Contacts of the helix formed by residues 919 - 941 (chain B) in PDB entry 6VSB
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 ASN 919 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B ASN* 5.8 0.2 + - - -
718B PHE* 3.9 22.4 - - + -
915B VAL* 3.1 17.9 + - - +
916B LEU 3.2 2.5 - - - -
918B GLU* 1.3 92.1 - - - +
920B GLN* 1.3 65.1 + - - +
921B LYS 3.2 3.4 - - - -
922B LEU* 3.0 22.7 + - + +
923B ILE* 3.0 29.8 + - + +
1109B PHE* 4.9 10.0 - - - -
1J NAG 4.8 6.9 + - - +
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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
----------------------------------------------------------
1130A ILE* 3.1 39.8 - - + +
798B GLY* 2.8 31.9 + - - +
800B PHE* 4.7 9.1 - - + -
899B ALA* 3.6 30.8 - - - +
916B LEU* 2.6 33.3 + - + +
917B TYR* 3.4 22.3 + - - +
918B GLU 3.5 0.6 - - - -
919B ASN* 1.3 73.4 - - - +
921B LYS* 1.3 59.0 + - - +
923B ILE* 3.2 0.9 + - - +
924B ALA* 2.9 29.6 + - + +
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Residues in contact with LYS 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130A ILE* 6.2 5.4 - - + -
918B GLU 5.3 0.8 + - - -
919B ASN 3.2 0.8 - - - -
920B GLN* 1.3 79.1 - - - +
922B LEU* 1.3 59.3 + - - +
924B ALA* 4.2 3.9 - - - +
925B ASN* 3.0 36.1 + - - +
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Residues in contact with LEU 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B ASN* 4.4 6.7 - - - +
718B PHE* 5.0 6.3 - - + -
919B ASN* 3.0 29.8 + - + +
921B LYS* 1.3 76.5 - - - +
923B ILE* 1.3 59.4 + - - +
925B ASN* 3.3 6.3 + - - +
926B GLN* 3.0 53.8 + - - +
1J NAG 3.5 41.3 - - - +
2J NAG 3.5 25.6 - - - +
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Residues in contact with ILE 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B PHE* 3.4 38.4 - - + -
720B ILE* 3.4 24.7 - - + +
800B PHE* 3.8 18.8 - - + -
902B MET* 5.4 2.5 - - + -
906B PHE* 3.5 21.1 - - + -
916B LEU* 3.4 35.4 - - + +
919B ASN* 3.0 20.6 + - + +
920B GLN 3.8 3.6 - - - +
922B LEU* 1.3 75.7 - - + +
924B ALA* 1.3 65.9 + - - +
926B GLN* 3.2 4.4 + - - -
927B PHE* 2.9 20.4 + - - +
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Residues in contact with ALA 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B GLY 4.6 1.8 - - - +
799B GLY* 3.8 30.5 - - - +
800B PHE* 3.8 22.8 - - + -
920B GLN* 2.9 17.2 + - + +
921B LYS* 4.2 4.9 - - - +
923B ILE* 1.3 77.1 - - - +
925B ASN* 1.3 65.5 + - - +
927B PHE* 3.4 1.2 + - - +
928B ASN* 3.0 32.2 + - - +
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Residues in contact with ASN 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B LYS* 3.0 24.7 + - - +
922B LEU* 3.3 7.4 + - - +
923B ILE 3.2 0.6 - - - -
924B ALA* 1.3 79.9 - - - +
926B GLN* 1.3 62.9 + - - +
928B ASN* 3.4 8.3 + - - +
929B SER* 3.0 30.6 + - - +
2J NAG 4.4 22.4 + - + +
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Residues in contact with GLN 926 (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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718B PHE* 3.3 18.8 + - - +
719B THR* 3.1 12.3 - - - -
720B ILE* 3.1 39.8 + - + +
922B LEU* 3.0 49.0 + - - +
923B ILE* 3.2 6.7 + - - +
925B ASN* 1.3 76.3 - - - +
927B PHE* 1.3 63.7 + - - +
929B SER* 3.6 4.7 + - - -
930B ALA* 2.9 25.5 + - - +
1J NAG 3.9 13.7 + - - +
2J NAG 4.1 16.6 - - + -
