Contacts of the helix formed by residues 805 - 816 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.2 35.6 + - - -
803B LYS* 3.8 2.4 + - - +
804B LEU* 1.3 74.4 - - - +
806B ASP* 1.3 67.2 + - - +
807B ASN* 4.2 4.9 + - - -
808B ALA* 3.0 19.3 + - - +
809B GLN* 3.0 11.4 + - - +
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Residues in contact with ASP 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B LYS* 3.5 22.7 + - - -
804B LEU 4.2 0.4 - - - +
805B SER* 1.3 74.4 - - - +
807B ASN* 1.3 57.3 + - - +
809B GLN* 4.0 9.7 + - - +
810B SER* 2.9 29.5 + - - -
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Residues in contact with ASN 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 4.7 4.3 + - - +
805B SER* 3.1 7.2 - - - +
806B ASP* 1.3 78.6 - - - +
808B ALA* 1.3 63.4 + - - +
810B SER* 3.1 8.7 + - - -
811B ALA* 3.0 19.9 + - - +
832B HIS* 3.4 6.3 - - - -
833B PRO* 3.2 40.6 + - - +
834B LEU* 3.6 22.3 - - + +
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Residues in contact with ALA 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 4.1 7.6 - - + +
772B LEU* 3.7 28.7 - - + -
804B LEU* 4.3 9.0 - - + -
805B SER* 3.0 21.2 + - - +
807B ASN* 1.3 78.0 - - - +
809B GLN* 1.3 63.4 + - - +
811B ALA* 3.1 3.3 + - - +
812B VAL* 2.9 29.7 + - - +
834B LEU* 3.8 16.7 - - + +
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Residues in contact with GLN 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B TRP* 3.6 57.6 + - + +
798B PRO 5.2 1.2 + - - -
803B LYS* 4.1 21.4 - - - +
804B LEU* 3.6 30.4 + - + +
805B SER 3.0 11.5 + - - +
806B ASP* 4.0 9.5 + - - +
808B ALA* 1.3 74.3 - - - +
810B SER* 1.3 62.8 + - - +
812B VAL* 3.9 0.5 - - - +
813B GLU* 2.9 40.4 + - - +
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Residues in contact with SER 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B ASP 2.9 19.6 + - - -
807B ASN* 3.1 8.3 + - - -
809B GLN* 1.3 78.1 - - - +
811B ALA* 1.3 63.3 + - - +
813B GLU* 3.3 8.8 + - - +
814B ILE* 2.9 33.0 + - - +
832B HIS* 2.6 25.8 + - - -
833B PRO* 5.3 2.6 - - - +
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Residues in contact with ALA 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B LEU* 3.9 9.2 - - + -
807B ASN 3.0 5.9 + - - -
808B ALA 3.1 2.4 + - - +
810B SER* 1.3 75.8 - - - +
812B VAL* 1.3 64.4 + - - +
814B ILE* 3.1 12.1 - - + +
815B LEU* 3.0 28.9 + - + +
832B HIS* 3.4 16.1 - - + +
834B LEU* 3.6 31.9 - - + -
835B PHE* 4.1 11.2 - - + -
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Residues in contact with VAL 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B GLY 3.8 10.1 - - - +
768B LEU* 3.8 26.2 - - + -
769B PHE* 4.0 22.0 - - + +
772B LEU* 4.5 6.3 - - + -
795B ILE* 4.8 0.2 - - + -
797B TRP* 3.7 28.3 - - + -
804B LEU* 5.3 0.2 - - + -
808B ALA 2.9 23.7 + - - +
811B ALA* 1.3 74.8 - - - +
813B GLU* 1.3 53.0 + - - +
815B LEU* 3.3 4.4 + - - +
816B LEU* 2.7 57.3 + - + +
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Residues in contact with GLU 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793B ARG* 3.7 14.5 + - - +
795B ILE* 5.5 0.2 - - - -
797B TRP* 3.6 27.2 + - + -
809B GLN* 2.9 32.5 + - - +
810B SER* 3.7 8.4 - - - +
812B VAL* 1.3 77.4 - - - +
814B ILE* 1.3 61.4 + - + +
815B LEU 3.1 1.0 + - - -
816B LEU* 3.2 15.7 + - - +
817B THR* 2.8 18.0 + - - -
902B EDO 3.8 12.5 + - - -
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Residues in contact with ILE 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B SER* 2.9 21.3 + - - +
811B ALA* 3.1 17.3 - - - +
813B GLU* 1.3 76.0 - - + +
815B LEU* 1.3 59.7 + - + +
817B THR* 3.4 11.8 + - - -
822B LYS 4.8 0.8 - - - +
823B ARG* 3.7 0.7 - - - +
824B ALA* 2.8 47.1 + - + -
828B GLU* 4.4 12.3 - - + +
829B LEU* 4.6 9.6 - - + -
832B HIS* 3.4 31.0 - - + +
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Residues in contact with LEU 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 5.5 2.0 - - + -
761B TRP* 3.3 50.3 - - + +
762B TRP* 3.9 9.2 - - - -
764B LEU* 4.3 11.7 - - + -
765B GLY* 3.6 28.0 - - - +
768B LEU* 4.7 12.6 - - + -
811B ALA* 3.0 22.0 + - + +
812B VAL 3.8 0.2 - - - +
814B ILE* 1.3 80.8 - - + +
816B LEU* 1.3 59.6 + - - +
817B THR 3.2 6.4 + - - -
823B ARG* 3.3 21.9 + - - +
824B ALA* 4.1 8.1 - - + +
829B LEU* 3.7 28.7 - - + -
835B PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B TRP* 3.3 53.2 - - + +
765B GLY* 3.5 20.2 - - - +
766B VAL* 3.6 7.6 - - + +
777B PRO* 4.1 14.1 - - + -
778B PHE* 4.0 15.0 - - + -
793B ARG* 3.4 24.9 + - + +
795B ILE* 3.8 22.4 - - + -
812B VAL* 2.7 40.9 + - + +
813B GLU 3.3 9.1 - - - +
815B LEU* 1.3 69.2 - - - +
817B THR* 1.3 57.7 + - - +
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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