Contacts of the helix formed by residues 929 - 946 (chain B) in PDB entry 2IVS
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 929 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B VAL* 3.5 17.9 - - - +
899B VAL* 6.0 0.7 - - - -
921B GLU* 4.7 2.9 + - - -
927B ILE* 3.6 22.2 - - + -
928B TYR* 1.3 80.0 - - - +
930B THR* 1.3 65.4 + - - +
931B GLN* 3.0 21.7 + - - +
932B SER* 2.8 26.3 + - - -
933B ASP 3.1 5.4 + - - -
992B PRO* 5.3 1.4 - - - +
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Residues in contact with THR 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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862B MET* 5.8 0.2 - - + -
866B ALA* 3.6 39.3 + - + +
869B LYS* 5.9 1.0 - - - -
870B LEU 4.5 3.8 + - - -
871B VAL* 3.7 12.7 - - - +
929B THR* 1.3 73.8 - - - +
931B GLN* 1.3 70.8 + - - +
933B ASP* 3.1 12.9 + - + +
934B VAL* 2.9 24.4 + - - +
997B VAL* 6.3 0.9 - - + -
998B PHE* 3.8 20.2 - - + +
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Residues in contact with GLN 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B THR* 3.0 11.4 + - - +
930B THR* 1.3 88.9 - - - +
932B SER* 1.3 56.5 + - - +
934B VAL* 3.4 15.0 + - - +
935B TRP 3.3 15.6 + - - -
992B PRO* 3.5 42.3 + - + +
993B ASP* 5.4 4.7 - - - +
995B ARG* 2.9 31.6 + - - +
996B PRO 3.0 25.8 + - - -
997B VAL* 3.9 20.4 - - - +
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Residues in contact with SER 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B VAL* 4.7 1.2 - - - +
873B ARG* 6.1 0.2 - - - -
919B ALA* 3.5 18.9 + - - +
921B GLU* 3.6 8.2 + - - -
922B SER* 3.5 22.9 - - - -
927B ILE 4.4 0.4 - - - -
928B TYR* 3.3 12.9 - - - +
929B THR* 2.8 37.1 + - - -
931B GLN* 1.3 74.6 - - - +
933B ASP* 1.3 66.0 + - - +
934B VAL 3.3 0.4 - - - -
935B TRP* 3.3 3.6 + - - +
936B SER* 3.2 24.3 + - - -
995B ARG* 3.9 0.8 - - - +
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Residues in contact with ASP 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B MET* 3.5 16.9 - - + +
870B LEU 4.4 0.9 - - - +
871B VAL* 3.5 17.6 - - - +
872B HIS* 2.8 27.4 + - - +
873B ARG* 2.8 29.8 + - - -
875B LEU* 3.5 10.2 - - + +
929B THR 3.1 5.6 + - - -
930B THR* 3.1 14.9 + - - +
932B SER* 1.3 75.3 + - - +
934B VAL* 1.3 59.0 + - - +
936B SER* 3.3 5.6 + - - -
937B PHE* 2.8 29.1 + - - +
998B PHE* 3.8 14.8 - - + -
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Residues in contact with VAL 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B THR 2.9 18.2 + - - +
931B GLN* 3.5 20.9 - - - +
932B SER 3.3 0.2 - - - -
933B ASP* 1.3 76.2 - - - +
935B TRP* 1.3 61.4 + - - +
937B PHE* 3.2 4.0 + - - +
938B GLY 3.0 18.2 + - - -
987B CYS* 3.5 23.9 - - - +
995B ARG* 4.0 15.0 - - + -
996B PRO* 3.3 29.4 - - + +
998B PHE* 3.6 31.2 - - + +
1001B ILE* 4.0 9.0 - - + -
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Residues in contact with TRP 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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916B LYS 5.1 1.2 + - - -
