Contacts of the helix formed by residues 829 - 844 (chain B) in PDB entry 4OL0
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 LEU 829 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B ILE* 4.0 19.7 - - + +
777B LEU* 3.7 35.4 - - + +
778B GLN* 3.7 37.0 - - + +
781B ILE* 3.9 15.0 - - + +
825B VAL* 4.2 1.3 - - + +
826B MET* 5.3 1.1 - - - -
828B GLN* 1.3 85.0 - - + +
830B GLY* 1.3 58.0 + - - +
832B GLN* 3.0 36.8 + - + +
833B LEU* 2.9 28.9 + - - +
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Residues in contact with GLY 830 (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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826B MET* 3.3 29.0 + - - -
827B ASN 5.0 0.2 + - - -
828B GLN 2.8 8.1 + - - -
829B LEU* 1.3 74.3 - - - +
831B GLN* 1.3 67.0 + - - +
833B LEU* 3.0 4.7 + - - +
834B VAL* 2.9 26.7 + - - +
871B TRP* 3.8 19.3 - - - -
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Residues in contact with GLN 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B ASN 5.9 0.2 + - - -
830B GLY* 1.3 73.5 - - - +
832B GLN* 1.3 66.5 + - - +
834B VAL* 3.2 1.4 + - - +
835B SER* 2.9 43.9 + - - +
871B TRP* 2.8 61.8 + - + +
874B ASN* 2.8 37.5 + - - +
875B SER* 3.3 12.9 + - - -
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Residues in contact with GLN 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ILE* 4.4 13.2 - - + +
828B GLN* 5.1 1.8 - - - +
829B LEU* 3.0 49.2 + - + +
831B GLN* 1.3 85.3 + - + +
833B LEU* 1.3 57.5 + - - +
835B SER* 3.8 4.9 - - - -
836B GLN* 2.8 34.1 + - - +
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Residues in contact with LEU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B LEU* 5.4 4.9 - - + -
781B ILE* 4.0 23.3 - - + +
784B THR* 5.3 0.9 - - + -
799B LEU* 3.9 38.4 - - + -
803B ILE* 4.4 8.5 - - + -
826B MET* 4.4 16.4 - - + -
829B LEU 2.9 20.9 + - - +
830B GLY 3.3 4.3 - - - +
832B GLN* 1.3 76.4 - - - +
834B VAL* 1.3 58.3 + - - +
836B GLN* 3.7 2.2 - - + +
837B LEU* 2.9 50.2 + - + +
856B VAL* 4.4 8.5 - - + -
860B ILE* 3.7 24.0 - - + -
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Residues in contact with VAL 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B GLY 2.9 18.0 + - - +
831B GLN 3.7 4.7 - - - +
833B LEU* 1.3 75.1 - - - +
835B SER* 1.3 56.9 + - - +
837B LEU* 3.2 11.2 + - - +
838B LEU* 2.9 28.0 + - + +
857B LEU* 4.4 7.2 - - + +
860B ILE* 4.1 18.8 - - + -
868B PHE* 4.1 17.5 - - + -
871B TRP* 3.9 25.8 - - + -
872B LEU* 4.1 30.3 - - + +
875B SER* 3.5 15.0 - - - +
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Residues in contact with SER 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B GLN* 2.9 31.8 + - - +
832B GLN* 3.8 4.7 - - - -
834B VAL* 1.3 72.9 - - - +
836B GLN* 1.3 59.7 + - - +
838B LEU* 3.2 2.4 + - - +
839B HIS* 2.9 41.0 + - - -
874B ASN 4.9 0.3 - - - -
875B SER* 2.8 34.0 + - - -
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Residues in contact with GLN 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ILE* 3.5 28.9 - - + +
782B ALA* 5.8 0.7 - - - -
784B THR* 3.3 19.1 - - + +
785B THR* 3.1 32.0 - - - +
832B GLN 2.8 22.0 + - - +
833B LEU* 3.7 2.5 - - + +
835B SER* 1.3 74.1 - - - +
837B LEU* 1.3 54.7 + - - +
839B HIS* 3.3 9.7 + - - +
840B THR* 2.5 52.7 + - - +
844B CYS* 5.3 1.6 - - - -
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Residues in contact with LEU 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 4.2 18.2 - - + -
796B MET* 4.2 22.2 - - + -
