.2 + - + +
812A VAL 4.3 0.4 - - - +
814A ILE* 1.3 79.8 - - - +
816A LEU* 1.3 59.3 + - - +
823A ARG* 3.3 25.0 - - - -
824A ALA* 3.9 17.3 - - + -
829A LEU* 4.0 26.5 - - + -
835A PHE* 5.9 0.4 - - + -
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Residues in contact with LEU 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A TRP* 3.2 60.1 - - + +
765A GLY* 3.8 12.3 - - - +
766A VAL* 3.7 11.7 - - + +
777A PRO* 4.4 9.4 - - + -
778A PHE* 4.0 14.6 - - + -
793A ARG* 3.0 28.8 + - - -
795A ILE* 3.7 20.9 - - + -
812A VAL* 3.0 36.6 + - + +
813A GLU 3.3 4.3 - - - +
815A LEU* 1.3 75.4 - - - +
817A THR* 1.3 57.2 + - - +
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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