Contacts of the helix formed by residues 919 - 933 (chain B) in PDB entry 6MZL
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 919 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLU* 3.3 24.0 - - + +
880B TYR* 4.3 23.6 - - + +
884B VAL* 5.0 12.8 - - + -
887B ARG* 4.3 11.9 - - - +
917B ASP* 3.4 2.8 - - - +
918B PRO* 1.3 79.3 - - + +
920B PRO* 1.3 74.5 - - + +
921B TYR* 3.7 15.5 - - + +
922B VAL* 3.3 36.4 - - + +
923B ARG* 3.7 12.5 - - - +
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Residues in contact with PRO 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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160B HIS* 3.4 29.6 - - + +
311B GLU* 3.6 16.8 - - + +
312B ALA 4.7 2.9 - - - +
313B TYR* 3.8 37.5 - - + +
918B PRO 3.4 6.3 - - - +
919B VAL* 1.3 84.5 - - + +
921B TYR* 1.3 61.9 + - - +
923B ARG* 2.8 28.2 + - + +
924B HIS* 2.9 12.8 + - - +
964B ASP* 4.5 9.0 - - - +
966B ARG* 4.1 1.9 + - - +
967B LEU* 4.7 2.8 - - + +
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Residues in contact with TYR 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 3.3 18.6 - - + +
313B TYR 3.7 20.6 - - - -
314B VAL* 5.1 1.1 - - - -
315B GLU* 4.8 29.7 - - + +
884B VAL* 4.6 12.6 - - + -
888B ILE* 3.8 19.5 - - + -
919B VAL* 3.4 8.3 - - + +
920B PRO* 1.3 81.4 - - - +
922B VAL* 1.3 57.7 + - - +
924B HIS* 3.4 25.0 + + - +
925B LYS* 3.0 59.3 + - + +
966B ARG* 4.1 1.8 - - - +
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Residues in contact with VAL 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B VAL* 4.9 15.0 - - + -
887B ARG* 4.3 35.0 - - + +
888B ILE* 5.1 7.9 - - + -
891B LEU* 4.5 13.9 - - + -
913B MET* 6.5 0.7 - - + -
917B ASP* 3.2 26.2 - - + +
919B VAL* 3.3 32.2 - - + +
921B TYR* 1.3 79.1 - - - +
923B ARG* 1.3 57.8 + - - +
925B LYS* 4.4 3.4 - - - +
926B ILE* 2.8 37.9 + - + +
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Residues in contact with ARG 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B ILE* 2.9 23.0 + - + +
915B GLN* 2.4 30.1 + - - +
916B ASN* 3.6 0.6 + - - +
917B ASP* 2.3 60.9 + - - +
918B PRO 5.5 0.9 - - - -
919B VAL 3.7 10.3 + - - +
920B PRO* 2.8 11.9 + - - +
922B VAL* 1.3 76.6 - - - +
924B HIS* 1.3 63.4 + - - +
926B ILE* 3.7 6.2 - - + +
927B LEU* 3.0 35.1 + - + +
963B HIS* 4.0 27.7 + - - +
967B LEU* 3.7 35.4 - - + +
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Residues in contact with HIS 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B TRP* 3.3 50.4 - + + +
920B PRO 2.9 4.6 + - - +
921B TYR* 3.4 28.6 + + - +
923B ARG* 1.3 75.7 - - - +
925B LYS* 1.3 86.7 + - + +
927B LEU* 4.0 2.9 - - - +
928B ASN* 2.9 36.5 + - + +
966B ARG* 3.2 47.5 + - - +
967B LEU* 4.3 5.0 - - - +
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Residues in contact with LYS 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B ILE* 3.6 28.5 - - + -
891B LEU* 6.2 0.7 - - - -
892B GLU* 5.4 5.4 - - + +
921B TYR* 3.0 47.3 + - + +
922B VAL 4.1 1.1 - - - +
924B HIS* 1.3 95.9 + - + +
926B ILE* 1.3 66.7 + - - +
928B ASN* 3.7 21.5 - - - +
929B MET* 3.0 42.2 + - + +
932B LYS* 5.1 4.2 - - - +
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Residues in contact with ILE 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B LEU* 3.7 37.2 - - + +
895B VAL* 4.8 5.2 - - + +
910B LEU* 3.7 32.5 - - + -
913B MET* 4.8 9.0 - - + -
914B ILE* 3.7 37.2 - - + +
917B ASP* 4.9 6.7 - - - +