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Residues in contact with PHE 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ILE* 3.7 14.9 - - + +
722B VAL* 4.1 9.9 - - + -
800B PHE* 3.6 30.5 - + + -
801B ASN 3.8 18.2 - - - -
802B PHE* 4.2 17.9 - + - -
805B ILE* 4.2 3.4 - - + -
898B PHE* 6.2 0.2 - + - -
923B ILE 2.9 16.7 + - - +
924B ALA 3.6 3.6 - - - +
926B GLN* 1.3 75.9 - - - +
928B ASN* 1.3 72.8 + - - +
930B ALA* 3.0 7.2 + - - +
931B ILE* 3.0 38.6 + - + +
1050B MET* 5.4 3.8 - - - -
1052B PHE* 4.0 19.1 - + - -
1065B VAL* 3.6 41.7 - - + -
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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
----------------------------------------------------------
799B GLY 3.4 19.6 + - - -
800B PHE 3.6 0.2 - - - -
801B ASN* 2.6 43.4 + - + +
804B GLN* 5.3 2.8 + - - +
924B ALA* 3.0 20.2 + - - +
925B ASN* 3.8 10.0 + - - +
927B PHE* 1.3 85.0 - - - +
929B SER* 1.3 61.9 + - - +
930B ALA 3.1 1.4 + - - -
931B ILE* 3.1 15.8 + - - +
932B GLY* 3.2 10.9 + - - -
1K NAG 5.7 0.6 + - - -
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Residues in contact with SER 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B ASN* 3.0 20.3 + - - +
926B GLN* 4.1 4.7 - - - -
928B ASN* 1.3 76.5 - - - +
930B ALA* 1.3 60.6 + - - +
932B GLY* 4.0 3.2 + - - +
933B LYS* 3.4 27.5 + - - +
2J NAG 5.7 4.5 - - - +
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Residues in contact with ALA 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ILE 4.4 8.3 - - - +
721B SER* 4.6 2.2 - - - -
722B VAL* 3.4 37.6 - - + +
926B GLN 2.9 19.1 + - - +
927B PHE* 3.3 7.4 - - - +
928B ASN 3.0 0.4 - - - -
929B SER* 1.3 76.5 - - - +
931B ILE* 1.3 65.9 + - - +
933B LYS* 3.1 23.3 + - + +
934B ILE* 3.5 3.6 + - - +
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Residues in contact with ILE 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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722B VAL* 4.1 25.8 - - + -
801B ASN 5.0 3.4 - - - +
804B GLN* 4.0 26.9 - - + +
805B ILE* 4.0 31.6 - - + -
818B ILE* 4.8 9.7 - - + +
927B PHE* 3.0 37.6 + - + +
928B ASN* 3.1 7.8 + - - +
930B ALA* 1.3 76.4 - - - +
932B GLY* 1.3 63.9 + - - +
933B LYS 3.0 1.7 + - - -
934B ILE* 3.0 18.6 + - + +
935B GLN* 3.3 10.4 + - + +
1052B PHE* 5.9 0.9 - - + -
1063B LEU* 4.6 15.5 - - + -
1065B VAL* 5.8 0.7 - - + -
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Residues in contact with GLY 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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804B GLN* 4.3 17.1 + - - +
928B ASN 3.2 11.0 + - - -
929B SER* 4.0 3.3 + - - -
931B ILE* 1.3 77.7 - - - +
933B LYS* 1.3 60.5 + - - +
935B GLN* 3.7 5.0 + - - +
936B ASP* 3.3 29.3 + - - +
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Residues in contact with LYS 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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929B SER* 3.4 18.9 + - - +
930B ALA* 3.1 15.1 + - - +
931B ILE 3.0 0.8 + - - -
932B GLY* 1.3 74.8 - - - +
934B ILE* 1.3 54.8 + - + +
936B ASP* 3.1 6.8 + - - +
937B SER* 2.6 36.9 + - - -
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Residues in contact with ILE 934 (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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722B VAL* 3.5 41.7 - - + +
