Contacts of the helix formed by residues 908 - 924 (chain B) in PDB entry 4DQL
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 VAL 908 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B THR* 5.2 0.2 - - + -
903B GLY 3.1 10.7 + - - +
905B GLY 3.1 17.6 + - - +
906B THR* 3.0 1.2 - - - -
907B GLY* 1.3 76.0 - - - +
909B ALA* 1.3 72.2 + - - +
910B PRO 3.4 0.4 - - - -
911B PHE* 2.8 21.0 + - + -
912B ARG* 3.1 13.1 + - + +
933B LEU* 4.1 24.2 - - + -
935B PHE* 3.8 20.9 - - + -
945B LEU* 4.1 13.9 - - + +
946B TYR* 4.0 28.0 - - + -
950B LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B SER* 3.8 25.1 - - - +
833B SER* 3.2 26.8 - - - -
846B THR* 4.0 18.4 - - - -
906B THR 3.0 16.1 + - - +
907B GLY 3.1 1.4 - - - -
908B VAL* 1.3 84.5 - - - +
910B PRO* 1.3 70.5 - - + +
911B PHE 3.2 0.2 + - - -
912B ARG* 3.2 8.4 + - - +
946B TYR* 5.5 0.2 - - - -
1101B FAD 4.0 6.7 - - - +
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Residues in contact with PRO 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLU* 5.6 0.9 - - - +
698B GLY* 5.3 7.8 + - - +
831B SER* 4.0 9.9 - - - +
832B ILE 3.8 15.0 - - - +
889B PHE* 3.9 25.8 - - + -
906B THR 4.6 0.2 - - - +
907B GLY* 3.4 12.8 - - - +
909B ALA* 1.3 94.5 - - + +
911B PHE* 1.3 59.8 + - + +
913B GLY* 3.0 17.8 + - - -
914B PHE* 3.1 17.9 + - + -
1000B CYS* 3.7 23.6 - - + -
1045B ASP* 3.8 14.1 - - - +
1047B TRP* 5.6 1.1 - - + -
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Residues in contact with PHE 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B PHE* 3.8 20.4 - + - -
901B MET* 3.6 31.2 - - + -
902B VAL 3.5 26.5 - - - -
903B GLY* 4.0 2.5 - - - -
907B GLY 3.5 23.1 - - - -
908B VAL* 2.8 10.4 + - + +
910B PRO* 1.3 76.0 - - - +
912B ARG* 1.3 59.6 + - - +
914B PHE* 3.1 13.9 + + - +
915B VAL* 2.8 33.5 + - + +
933B LEU* 3.9 27.6 - - + -
950B LEU* 5.9 0.2 - - - -
998B TYR* 3.4 41.5 - + + -
1000B CYS* 3.8 6.3 - - + -
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Residues in contact with ARG 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B HIS* 3.6 13.7 + - - -
686B GLU* 4.5 4.2 + - - -
833B SER* 2.8 36.9 + - - +
834B SER* 4.2 2.4 - - - -
844B SER* 3.0 18.6 + - - -
908B VAL* 3.1 12.3 + - + +
909B ALA* 3.2 8.5 + - - +
911B PHE* 1.3 76.5 - - - +
913B GLY* 1.3 57.6 - - - +
915B VAL* 3.4 7.8 + - + +
916B GLN* 3.0 54.9 + - + +
946B TYR* 3.5 35.3 - - + -
949B GLU* 2.7 41.2 + - - +
950B LEU* 5.4 7.4 - - + -
1104B PG4 3.6 17.0 - - - -
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Residues in contact with GLY 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLU* 4.1 10.7 - - - +
832B ILE 5.1 0.9 - - - -
833B SER* 3.7 4.0 + - - -
834B SER* 3.7 29.4 - - - -
835B SER* 3.5 9.6 - - - -
909B ALA 3.7 0.8 + - - -
910B PRO 3.0 10.7 + - - -
912B ARG* 1.3 76.4 - - - +
914B PHE* 1.3 64.9 + - - +
916B GLN 3.3 1.6 + - - -
917B ALA* 3.0 20.1 + - - +
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Residues in contact with PHE 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLU* 4.2 15.7 - - + -
698B GLY 4.8 1.6 - - - -
889B PHE* 3.8 38.1 - + - -
890B THR* 3.8 15.9 - - - -
891B LEU* 3.6 32.2 - - + +
901B MET* 3.8 22.9 - - - -
910B PRO 3.1 17.1 + - - -
911B PHE* 3.1 19.9 + + - +
913B GLY* 1.3 76.9 - - - +
915B VAL* 1.3 56.6 + - + +
917B ALA* 3.3 3.4 + - - +
918B ARG* 2.9 35.6 + - - +
998B TYR* 3.6 39.3 - + - -
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Residues in contact with VAL 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B MET* 5.5 3.6 - - + -
911B PHE* 2.8 22.2 + - + +
912B ARG* 3.8 7.9 - - + +
914B PHE* 1.3 73.9 - - + +
916B GLN* 1.3 67.2 + - + +
918B ARG* 3.2 3.0 + - - +
919B LYS* 2.9 26.5 + - + +
933B LEU* 5.1 3.6 - - + -
949B GLU* 5.0 4.5 - - + +
950B LEU* 4.2 21.8 - - + -
953B ALA* 3.5 31.0 - - + -
958B ILE* 4.0 9.3 - - + +
959B ILE* 3.7 26.2 - - + -
