Contacts of the helix formed by residues 859 - 874 (chain B) in PDB entry 1LD7
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 ASP 859 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B TYR* 3.2 11.2 - - - -
593B TYR* 3.5 15.5 - - + +
850B LEU 3.7 2.8 + - - +
857B SER 4.1 7.3 - - - +
858B ARG* 1.3 76.9 - - - +
860B PHE* 1.3 61.3 + - - +
861B TYR* 3.0 11.9 + - + +
862B HIS* 2.6 59.5 + - - -
863B THR* 3.0 22.1 + - - -
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Residues in contact with PHE 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B TYR* 3.5 52.7 - + - -
582B LEU* 4.1 11.8 - - + +
585B GLY* 3.7 19.3 - - - -
589B LEU* 3.6 23.6 - - + -
593B TYR* 3.1 37.4 + + + -
603B LEU* 4.1 8.7 - - + -
606B TRP* 3.6 25.3 - - + +
607B ILE* 3.6 28.0 - - + +
610B SER* 4.7 0.2 + - - -
859B ASP* 1.3 71.8 - - - +
861B TYR* 1.3 60.6 + - - +
863B THR* 3.6 4.8 - - - -
864B CYS* 2.9 30.3 + - - +
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Residues in contact with TYR 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TRP* 3.5 43.6 - + + -
799B CYS* 3.3 33.8 - - + -
803B TRP* 2.9 25.7 + - - -
859B ASP* 3.0 7.5 + - + +
860B PHE* 1.3 78.5 - - - +
862B HIS* 1.3 82.5 + + - +
864B CYS* 3.2 2.6 + - - +
865B TYR* 3.1 54.9 + + - -
1003B U66 3.6 59.4 + + - +
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Residues in contact with HIS 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ASP* 3.3 11.7 + - - -
799B CYS* 3.6 15.7 - - + -
850B LEU 3.6 4.3 - - - +
851B LEU* 3.6 21.3 - - - +
852B ASP* 3.5 25.2 + - + +
857B SER 5.2 1.2 + - - -
859B ASP* 2.6 40.5 + - - +
861B TYR* 1.3 82.6 - + - +
863B THR* 1.3 65.1 + - - +
865B TYR 4.5 0.2 - - - +
866B CYS* 2.9 30.7 + - - +
1001B ZN 2.1 36.5 - - - -
1003B U66 3.6 13.0 - + - -
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Residues in contact with THR 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 5.5 1.6 - - + -
581B TYR* 3.5 6.0 - - + -
582B LEU* 3.9 20.6 - - + -
610B SER* 3.8 12.8 - - - +
849B GLY* 3.4 11.0 - - - -
850B LEU* 2.9 37.1 + - + +
859B ASP 3.0 17.9 + - - -
860B PHE* 3.6 9.2 - - - -
861B TYR 3.2 0.2 - - - -
862B HIS* 1.3 77.0 - - - +
864B CYS* 1.3 64.5 + - - +
866B CYS* 4.2 0.5 - - - +
867B LEU* 3.1 40.4 + - + +
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Residues in contact with CYS 864 (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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605B TYR* 4.2 5.2 - - - -
606B TRP* 3.7 43.1 - - + +
609B HIS* 3.9 24.5 - - - -
610B SER* 3.3 10.9 + - - +
613B LEU* 4.2 1.4 - - - +
860B PHE 2.9 18.1 + - - +
861B TYR 3.5 4.7 - - - +
863B THR* 1.3 77.7 - - - +
865B TYR* 1.3 71.5 + - - +
867B LEU* 3.9 2.8 - - - +
868B SER* 2.7 32.5 + - - -
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Residues in contact with TYR 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TRP* 3.7 9.4 - + - -
605B TYR* 3.7 12.5 + - - -
606B TRP* 3.5 26.9 + + - -
654B TYR* 5.0 3.3 + - - -
798B GLY 4.4 2.0 - - - -
799B CYS* 3.6 23.8 - - - +
801B SER* 4.1 0.7 - - - -
802B PHE* 3.5 35.7 + + + +
803B TRP* 3.3 32.8 - + - -
861B TYR* 3.1 55.2 + + - +
862B HIS 4.6 0.2 - - - +
864B CYS* 1.3 78.6 - - - +
866B CYS* 1.3 61.1 + - - +
868B SER* 4.0 1.6 - - - -
869B GLY* 2.9 24.4 + - - -
902B ASN* 3.4 23.6 - - - -
1003B U66 5.3 0.2 - + - -
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Residues in contact with CYS 866 (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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798B GLY* 3.7 27.6 + - - -
799B CYS 4.3 0.4 - - - -
801B SER* 4.6 2.2 - - - -
839B ILE* 3.5 14.1 - - + +
843B CYS* 3.8 12.8 - - - -
850B LEU* 3.6 25.1 - - + -
851B LEU 3.2 27.8 - - - -
862B HIS 2.9 22.8 + - - +
865B TYR* 1.3 75.8 - - - +
867B LEU* 1.3 59.0 + - - +
869B GLY 3.3 0.9 + - - -
870B LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 867 (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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573B LEU* 4.1 21.5 - - + -
578B HIS* 4.9 1.8 - - + -
610B SER* 3.9 28.3 - - - +
