Contacts of the helix formed by residues 899 - 913 (chain B) in PDB entry 3H44
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 LYS 899 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASP* 3.7 39.3 - - + +
427B LYS 4.1 9.2 - - - +
428B GLU* 6.1 1.1 - - - +
429B ARG* 3.6 37.7 - - - +
567B PHE* 3.5 14.5 - - - -
569B LEU* 6.4 1.1 - - - -
897B PRO* 4.2 0.3 - - - +
898B LYS* 1.3 77.5 - - - +
900B LEU* 1.3 66.8 + - - +
901B SER* 3.7 23.0 + - - +
902B ALA* 3.2 23.1 + - + +
903B GLU 3.4 3.6 + - - -
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Residues in contact with LEU 900 (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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426B ASP* 5.3 5.6 + - - +
564B ASP* 4.2 17.5 - - - +
567B PHE* 3.6 19.3 - - + +
569B LEU* 6.0 3.3 - - + +
571B LYS* 4.0 28.7 - - + +
572B ALA* 4.1 2.0 - - - -
573B ASN* 3.6 39.7 - - - +
730B HIS* 3.5 33.4 - - + +
731B GLY* 3.9 12.8 - - - -
899B LYS* 1.3 73.7 - - - +
901B SER* 1.3 57.2 + - - +
903B GLU* 2.9 22.0 + - - +
904B SER* 2.9 15.1 + - - +
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Residues in contact with SER 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ASP* 4.8 4.5 + - - -
573B ASN* 3.3 22.6 - - - +
632B LYS* 4.4 21.6 + - - -
899B LYS* 3.7 23.1 + - - +
900B LEU* 1.3 80.0 - - - +
902B ALA* 1.3 63.3 + - - +
904B SER* 3.8 2.1 - - - -
905B ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ARG* 4.4 16.4 - - - +
897B PRO* 4.0 16.4 - - + +
898B LYS* 4.4 3.4 - - + +
899B LYS* 3.2 27.2 + - + +
900B LEU 3.1 0.4 - - - -
901B SER* 1.3 82.5 + - - +
903B GLU* 1.3 61.5 + - - +
905B ALA* 3.5 6.1 + - - +
906B LYS* 3.3 20.6 + - - +
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Residues in contact with GLU 903 (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 LYS* 3.2 13.2 + - - -
564B ASP* 4.8 0.7 - - - +
566B LYS* 3.7 19.4 + - - +
567B PHE* 3.1 24.8 - - - -
730B HIS* 3.4 15.3 + - - +
897B PRO* 3.7 26.3 - - + +
899B LYS 3.4 4.1 + - - +
900B LEU 2.9 10.1 + - - +
902B ALA* 1.3 78.9 - - - +
904B SER* 1.3 63.2 + - - +
906B LYS* 2.9 19.2 + - + +
907B TYR* 2.7 52.1 + - + +
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Residues in contact with SER 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASN* 3.1 33.3 + - - +
575B ASN* 4.7 7.2 - - - -
632B LYS* 5.1 3.8 - - - -
728B LEU* 3.9 14.9 - - - +
730B HIS* 2.9 30.4 - - - +
900B LEU 2.9 6.1 + - - -
901B SER 3.8 3.8 - - - -
902B ALA 3.4 0.2 - - - -
903B GLU* 1.3 76.1 - - - +
905B ALA* 1.3 52.4 + - - +
907B TYR* 3.1 4.1 + - - +
908B TRP* 2.7 37.4 + - - +
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Residues in contact with ALA 905 (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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632B LYS* 5.9 0.6 - - - +
901B SER 3.0 18.0 + - - +
902B ALA* 3.7 7.2 - - - +
903B GLU 3.3 0.2 - - - -
904B SER* 1.3 73.9 - - - +
906B LYS* 1.3 57.7 + - - +
908B TRP* 3.7 6.6 - - - +
909B GLY* 2.8 30.8 + - - -
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Residues in contact with LYS 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B ARG 5.0 1.2 + - - -
895B ASP 5.5 4.2 + - - +
897B PRO* 3.9 31.2 - - + -
902B ALA 3.3 8.6 + - - +
903B GLU* 2.9 12.7 + - - +
905B ALA* 1.3 78.1 - - - +
907B TYR* 1.3 71.1 + - + +
909B GLY* 3.8 1.6 + - - -
910B GLU* 3.6 22.7 + - - +
918B PHE 5.3 6.2 + - - -
