Contacts of the helix formed by residues 831 - 843 (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 HIS 831 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A THR 3.7 18.6 - - - -
351A ILE* 3.4 24.4 + - + +
353A LYS* 3.3 37.1 + - - +
524B TYR* 3.5 40.7 - + + -
527B ARG* 6.0 0.6 + - - -
781B GLN* 2.8 30.7 + - - +
830B PHE* 1.3 71.3 - - - +
832B GLN* 1.3 66.2 + - - +
833B GLN* 3.6 19.6 + - + -
834B ALA* 2.9 31.7 + - + +
835B LEU 3.1 8.8 + - - -
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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
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353A LYS* 5.0 2.6 - - - +
826B SER 5.2 0.2 + - - -
827B HIS* 3.3 24.9 - - + +
828B TRP* 2.9 41.7 + - + +
830B PHE* 3.0 37.9 + - + +
831B HIS* 1.3 72.9 + - - +
833B GLN* 1.3 62.1 + - - +
835B LEU 3.5 0.3 + - - -
836B GLN* 3.2 31.7 + - - +
873B ALA* 2.9 33.2 + - - +
874B GLN 4.7 4.4 - - - -
876B PHE* 4.8 9.3 - - - +
883B HIS 5.3 0.6 + - - -
885B VAL* 4.5 19.4 - - + +
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Residues in contact with GLN 833 (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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353A LYS* 5.9 0.2 - - - +
522B PRO 3.8 14.8 + - - -
523B LEU* 3.9 0.2 - - - +
524B TYR* 3.4 18.9 - - - +
527B ARG* 4.9 8.6 + - - +
831B HIS* 3.3 16.8 + - + -
832B GLN* 1.3 76.5 - - - +
834B ALA* 1.3 66.2 + - - +
836B GLN* 3.0 12.4 + - - +
837B GLU* 2.7 48.8 + - - +
885B VAL* 5.4 11.3 - - + +
887B LEU* 4.3 22.7 - - + +
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Residues in contact with ALA 834 (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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351A ILE* 3.7 20.4 - - + -
524B TYR* 3.8 17.0 - - + -
525B SER* 4.9 1.5 + - - +
781B GLN* 4.1 0.4 - - - +
785B GLU 4.6 0.2 - - - +
786B GLY* 3.8 14.5 - - - +
831B HIS* 2.9 30.9 + - + +
833B GLN* 1.3 75.5 - - - +
835B LEU* 1.3 63.5 + - - +
837B GLU* 3.1 10.4 + - - +
838B TYR* 2.9 23.4 + - - +
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Residues in contact with LEU 835 (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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781B GLN* 4.0 5.4 - - - +
786B GLY 3.5 6.6 + - - +
787B GLY* 3.8 24.0 - - - -
788B PHE* 4.0 9.2 - - + -
801B SER* 3.5 31.4 - - - +
805B ALA* 3.7 20.6 - - + -
830B PHE* 3.7 22.0 - - + -
831B HIS 3.1 16.9 + - - +
832B GLN 3.8 4.0 - - - +
834B ALA* 1.3 75.4 - - - +
836B GLN* 1.3 63.9 + - - +
838B TYR* 3.3 1.4 + - + -
839B ILE* 3.0 37.5 + - + +
869B GLY 4.2 5.4 - - - +
873B ALA* 4.1 12.8 - - + -
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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
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832B GLN 3.2 13.2 + - - +
833B GLN* 3.0 8.7 + - - +
835B LEU* 1.3 76.9 - - - +
837B GLU* 1.3 57.9 + - - +
839B ILE* 3.9 0.6 - - - +
840B LEU* 2.9 38.7 + - + +
870B LEU* 3.6 25.5 - - + +
873B ALA* 3.1 31.2 + - + -
874B GLN* 3.7 15.4 + - - +
885B VAL* 2.8 32.0 + - - +
887B LEU* 3.0 41.2 + - + +
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Residues in contact with GLU 837 (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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523B LEU* 3.5 13.0 - - + +
