Contacts of the helix formed by residues 852 - 868 (chain B) in PDB entry 3U44
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 THR 852 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850B ASP 4.4 5.6 - - - +
851B LEU* 1.3 78.5 - - - +
853B LYS* 1.3 56.7 + - - +
854B GLU* 2.8 38.4 + - - +
855B GLN* 3.0 20.3 + - - +
856B CYS* 2.7 37.0 + - - -
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Residues in contact with LYS 853 (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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852B THR* 1.3 73.3 - - - +
854B GLU* 1.3 62.0 + - - +
856B CYS* 3.8 9.3 + - - +
857B GLU* 3.6 19.8 + - - +
894B THR* 5.3 1.6 - - - +
902B GLU* 5.6 6.1 - - - -
1028B GLU* 3.9 28.1 + - - +
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Residues in contact with GLU 854 (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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852B THR* 2.8 24.9 + - - +
853B LYS* 1.3 81.0 - - - +
855B GLN* 1.3 84.8 + - + +
857B GLU* 3.5 7.7 + - - +
858B LEU* 3.4 18.1 + - - +
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Residues in contact with GLN 855 (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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844B GLU* 5.2 1.8 + - - -
846B LEU* 4.1 12.3 - - - +
850B ASP 3.9 5.9 - - - +
851B LEU* 3.2 20.2 - - + +
852B THR* 3.0 27.5 + - - +
854B GLU* 1.3 89.2 + - + +
856B CYS* 1.3 66.5 + - - +
857B GLU 3.1 2.4 + - - -
858B LEU* 3.1 10.3 + - + -
859B PHE* 2.8 61.4 + - + -
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Residues in contact with CYS 856 (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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851B LEU* 4.1 16.4 - - - +
852B THR 2.7 32.4 + - - +
853B LYS* 3.9 10.1 - - - +
855B GLN* 1.3 71.2 - - - +
857B GLU* 1.3 60.9 + - - +
859B PHE* 4.1 2.1 - - - +
860B SER* 2.8 33.0 + - - -
894B THR* 3.9 18.8 - - + +
897B SER* 4.0 10.7 - - - -
898B GLY* 3.6 28.7 - - - -
901B SER* 4.1 11.4 - - - -
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Residues in contact with GLU 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B LYS 3.6 8.5 + - - +
854B GLU* 3.5 11.8 + - - +
855B GLN 3.1 0.6 - - - -
856B CYS* 1.3 76.5 - - - +
858B LEU* 1.3 68.5 + - - +
860B SER* 3.1 2.6 + - - -
861B TYR* 3.0 60.7 + - + -
894B THR* 3.5 21.0 - - + +
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Residues in contact with LEU 858 (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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840B ARG* 5.2 3.1 - - - +
854B GLU 3.4 9.2 + - - +
855B GLN* 3.1 12.2 + - + +
857B GLU* 1.3 81.5 - - - +
859B PHE* 1.3 83.6 + - + +
860B SER 3.1 0.3 + - - -
861B TYR* 3.1 12.9 + - + +
862B ASP* 3.2 43.1 + - - +
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Residues in contact with PHE 859 (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 ILE* 3.1 29.5 - - + +
840B ARG* 3.0 53.0 - - - +
841B LEU* 4.5 10.3 - - + -
844B GLU* 3.7 22.2 - - - -
846B LEU* 5.1 1.8 - - + -
851B LEU* 3.1 41.3 - - + -
855B GLN* 2.8 50.5 + - + +
856B CYS* 4.1 2.7 - - - +
858B LEU* 1.3 86.0 - - + +
860B SER* 1.3 63.1 + - - +
862B ASP* 3.8 2.9 + - - +
863B ALA* 3.5 10.4 + - - +
897B SER* 6.0 0.9 - - - +
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Residues in contact with SER 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B ILE* 4.0 8.4 - - - +
856B CYS 2.8 19.7 + - - -
857B GLU 3.5 2.9 - - - -
859B PHE* 1.3 73.7 - - - +
861B TYR* 1.3 67.9 + - - +
863B ALA* 3.0 19.2 + - - +
864B VAL* 3.4 6.1 + - - +
890B GLN* 4.5 1.3 - - - -
893B VAL* 3.3 28.5 + - - +
894B THR* 3.3 16.3 - - - -