922B VAL* 2.8 34.6 + - + +
923B ARG* 3.7 6.5 - - - +
925B LYS* 1.3 71.9 - - - +
927B LEU* 1.3 60.8 + - + +
930B LEU* 2.7 35.2 + - + +
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Residues in contact with LEU 927 (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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914B ILE* 3.7 43.3 - - + -
923B ARG 3.0 20.7 + - - +
924B HIS* 4.0 2.9 - - - +
926B ILE* 1.3 75.0 - - + +
928B ASN* 1.3 62.4 - - - +
930B LEU* 3.7 9.4 - - + +
931B THR* 2.6 33.8 + - - -
966B ARG 6.0 0.2 - - - +
967B LEU* 4.1 29.4 - - + +
970B GLY* 4.5 18.6 - - - +
971B ALA* 5.0 1.1 - - + +
974B LEU* 3.8 26.9 - - + -
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Residues in contact with ASN 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B TRP* 5.5 7.2 - - - +
444B GLU* 3.6 18.1 - - - +
924B HIS* 2.9 30.4 + - + +
925B LYS* 3.7 31.2 - - + +
926B ILE 3.4 0.2 - - - -
927B LEU* 1.3 75.0 - - - +
929B MET* 1.3 61.9 + - + +
931B THR* 3.0 8.4 + - - -
932B LYS* 2.9 51.3 + - - +
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Residues in contact with MET 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892B GLU* 3.7 45.3 - - + +
895B VAL* 3.7 7.4 - - + +
925B LYS* 3.0 28.2 + - - +
928B ASN* 1.3 79.3 - - - +
930B LEU* 1.3 60.1 + - - +
931B THR 3.2 0.4 - - - -
932B LYS* 3.7 34.1 - - + +
933B ASN* 3.0 51.0 + - - +
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Residues in contact with LEU 930 (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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895B VAL* 3.8 28.2 - - + +
898B THR* 6.4 1.1 - - - -
907B LEU* 5.3 4.9 - - + -
910B LEU* 4.4 17.9 - - + -
911B LEU* 5.0 8.3 - - + -
914B ILE* 4.9 5.4 - - + -
926B ILE* 2.7 22.3 + - + +
927B LEU* 3.7 16.2 - - + +
929B MET* 1.3 77.7 - - - +
931B THR* 1.3 58.8 + - - +
933B ASN 3.0 23.8 - - - +
934B PRO* 3.3 7.6 - - - +
935B PRO* 3.8 25.4 - - + -
974B LEU* 3.8 24.9 - - + +
978B LEU* 6.4 0.2 - - + -
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Residues in contact with THR 931 (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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444B GLU* 5.4 7.6 - - - +
927B LEU 2.6 23.4 + - - -
928B ASN* 3.5 4.7 - - - -
930B LEU* 1.3 76.5 - - - +
932B LYS* 1.3 64.0 + - - +
934B PRO* 3.8 13.1 - - - +
970B GLY 4.4 1.0 + - - -
973B ASP* 3.6 31.0 - - + +
974B LEU* 3.5 19.7 - - - +
976B PHE* 6.0 0.4 - - + -
977B THR* 3.3 29.3 + - - +
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Residues in contact with LYS 932 (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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408B LYS* 5.0 12.6 - - - +
444B GLU* 3.7 22.4 - - - +
925B LYS* 5.1 4.0 - - - +
928B ASN* 2.9 44.0 + - - +
929B MET* 3.8 32.6 - - + +
930B LEU 3.4 0.2 - - - -
931B THR* 1.3 77.9 - - - +
933B ASN* 1.3 70.7 + - - +
934B PRO* 3.5 7.2 - - - +
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Residues in contact with ASN 933 (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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892B GLU 5.9 0.8 + - - -
895B VAL* 3.3 23.8 - - + +
896B ASP* 3.8 29.5 + - - +
899B LYS* 4.9 13.1 + - + +
929B MET* 3.0 41.3 + - - +
930B LEU 3.0 8.4 - - - +
932B LYS* 1.3 84.8 - - - +
934B PRO* 1.3 64.9 - - - +
935B PRO* 3.8 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