917B TRP 3.8 5.8 - - - -
918B MET 3.2 22.7 + - - -
919B ALA* 3.5 21.1 - - + -
920B ILE* 3.9 26.0 - - + -
931B GLN 3.3 8.8 + - - +
932B SER 3.5 9.0 - - - +
933B ASP 3.3 0.4 - - - -
934B VAL* 1.3 79.2 - - - +
936B SER* 1.3 64.0 + - - +
938B GLY 3.0 10.7 + - - -
939B VAL* 3.2 19.6 + - + +
952B TYR* 4.3 6.8 + - - -
964B LEU* 3.8 30.7 - - + -
969B ARG* 3.7 25.6 - - - -
987B CYS 3.4 12.1 + - - +
988B TRP* 3.4 50.8 + + + -
989B LYS 3.8 6.5 - - - -
995B ARG* 3.5 18.8 - - - +
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Residues in contact with SER 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B ARG 4.5 10.0 + - - -
875B LEU* 3.7 34.1 - - - +
913B ILE* 5.7 0.2 - - - +
917B TRP* 2.6 29.7 + - - +
918B MET* 4.6 2.1 - - - -
919B ALA 4.9 0.2 + - - -
932B SER 3.2 11.4 + - - -
933B ASP* 3.6 10.6 + - - -
935B TRP* 1.3 74.4 - - - +
937B PHE* 1.3 61.0 + - - +
939B VAL* 3.1 7.2 + - - +
940B LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B ALA* 3.6 32.5 - - + -
858B ILE* 3.8 27.1 - - + -
859B SER* 3.9 9.2 - - - -
862B MET* 4.8 0.2 - - + -
875B LEU* 3.9 10.2 - - + +
933B ASP 2.8 18.2 + - - +
934B VAL* 3.4 9.2 - - - +
935B TRP 3.2 0.2 - - - -
936B SER* 1.3 73.2 - - - +
938B GLY* 1.3 52.6 + - - +
940B LEU* 3.1 14.5 + - + +
941B LEU* 2.7 60.9 + - + +
944B ILE* 6.1 0.7 - - + -
983B LEU* 5.4 0.2 - - + -
987B CYS* 4.4 4.3 - - - -
998B PHE* 3.7 22.0 - + + -
1001B ILE* 3.5 39.5 - - + -
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Residues in contact with GLY 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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934B VAL 3.0 7.3 + - - -
935B TRP 3.0 9.8 + - - -
937B PHE* 1.3 75.4 - - - +
939B VAL* 1.3 59.9 + - - +
941B LEU* 3.3 9.6 + - - +
942B TRP* 3.1 17.2 + - - +
984B MET* 4.0 5.4 - - - +
987B CYS* 3.6 24.9 - - - +
988B TRP* 3.4 19.6 - - - -
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Residues in contact with VAL 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916B LYS 3.8 20.0 - - - +
917B TRP* 3.4 30.7 - - + +
935B TRP* 3.6 27.4 - - + +
936B SER 3.1 8.0 + - - +
938B GLY* 1.3 74.3 - - - +
940B LEU* 1.3 57.4 + - - +
942B TRP* 3.1 7.1 + - - +
943B GLU* 2.9 26.0 + - - +
951B PRO* 3.7 26.0 - - + -
952B TYR* 4.7 6.1 - - - +
970B MET* 4.6 4.0 - - + -
988B TRP* 3.6 18.6 - - + +
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Residues in contact with LEU 940 (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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812B LEU* 4.2 6.7 - - + -
858B ILE* 3.9 29.2 - - + -
875B LEU* 4.1 18.2 - - + -
876B ALA* 4.5 8.5 - - - +
877B ALA* 3.7 33.0 - - + +
880B ILE* 4.0 13.0 - - + -
917B TRP* 4.6 0.6 - - - +
936B SER 2.9 12.7 + - - +
937B PHE* 3.3 15.9 - - + +
939B VAL* 1.3 75.9 - - - +
941B LEU* 1.3 57.2 + - - +
943B GLU* 3.1 12.2 + - - +
944B ILE* 2.9 47.2 + - + +
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Residues in contact with LEU 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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855B ALA* 3.7 30.1 - - + -