613B LEU* 3.7 13.9 - - + -
614B LEU* 4.1 28.3 - - + -
850B LEU* 3.9 23.1 - - + -
863B THR* 3.1 28.3 + - + +
864B CYS 3.9 0.7 - - - +
865B TYR 3.3 0.2 - - - -
866B CYS* 1.3 78.3 - - - +
868B SER* 1.3 65.7 + - - +
870B LEU* 3.1 5.1 + - + -
871B SER* 3.0 21.0 + - - -
894B LEU* 3.3 22.4 - - + +
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Residues in contact with SER 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B HIS* 3.2 23.4 + - - -
613B LEU* 3.6 8.7 - - - +
802B PHE* 3.8 11.9 - - - -
864B CYS 2.7 23.5 + - - -
865B TYR* 3.7 7.6 - - - -
866B CYS 3.3 0.2 - - - -
867B LEU* 1.3 76.0 - - - +
869B GLY* 1.3 61.6 + - - +
871B SER* 3.3 5.4 + - - -
872B ILE* 3.2 25.8 + - - +
897B THR* 4.0 2.1 - - - +
902B ASN* 3.3 27.5 + - - -
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Residues in contact with GLY 869 (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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801B SER* 3.4 29.3 - - - +
802B PHE* 4.0 2.8 - - - +
835B LEU* 4.2 4.4 - - - +
839B ILE* 4.1 5.2 - - - -
865B TYR 2.9 16.9 + - - -
866B CYS 3.7 1.6 - - - -
868B SER* 1.3 76.0 - - - +
870B LEU* 1.3 64.5 + - - +
872B ILE* 3.3 5.6 + - - +
873B ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 870 (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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573B LEU* 4.1 18.6 - - + -
836B GLN* 3.6 36.3 - - + +
839B ILE* 3.6 18.5 - - + +
840B LEU* 4.0 28.7 - - + -
866B CYS 2.9 17.8 + - - +
867B LEU* 3.1 8.7 + - + +
869B GLY* 1.3 74.2 - - - +
871B SER* 1.3 57.9 + - - +
873B ALA* 3.3 3.8 + - - +
874B GLN* 3.0 52.9 + - - +
892B ASN* 4.8 0.7 - - + +
894B LEU* 3.8 15.0 - - + -
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Residues in contact with SER 871 (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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613B LEU* 4.2 8.7 - - - -
867B LEU 3.0 12.7 + - - -
868B SER 3.5 9.2 - - - -
870B LEU* 1.3 76.5 - - - +
872B ILE* 1.3 62.3 + - - +
874B GLN* 3.2 12.0 + - - -
875B HIS* 3.0 32.1 + - - +
894B LEU* 3.9 8.9 - - - +
895B GLN 2.8 27.8 + - - -
896B PRO* 3.5 12.1 - - - +
897B THR* 3.7 7.0 + - - -
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Residues in contact with ILE 872 (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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801B SER 5.2 0.7 - - - +
802B PHE* 3.6 37.7 - - + +
805B ALA* 4.2 13.0 - - + +
806B GLY* 3.8 16.4 - - - +
809B PRO* 3.8 28.9 - - + -
828B TRP* 2.9 32.6 + - + +
830B PHE* 4.4 5.6 - - + -
868B SER 3.2 9.9 + - - +
869B GLY* 3.3 8.5 + - - +
871B SER* 1.3 76.5 - - - +
873B ALA* 1.3 62.1 + - - +
874B GLN 3.3 0.2 + - - -
875B HIS* 3.2 9.3 - - - +
897B THR* 3.7 17.7 - - + +
899B PRO* 5.1 7.6 - - + -
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Residues in contact with ALA 873 (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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830B PHE* 3.9 21.8 - - + -
832B GLN* 2.9 35.0 + - - +
835B LEU* 4.1 10.5 - - + -
836B GLN* 3.1 33.0 + - + -
869B GLY 3.0 16.6 + - - +
870B LEU* 3.6 6.1 - - - +
872B ILE* 1.3 77.5 - - - +
874B GLN* 1.3 57.1 + - - +
885B VAL* 4.1 0.9 - - - +
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Residues in contact with GLN 874 (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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832B GLN* 4.7 1.3 + - - -
836B GLN* 3.7 18.2 + - - +
840B LEU* 6.2 0.4 - - - +
870B LEU* 3.0 41.7 + - + +
871B SER* 3.6 5.4 - - - +
872B ILE 3.1 0.4 - - - -
873B ALA* 1.3 79.1 - - - +
875B HIS* 1.3 73.2 + - + +
876B PHE 4.3 0.2 - - - -
883B HIS 4.1 0.5 - - - +
884B ASP* 3.3 8.7 - - - +
885B VAL* 2.9 35.6 + - - +
886B VAL* 4.0 13.9 - - + +
887B LEU 5.4 0.4 + - - -
892B ASN* 2.9 32.3 + - - +
893B ALA* 3.8 4.8 - - - +
894B LEU* 2.9 29.1 + - - +
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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
------------------------------------------------------------
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