799B LEU* 4.6 1.8 - - + -
833B LEU* 2.9 41.2 + - + +
834B VAL* 3.5 4.0 - - - +
836B GLN* 1.3 76.7 - - - +
838B LEU* 1.3 57.1 + - - +
840B THR* 3.2 6.5 + - - +
841B CYS* 2.8 36.1 + - - -
853B VAL* 4.0 26.5 - - + -
856B VAL* 3.8 27.8 - - + -
857B LEU* 3.8 23.8 - - + -
860B ILE* 4.7 0.4 - - + -
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Residues in contact with LEU 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B VAL 2.9 13.5 + - - +
835B SER* 3.2 8.7 + - - +
837B LEU* 1.3 77.1 - - - +
839B HIS* 1.3 64.0 + - + +
841B CYS* 3.2 4.9 + - + +
842B CYS* 2.9 32.1 + - - -
857B LEU* 6.0 0.6 - - - +
872B LEU* 4.8 7.0 - - + -
875B SER* 3.8 30.3 - - - +
876B LEU* 3.7 25.4 - - + -
879B LEU* 4.3 15.5 - - + -
898B PHE* 3.8 27.1 - - + -
915B LEU* 5.0 8.5 - - + -
918B PHE* 3.9 17.3 - - + -
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Residues in contact with HIS 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B SER* 2.9 32.3 + - - +
836B GLN* 3.6 12.8 - - - +
838B LEU* 1.3 77.1 - - + +
840B THR* 1.3 58.0 + - - +
842B CYS 3.3 0.2 + - - -
843B PHE* 2.8 53.6 + + + +
844B CYS* 3.8 3.5 + - - -
875B SER 5.1 4.3 - - - -
878B GLY 3.2 26.5 + - - -
879B LEU* 3.8 13.9 - - + +
880B PRO* 3.8 19.1 - - + -
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Residues in contact with THR 840 (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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784B THR* 3.3 35.7 + - - +
785B THR* 4.2 1.3 - - - -
836B GLN* 2.5 46.7 + - - +
837B LEU* 3.5 8.6 - - - -
839B HIS* 1.3 74.2 - - - +
841B CYS* 1.3 63.7 + - - +
844B CYS* 2.9 34.7 + - + -
845B LEU* 3.0 36.6 + - + -
853B VAL* 6.3 2.2 - - + -
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Residues in contact with CYS 841 (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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837B LEU 2.8 20.3 + - - +
838B LEU* 3.6 6.5 - - + +
840B THR* 1.3 78.0 - - - +
842B CYS* 1.3 65.1 + - - +
845B LEU* 3.7 14.1 - - - +
849B THR* 5.0 4.7 - - - -
850B LEU* 3.7 28.0 - - + +
853B VAL* 3.6 40.4 - - - -
915B LEU* 4.5 13.5 - - + -
919B THR* 3.6 21.6 - - - +
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Residues in contact with CYS 842 (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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838B LEU* 2.9 27.8 + - - +
839B HIS 3.9 1.8 - - - +
841B CYS* 1.3 82.4 - - - +
843B PHE* 1.3 85.9 + - + +
879B LEU* 4.3 5.2 - - - -
918B PHE* 3.7 20.9 - - - -
919B THR* 4.8 10.5 - - - +
922B PHE* 3.5 48.6 - - + +
923B ARG 5.7 1.6 - - - -
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Residues in contact with PHE 843 (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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839B HIS* 2.8 39.0 + - + +
841B CYS 5.1 0.2 - - - -
842B CYS* 1.3 83.3 - - + +
844B CYS* 1.3 67.7 + - - +
845B LEU 5.3 0.4 - - - -
879B LEU* 3.6 29.2 - - + -
880B PRO* 3.6 40.4 - - + -
922B PHE* 3.7 27.1 - + + -
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Residues in contact with CYS 844 (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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785B THR* 4.5 29.6 - - - +
787B ASP* 5.7 1.9 - - - +
836B GLN* 5.3 1.6 - - - -
839B HIS* 4.4 4.7 - - - -
840B THR* 2.9 32.6 + - + +
843B PHE* 1.3 86.2 - - - +
845B LEU* 1.3 67.8 + - + +
846B PRO* 4.1 3.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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