937B PHE* 2.7 35.4 + - + +
938B GLY* 3.4 11.0 - - - +
940B LEU* 1.3 72.3 - - - +
942B TRP* 1.3 63.5 + - - +
944B ILE* 3.2 9.0 + - + +
945B VAL* 3.0 31.1 + - + +
980B MET* 3.8 22.9 - - + -
983B LEU* 3.8 34.3 - - + -
984B MET* 3.9 24.7 - - + +
987B CYS* 5.2 1.1 - - - -
1005B LEU* 5.1 0.4 - - + -
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Residues in contact with TRP 942 (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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938B GLY 3.1 9.2 + - - +
939B VAL 3.1 10.5 + - - +
941B LEU* 1.3 80.7 - - - +
943B GLU* 1.3 64.9 + - + +
945B VAL* 3.9 0.5 - - - +
946B THR* 2.9 48.8 + - + +
949B GLY* 3.5 25.1 - - - -
950B ASN 3.3 19.5 - - - -
951B PRO* 3.4 33.7 - - + -
953B PRO* 4.7 10.1 - - + -
970B MET* 3.5 40.4 - - + +
971B GLU 4.1 8.6 + - - -
973B PRO* 4.0 24.3 - - + +
981B TYR* 5.9 0.2 - + - -
984B MET* 4.0 26.4 - - - +
988B TRP* 4.4 2.2 - + + -
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Residues in contact with GLU 943 (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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813B ARG* 4.7 11.1 + - - +
816B LEU* 3.9 2.1 - - - +
877B ALA* 2.8 45.8 + - + +
878B ARG* 4.6 2.1 + - - -
917B TRP* 2.9 37.9 + - - -
939B VAL 2.9 13.4 + - - +
940B LEU* 3.3 14.5 - - - +
942B TRP* 1.3 79.9 - - + +
944B ILE* 1.3 60.1 + - - +
946B THR* 3.2 8.4 + - - -
948B GLY* 2.7 32.4 + - - -
949B GLY 4.1 17.4 - - - +
951B PRO* 4.2 10.7 - - + +
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Residues in contact with ILE 944 (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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812B LEU* 4.1 13.5 - - + -
816B LEU* 3.8 10.0 - - + +
851B LEU* 3.7 42.6 - - + +
854B PHE* 4.6 4.5 - - + -
855B ALA* 4.2 24.2 - - + +
858B ILE* 4.1 19.5 - - + -
937B PHE* 6.1 0.9 - - + -
940B LEU* 2.9 39.8 + - + +
941B LEU* 3.2 10.7 + - + +
943B GLU* 1.3 77.5 - - - +
945B VAL* 1.3 62.3 + - + +
947B LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 945 (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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848B MET* 4.9 11.3 - - + +
851B LEU* 4.5 13.0 - - + +
941B LEU* 3.0 19.4 + - + +
942B TRP 4.0 2.9 - - - +
944B ILE* 1.3 81.1 - - + +
946B THR* 1.3 57.6 + - - +
947B LEU* 3.2 5.2 + - - +
973B PRO* 3.8 12.8 - - + -
975B ASN* 4.1 19.9 + - - +
976B CYS* 3.5 32.8 - - + -
980B MET* 3.8 34.5 - - + -
984B MET* 4.0 5.4 - - + -
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Residues in contact with THR 946 (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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942B TRP* 2.9 46.6 + - + +
943B GLU* 3.2 4.9 + - - -
945B VAL* 1.3 74.5 - - - +
947B LEU* 1.3 67.8 - - - +
949B GLY* 2.9 31.3 + - - -
973B PRO* 3.7 24.0 - - + -
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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