897B SER* 2.7 27.5 + - - -
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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
----------------------------------------------------------
857B GLU* 3.0 47.3 + - + +
858B LEU* 3.7 8.7 - - + +
860B SER* 1.3 76.4 - - - +
862B ASP* 1.3 66.7 + - - +
864B VAL* 2.8 28.7 - - - +
865B GLU* 3.1 11.2 + - + +
887B GLU* 4.3 7.9 + - + -
890B GLN* 2.9 44.6 - - + +
891B LYS* 3.5 24.7 - - - +
894B THR* 3.1 23.6 - - - -
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Residues in contact with ASP 862 (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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840B ARG* 3.6 17.7 + - - +
858B LEU* 3.2 36.1 + - - +
859B PHE 4.1 0.9 - - - +
861B TYR* 1.3 77.2 - - - +
863B ALA* 1.3 63.2 + - - +
865B GLU* 3.0 22.5 + - - +
866B ARG* 3.1 38.9 + - - +
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Residues in contact with ALA 863 (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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833B SER* 4.2 20.9 - - - +
836B LEU* 3.7 7.0 - - + +
837B ILE* 3.6 26.9 - - + -
859B PHE 3.5 2.2 + - - +
860B SER 3.0 15.3 + - - +
861B TYR 3.0 0.2 + - - -
862B ASP* 1.3 79.8 - - - +
864B VAL* 1.3 58.4 + - - +
866B ARG* 3.4 18.2 + - - +
867B LEU* 3.2 28.1 + - - +
893B VAL* 5.6 0.7 - - + -
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Residues in contact with VAL 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829B LEU* 4.7 17.5 - - + -
833B SER* 5.0 3.6 + - - +
860B SER 3.4 3.7 + - - +
861B TYR* 2.8 25.5 + - - +
863B ALA* 1.3 77.4 - - - +
865B GLU* 1.3 58.9 + - - +
867B LEU* 4.2 7.9 - - - -
868B ALA* 2.6 50.1 + - + +
876B LEU* 4.8 4.9 - - + -
886B LYS* 4.5 12.1 - - + +
889B LEU* 5.1 4.0 - - + -
890B GLN* 3.1 46.0 - - + +
893B VAL* 6.0 3.8 - - + -
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Residues in contact with GLU 865 (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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861B TYR* 3.1 18.0 + - + +
862B ASP* 3.1 19.7 - - - +
864B VAL* 1.3 76.4 - - - +
866B ARG* 1.3 64.9 + - + +
869B PRO* 2.9 24.0 - - - +
886B LYS* 2.9 29.3 + - - +
890B GLN* 3.2 21.1 + - - -
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Residues in contact with ARG 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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836B LEU* 3.1 45.2 - - + +
840B ARG* 2.7 46.2 - - - +
859B PHE 4.7 0.2 + - - -
862B ASP* 3.1 22.0 + - - +
863B ALA* 3.6 21.2 - - - +
865B GLU* 1.3 77.5 - - + +
867B LEU* 1.3 62.5 + - + +
869B PRO* 3.9 8.5 - - - +
870B LYS* 4.3 15.1 - - - +
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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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829B LEU* 4.1 18.6 - - + +
832B SER* 3.9 21.8 - - - +
833B SER* 3.0 45.1 - - - +
836B LEU* 4.2 12.8 - - + -
863B ALA 3.2 19.2 + - - +
864B VAL* 3.1 3.1 + - - +
865B GLU 3.1 0.6 - - - -
866B ARG* 1.3 76.1 - - - +
868B ALA* 1.3 68.6 + - - +
869B PRO* 3.2 3.8 - - - -
870B LYS* 2.7 26.3 + - + +
871B LEU* 3.5 6.6 + - + +
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Residues in contact with ALA 868 (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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829B LEU* 5.3 1.8 - - - -
864B VAL* 2.6 29.7 + - + +
865B GLU 4.4 0.4 - - - +
867B LEU* 1.3 71.5 - - - +
869B PRO* 1.3 67.7 - - + +
871B LEU* 3.1 24.1 + - - +
874B GLU* 4.7 1.4 - - - -
876B LEU* 3.5 41.3 - - + +
877B LEU* 5.1 4.7 - - + -
886B LYS* 4.5 15.9 - - + +
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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