524B TYR* 2.8 15.9 + - - +
525B SER* 2.5 46.5 + - - +
559B PHE* 4.9 0.7 - - - -
571B LEU* 4.3 3.4 - - + -
833B GLN* 2.7 46.8 + - - +
834B ALA* 3.1 7.8 + - - +
836B GLN* 1.3 77.8 - - - +
838B TYR* 1.3 61.4 + - - +
841B MET* 3.0 47.8 + - + +
887B LEU* 3.4 20.4 - - + -
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Residues in contact with TYR 838 (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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555B ILE* 4.1 12.3 - - + -
559B PHE* 4.9 1.3 - - - -
785B GLU* 3.4 33.1 + - + +
787B GLY* 3.7 23.8 - - - +
796B VAL* 3.5 29.6 - - + +
797B ASP 4.4 0.7 - - - -
798B GLY* 3.9 13.9 + - - -
801B SER* 4.9 0.4 - - - -
834B ALA 2.9 8.8 + - - +
835B LEU* 3.7 7.6 - - + +
837B GLU* 1.3 76.2 - - - +
839B ILE* 1.3 64.8 + - + +
842B CYS* 2.8 56.7 + - + +
843B CYS* 3.1 24.8 + - - -
852B ASP 2.9 18.9 + - - -
853B LYS* 3.4 17.5 - - - +
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Residues in contact with ILE 839 (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* 3.5 29.4 - - - +
835B LEU* 3.0 27.3 + - + +
836B GLN* 3.9 3.6 - - - +
838B TYR* 1.3 77.8 - - + +
840B LEU* 1.3 62.4 + - + +
843B CYS* 3.0 35.6 + - + +
844B GLN* 3.8 5.2 + - - +
850B LEU* 4.1 20.0 - - + -
866B CYS* 3.5 32.1 - - + +
870B LEU* 3.6 37.0 - - + +
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Residues in contact with LEU 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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562B TYR* 4.3 5.9 + - - -
571B LEU* 3.9 37.2 - - + -
572B VAL 4.6 1.1 - - - +
573B LEU* 3.9 34.8 - - + +
836B GLN* 2.9 32.9 + - + +
839B ILE* 1.3 76.6 - - + +
841B MET* 1.3 59.7 + - - +
844B GLN* 2.8 34.2 - - - +
870B LEU* 4.0 24.5 - - + -
874B GLN* 6.2 0.2 - - - +
887B LEU* 4.1 13.2 - - + +
892B ASN* 4.1 14.6 - - + +
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Residues in contact with MET 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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523B LEU* 3.8 22.9 - - + -
525B SER* 4.3 3.4 - - - -
526B LEU* 4.8 2.7 - - + -
558B VAL* 3.2 15.7 - - + +
559B PHE* 3.8 28.0 - - + +
562B TYR* 3.4 54.8 + - + -
571B LEU* 3.6 22.2 - - + -
837B GLU* 3.0 51.1 + - + +
840B LEU* 1.3 76.5 - - - +
842B CYS* 1.3 67.6 + - - +
844B GLN 5.2 1.5 + - - -
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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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555B ILE* 4.0 14.8 - - - -
558B VAL* 3.9 14.4 - - - -
559B PHE* 3.8 28.3 - - - -
838B TYR* 2.8 42.3 + - + +
841B MET* 1.3 78.7 - - - +
843B CYS* 1.3 58.4 + - - +
844B GLN 3.7 2.9 + - - +
851B LEU* 3.6 6.4 - - - +
854B PRO* 3.4 38.4 - - + +
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Residues in contact with CYS 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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798B GLY* 3.9 6.5 - - - -
838B TYR* 3.1 48.2 - - - -
839B ILE* 3.0 21.7 + - + +
842B CYS* 1.3 78.5 - - - +
844B GLN* 1.3 60.4 + - - +
850B LEU* 3.0 7.9 - - + +
851B LEU* 2.7 56.3 + - - +
852B ASP 3.9 3.1 - - - -
866B CYS* 3.8 10.8 - - - -
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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