724B THR* 3.6 35.9 - - + -
818B ILE* 5.5 7.2 - - + -
930B ALA 3.5 5.3 + - - +
931B ILE* 3.0 12.5 + - + +
933B LYS* 1.3 76.7 - - + +
935B GLN* 1.3 57.6 + - - +
937B SER* 3.8 9.2 - - - -
938B LEU* 2.6 54.9 + - + +
1063B LEU* 3.7 19.5 - - + -
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Residues in contact with GLN 935 (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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804B GLN* 2.3 44.3 + - - +
817B PHE* 3.3 39.5 - - + -
818B ILE* 5.4 10.6 - - + +
821B LEU* 3.6 12.4 - - + +
931B ILE* 3.3 9.6 + - + +
932B GLY* 3.8 9.4 - - - +
934B ILE* 1.3 78.4 - - - +
936B ASP* 1.3 65.4 + - - +
938B LEU* 4.8 2.5 - - - -
939B SER* 3.2 28.8 + - - -
1K NAG 5.4 0.6 + - - -
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Residues in contact with ASP 936 (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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932B GLY 3.3 14.9 + - - +
933B LYS* 3.1 8.4 + - - +
934B ILE 3.1 0.4 - - - -
935B GLN* 1.3 87.9 - - - +
937B SER* 1.3 62.0 + - - +
938B LEU 3.3 0.2 - - - -
939B SER* 4.1 5.2 + - - -
940B SER* 2.9 40.5 + - - +
941B THR* 4.0 0.3 + - - -
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Residues in contact with SER 937 (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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933B LYS 2.6 22.0 + - - -
934B ILE* 3.5 12.1 - - - -
936B ASP* 1.3 73.5 - - - +
938B LEU* 1.3 63.9 + - - +
941B THR* 3.2 33.0 - - - +
944B ALA* 4.7 2.1 - - - +
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Residues in contact with LEU 938 (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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724B THR* 5.4 11.0 - - + +
726B ILE* 6.1 1.8 - - + -
818B ILE* 4.2 17.9 - - + -
821B LEU* 3.6 17.3 - - + -
822B LEU* 3.7 31.6 - - + -
825B LYS* 2.7 32.9 + - + +
934B ILE* 2.6 39.4 + - + +
935B GLN* 4.1 3.4 - - - +
937B SER* 1.3 74.2 - - - +
939B SER* 1.3 52.8 + - - +
941B THR 3.0 11.9 - - - +
944B ALA* 4.3 19.8 - - + +
945B LEU* 4.9 11.4 - - + -
1061B VAL* 5.9 4.7 - - + -
1063B LEU* 6.2 0.7 - - + -
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Residues in contact with SER 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B LEU* 3.6 19.7 - - - -
825B LYS* 2.5 29.1 + - - +
935B GLN* 3.2 18.7 + - - -
936B ASP* 3.8 4.0 + - - -
938B LEU* 1.3 79.2 - - - +
940B SER* 1.3 70.8 + - - +
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Residues in contact with SER 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936B ASP* 2.9 25.0 + - - +
939B SER* 1.3 83.8 + - - +
941B THR* 1.3 60.3 + - - +
942B ALA 4.0 1.5 + - - -
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Residues in contact with THR 941 (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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825B LYS* 3.6 1.6 + - - +
937B SER* 3.2 23.9 + - - +
938B LEU 3.0 18.3 - - - +
940B SER* 1.3 80.0 + - - +
942B ALA* 1.3 74.1 + - - +
944B ALA* 3.7 13.8 - - + +
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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
------------------------------------------------------------
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