921B ASP* 2.3 34.6 + - - -
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Residues in contact with TYR 907 (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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546B PRO 3.4 19.9 + - - -
547B TYR* 3.7 19.9 - + - -
548B PRO* 3.5 40.2 - - + -
562B LYS* 3.5 12.1 + - + -
566B LYS* 4.9 1.7 + - - -
728B LEU* 3.9 15.0 - - + -
730B HIS* 4.1 17.0 - + - -
903B GLU* 2.7 49.3 + - + +
904B SER* 3.4 6.1 - - - +
906B LYS* 1.3 85.3 - - + +
908B TRP* 1.3 66.6 + - - +
910B GLU* 3.0 16.3 + - - +
911B ILE* 3.0 16.1 + - - +
918B PHE* 3.8 17.8 - + + -
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Residues in contact with TRP 908 (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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575B ASN* 3.6 28.7 - - + +
576B PHE* 3.8 8.5 - - - -
577B GLU* 3.5 38.7 + - + +
628B TYR* 3.9 30.5 - + - -
726B GLU* 4.1 4.0 - - + -
727B ALA* 4.3 2.0 - - - -
728B LEU* 3.9 28.8 - - + +
904B SER 2.7 20.1 + - - +
905B ALA* 3.7 7.6 - - - +
907B TYR* 1.3 71.6 - - - +
909B GLY* 1.3 64.9 + - - +
911B ILE* 2.7 21.9 + - + -
912B ILE* 2.7 68.2 + - + +
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Residues in contact with GLY 909 (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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905B ALA 2.8 20.3 + - - -
906B LYS* 4.1 2.5 - - - -
908B TRP* 1.3 75.8 - - - +
910B GLU* 1.3 58.0 + - - +
912B ILE* 3.7 10.9 - - - +
913B SER* 2.9 30.6 + - - -
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Residues in contact with GLU 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B LYS 3.6 15.6 + - - +
907B TYR* 3.0 8.8 + - + +
909B GLY* 1.3 73.1 - - - +
911B ILE* 1.3 59.5 + - - +
913B SER* 3.3 4.5 + - - -
914B GLN 3.9 0.3 - - - -
915B GLN* 3.1 13.5 + - - +
916B TYR* 2.8 24.3 + - - -
917B ASN 2.9 48.6 + - - +
918B PHE* 3.6 22.0 - - + -
920B ARG* 2.8 41.2 + - + +
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Residues in contact with ILE 911 (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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548B PRO* 5.5 0.2 - - + -
560B TRP* 3.6 28.0 - - + -
726B GLU* 3.8 35.4 - - + +
727B ALA 4.7 0.2 - - - +
728B LEU* 3.9 31.4 - - + -
765B ARG* 5.1 0.2 + - - -
907B TYR 3.0 13.4 + - - +
908B TRP* 2.7 29.1 + - + +
910B GLU* 1.3 68.9 - - - +
912B ILE* 1.3 69.2 + - + +
913B SER 3.0 1.1 - - - -
914B GLN* 2.8 18.4 + - - -
916B TYR* 4.1 15.6 + - + -
918B PHE* 4.0 20.2 - - + -
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Residues in contact with ILE 912 (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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577B GLU* 4.1 18.8 - - + +
579B PHE* 6.5 1.3 - - - -
625B TYR* 5.8 0.5 - - - -
726B GLU* 6.0 0.4 - - - -
765B ARG* 3.0 29.6 + - - +
908B TRP* 2.7 89.5 + - + +
909B GLY* 3.7 16.2 - - - +
911B ILE* 1.3 72.9 - - + +
913B SER* 1.3 57.3 + - - +
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Residues in contact with SER 913 (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 ARG* 5.7 0.6 - - - -
909B GLY 2.9 22.2 + - - -
910B GLU* 3.3 8.8 + - - -
911B ILE 3.0 1.0 + - - -
912B ILE* 1.3 81.3 - - - +
914B GLN* 1.3 67.6 + - - +
915B GLN* 3.3 33.7 + - - +
1008B VAL* 5.8 1.7 - - - +
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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