Contacts of the helix formed by residues 806 - 818 (chain B) in PDB entry 1LD8
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 GLY 806 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753B PHE* 4.6 8.1 - - - -
801B SER 4.1 0.6 + - - -
802B PHE* 2.7 30.7 + - - -
805B ALA* 1.3 72.2 - - - +
807B LEU* 1.3 56.8 + - - +
808B LEU 3.2 0.2 - - - -
809B PRO* 3.1 16.1 - - - +
810B LEU* 3.5 18.0 + - - +
872B ILE* 3.7 22.4 - - - +
899B PRO* 4.3 4.1 - - - +
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Residues in contact with LEU 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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752B THR* 3.4 36.1 - - + +
753B PHE* 3.5 25.6 - - + -
756B LEU* 3.9 21.5 - - + -
773B LEU* 4.6 2.0 - - + -
777B VAL* 3.6 23.1 - - + -
803B TRP 3.5 12.7 + - - +
804B GLN* 2.9 33.6 + - - +
806B GLY* 1.3 77.9 - - - +
808B LEU* 1.3 58.3 + - - +
810B LEU* 3.3 8.8 + - + +
811B LEU* 2.8 36.1 + - + +
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Residues in contact with LEU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B LEU* 3.9 20.2 - - + -
777B VAL* 4.5 15.0 - - + -
778B THR* 4.0 6.7 - - + -
788B PHE* 4.5 3.4 - - + -
804B GLN 4.3 3.8 - - - +
805B ALA* 3.1 15.9 + - - +
807B LEU* 1.3 76.7 - - - +
809B PRO* 1.3 67.9 - - + +
811B LEU* 3.8 3.2 - - + +
812B HIS* 2.8 29.5 + - - +
828B TRP* 4.2 9.7 - - + -
829B MET* 3.3 39.8 + - + +
830B PHE* 3.3 41.3 - - + -
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Residues in contact with PRO 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B ALA 3.1 12.1 - - - +
806B GLY* 3.1 14.4 - - - +
808B LEU* 1.3 92.5 - - + +
810B LEU* 1.3 56.2 + - - +
812B HIS* 3.4 2.6 + - - +
813B ARG* 3.0 29.1 + - - +
828B TRP* 3.5 47.0 - - + -
872B ILE* 3.8 18.2 - - + -
899B PRO* 3.9 25.2 - - + +
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Residues in contact with LEU 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B PHE* 4.0 20.9 - - + -
756B LEU* 3.7 21.8 - - + -
757B ALA* 3.9 28.5 - - + +
760B VAL* 4.3 16.9 - - + +
806B GLY 3.5 16.2 - - - +
807B LEU* 3.3 10.3 + - + +
808B LEU 3.2 0.2 - - - -
809B PRO* 1.3 79.3 - - - +
811B LEU* 1.3 56.8 + - - +
813B ARG* 3.4 7.5 + - + +
814B ALA* 3.0 27.5 + - - +
899B PRO* 3.8 20.0 - - + +
900B VAL* 3.6 30.1 - - + -
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Residues in contact with LEU 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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756B LEU* 3.8 18.4 - - + -
770B LEU* 4.0 36.6 - - + +
773B LEU* 4.1 13.9 - - + -
774B LEU* 3.6 42.8 - - + -
777B VAL* 3.9 15.9 - - + -
807B LEU 2.8 22.5 + - - +
808B LEU* 3.8 6.1 - - + +
810B LEU* 1.3 73.6 - - - +
812B HIS* 1.3 60.1 + - - +
814B ALA* 3.2 3.3 + - + +
815B LEU* 2.8 44.6 + - + +
829B MET* 5.2 1.8 - - + -
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Residues in contact with HIS 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LEU 2.8 19.0 + - - +
809B PRO 3.5 5.8 - - - +
810B LEU 3.3 0.2 - - - -
811B LEU* 1.3 77.5 - - - +
813B ARG* 1.3 58.9 + - - +
816B HIS* 2.8 35.8 + - + +
823B LEU* 3.4 38.2 - - + +
824B SER 3.0 29.8 + - - -
827B HIS 4.6 4.7 + - - -
828B TRP* 3.7 20.9 - + + -
829B MET* 5.2 8.5 + - + +
876B PHE* 3.7 13.3 - + - -
877B GLY 5.1 0.4 - - - -
878B SER* 3.1 37.1 + - - -
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Residues in contact with ARG 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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760B VAL* 5.5 11.9 - - + -
765B GLU* 5.5 3.4 - - - +
809B PRO 3.0 17.0 + - - +
810B LEU* 3.6 8.1 - - + +
812B HIS* 1.3 78.3 - - - +
814B ALA* 1.3 58.5 + - - +
816B HIS* 3.3 15.4 + - - +
817B ALA* 3.0 31.0 + - + +
877B GLY 4.9 9.8 + - - -
878B SER* 5.8 2.8 - - - +
879B GLY 5.5 7.5 - - - +
899B PRO* 6.1 3.6 - - - +
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Residues in contact with ALA 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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756B LEU* 5.5 1.6 - - + -
760B VAL* 6.2 0.2 - - - +
765B GLU* 4.1 32.8 - - + +
770B LEU* 4.0 22.7 - - + -
810B LEU 3.0 19.2 + - - +
811B LEU* 3.6 7.9 - - + +
813B ARG* 1.3 77.2 - - - +
815B LEU* 1.3 61.4 + - - +
817B ALA* 3.3 11.5 + - - +
818B GLN* 3.1 21.7 + - - +
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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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358A TYR* 3.8 21.1 - - + +
770B LEU* 4.0 26.2 - - + +
774B LEU* 4.5 9.6 - - + -
811B LEU* 2.8 28.3 + - + +
814B ALA* 1.3 70.9 - - - +
816B HIS* 1.3 66.0 + - - +
818B GLN* 3.0 31.6 + - - +
820B ASP* 3.2 31.4 + - + +
823B LEU* 3.8 26.0 - - + -
829B MET* 4.1 14.8 - - + -
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Residues in contact with HIS 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B HIS* 2.8 24.6 + - + +
813B ARG* 3.6 16.6 - - - +
815B LEU* 1.3 76.7 - - - +
817B ALA* 1.3 63.5 + - - +
819B GLY* 3.1 14.1 + - - +
820B ASP 4.6 3.8 + - - +
823B LEU* 3.3 16.7 - - + +
878B SER* 4.2 19.1 + - - -
879B GLY* 5.2 11.6 + - - -
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Residues in contact with ALA 817 (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 GLU* 5.4 5.2 - - - +
766B ARG* 5.4 0.2 + - - -
813B ARG* 3.0 17.8 + - + +
814B ALA* 3.5 9.9 - - - +
815B LEU 3.2 0.4 - - - -
816B HIS* 1.3 79.9 - - - +
818B GLN* 1.3 60.3 + - + +
819B GLY 3.2 0.8 + - - -
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Residues in contact with GLN 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B ARG* 3.1 61.8 + - - +
770B LEU* 3.8 19.1 - - - +
814B ALA 3.1 17.8 + - - +
815B LEU* 3.0 22.9 + - - +
817B ALA* 1.3 78.3 - - + +
819B GLY* 1.3 61.0 + - - +
820B ASP* 3.5 2.2 - - + +
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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