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Residues in contact with GLN 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B SER* 3.3 10.4 - - - -
835B SER* 2.9 29.8 + - - +
838B VAL* 4.0 23.5 - - + +
912B ARG* 3.0 55.5 + - + +
913B GLY 3.6 6.7 - - - +
915B VAL* 1.3 77.8 - - + +
917B ALA* 1.3 63.2 + - - +
919B LYS* 3.3 10.2 + - + +
920B GLN* 3.0 27.8 + - - +
949B GLU* 4.9 2.6 + - - +
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Residues in contact with ALA 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLU* 3.3 26.9 - - - +
835B SER* 3.7 5.8 - - - +
837B ARG* 4.7 8.5 - - + +
891B LEU* 3.8 18.2 - - + -
913B GLY 3.0 10.3 + - - +
914B PHE 3.6 7.0 - - - +
916B GLN* 1.3 77.7 - - - +
918B ARG* 1.3 62.3 + - - +
920B GLN* 3.1 7.7 + - - +
921B LEU* 3.0 29.4 + - + +
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Residues in contact with ARG 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B LEU* 4.2 14.1 - - + +
895B PRO* 3.5 25.6 + - + +
897B THR 4.9 1.2 + - - -
899B LEU* 4.0 26.8 - - - +
901B MET* 5.8 1.6 - - - -
914B PHE* 2.9 22.7 + - - +
915B VAL* 3.2 1.3 + - - +
917B ALA* 1.3 77.0 - - - +
919B LYS* 1.3 57.0 + - - +
921B LEU* 3.5 10.5 + - + +
922B LYS* 2.9 24.3 + - - +
928B LEU* 3.5 33.4 - - + +
929B GLY 3.0 25.9 + - - +
930B GLU 4.8 1.4 + - - -
931B ALA* 3.4 19.2 - - - +
957B GLY 4.6 0.8 + - - -
958B ILE* 3.0 41.7 + - + -
959B ILE* 4.8 3.3 - - - +
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Residues in contact with LYS 919 (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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915B VAL* 2.9 21.7 + - + +
916B GLN* 3.5 9.6 - - + +
918B ARG* 1.3 78.6 - - - +
920B GLN* 1.3 57.1 + - + +
922B LYS* 4.1 2.1 - - - +
923B GLU* 3.2 55.1 + - + +
952B ASN* 3.7 14.5 - - - +
953B ALA* 5.8 2.0 - - + +
956B GLU* 3.5 19.6 + - - +
958B ILE* 3.5 31.0 - - + +
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Residues in contact with GLN 920 (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 ARG* 3.7 30.2 + - + +
838B VAL* 4.1 28.1 - - + +
916B GLN 3.0 18.1 + - - +
917B ALA 3.1 6.7 + - - +
919B LYS* 1.3 75.1 - - + +
921B LEU* 1.3 63.7 + - + +
923B GLU* 3.9 16.0 - - - +
924B GLN* 3.2 43.0 + - - +
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Residues in contact with LEU 921 (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 ARG* 6.4 3.6 - - + -
891B LEU* 5.6 6.3 - - + -
895B PRO* 3.9 29.6 - - + -
917B ALA* 3.0 20.9 + - + +
918B ARG* 3.7 13.9 - - + +
920B GLN* 1.3 78.4 - - + +
922B LYS* 1.3 58.0 + - - +
924B GLN* 3.5 20.9 + - - +
926B GLN* 3.0 39.1 + - + +
928B LEU* 4.3 7.9 - - + -
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Residues in contact with LYS 922 (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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918B ARG 2.9 18.4 + - - +
919B LYS* 4.1 5.2 - - + +
921B LEU* 1.3 74.1 - - - +
923B GLU* 1.3 61.3 + - + +
925B GLY* 2.9 20.6 + - - -
926B GLN 3.6 10.6 - - - +
928B LEU* 3.7 20.4 - - + +
956B GLU* 5.7 5.8 - - - +
958B ILE* 5.0 6.1 - - + -
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Residues in contact with GLU 923 (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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919B LYS* 3.2 49.1 + - + +
920B GLN* 3.9 20.2 - - - +
922B LYS* 1.3 71.6 - - + +
924B GLN* 1.3 57.3 + - + +
925B GLY 3.0 8.0 + - - -
956B GLU* 4.6 12.0 - - - +
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Residues in contact with GLN 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920B GLN* 3.2 32.3 + - - +
921B LEU* 3.8 20.0 - - - +
922B LYS 3.2 1.2 - - - -
923B GLU* 1.3 75.2 - - + +
925B GLY* 1.3 55.3 + - - +
926B GLN* 3.1 13.0 + - + +
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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