Contacts of the helix formed by residues 915 - 935 (chain B) in PDB entry 1VDV
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 GLY 915 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B PHE* 5.0 0.7 - - - -
877B ILE* 3.6 23.6 - - - -
881B ALA* 3.6 18.0 - - - +
913B GLY 3.4 0.4 - - - -
914B PHE* 1.3 72.4 - - - +
916B GLY* 1.3 62.9 + - - +
918B GLN* 3.4 19.0 + - - +
919B ALA 3.3 16.5 + - - -
5202B ACY 2.9 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 916 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B ARG* 4.0 11.4 - - - +
884B HIS* 4.5 14.8 - - - -
913B GLY 3.0 10.0 + - - -
914B PHE 3.2 2.2 + - - -
915B GLY* 1.3 76.3 - - - +
917B PRO* 1.3 62.3 - - - +
919B ALA* 3.1 2.5 + - - +
920B LEU* 2.8 39.6 + - - +
1005B PHE* 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 917 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ILE* 5.1 1.1 - - - -
839B ARG* 3.8 12.1 - - - +
913B GLY* 3.3 32.3 - - - -
916B GLY* 1.3 88.1 - - - +
918B GLN* 1.3 66.0 + - - +
920B LEU* 3.7 2.8 - - + -
921B PHE* 2.8 32.9 + - - +
1005B PHE* 5.0 2.2 - - + -
1205B LEU* 4.2 12.6 - - + -
1206B PHE* 4.2 5.5 - - + -
1264B LEU* 3.8 27.8 - - + -
1265B PHE* 3.8 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 918 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ILE* 4.0 26.9 - - + -
737B GLY 6.1 0.2 - - - +
839B ARG* 3.4 14.2 + - - +
840B HIS 3.2 19.8 + - - +
842B PHE* 3.5 44.3 - - + -
915B GLY* 3.4 18.4 - - - +
916B GLY 3.2 0.2 - - - -
917B PRO* 1.3 82.1 - - - +
919B ALA* 1.3 61.6 + - - +
921B PHE* 3.2 2.9 + - - +
922B ILE* 3.0 30.5 + - - +
5202B ACY 2.9 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 919 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B HIS* 4.5 8.7 - - - +
881B ALA* 2.9 45.9 - - + +
884B HIS* 4.0 13.8 - - + +
885B MET* 4.0 6.2 - - - +
915B GLY 3.3 1.6 + - - -
916B GLY 3.1 6.1 + - - +
918B GLN* 1.3 79.2 - - - +
920B LEU* 1.3 63.3 + - - +
922B ILE* 3.4 11.7 + - - +
923B ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 920 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B HIS* 3.3 31.0 - - + +
887B ASN* 3.2 35.4 - - - +
916B GLY* 2.8 32.2 + - - +
917B PRO* 5.3 0.4 - - + -
919B ALA* 1.3 71.7 - - - +
921B PHE* 1.3 57.9 + - - +
923B ALA* 3.3 4.6 + - - +
924B GLU* 3.0 25.6 + - - +
1003B THR* 3.7 18.4 - - - +
1004B LYS 4.4 10.1 - - - +
1005B PHE* 4.9 8.1 - - + -
1265B PHE* 3.3 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 921 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B LEU* 3.6 31.4 - - + -
736B ILE* 4.0 20.4 - - + -
917B PRO 2.8 19.1 + - - +
918B GLN 3.2 5.1 + - - +
920B LEU* 1.3 73.7 - - - +
922B ILE* 1.3 66.7 + - + +
924B GLU* 3.4 2.0 + - - +
925B ASN* 3.0 23.4 + - + +
1206B PHE* 3.6 26.7 - + + -
1265B PHE* 3.3 9.6 - + + -
1268B ALA* 4.8 1.3 - - + -
1271B PHE* 3.6 52.7 - + - -
1272B PHE* 3.9 15.0 - + - -
1296B LEU 4.5 2.7 - - - -
1298B SER* 3.6 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 922 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B LEU* 3.9 21.1 - - + +
736B ILE* 5.7 2.7 - - + -
842B PHE* 4.5 16.2 - - + -
844B ALA* 3.5 34.5 - - + -
846B TYR* 5.0 7.8 - - + -
861B VAL* 4.0 19.1 - - + -
863B HIS* 3.7 24.0 - - + +
918B GLN* 3.0 20.9 + - - +
919B ALA 3.7 4.7 - - - +
921B PHE* 1.3 79.4 - - + +
923B ALA* 1.3 63.2 + - - +
925B ASN* 3.3 11.3 + - - +
926B TRP* 3.3 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 923 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B MET 3.5 26.5 - - - +
886B ASP 4.9 0.7 - - - +
887B ASN* 4.4 14.6 - - + -
889B TYR* 5.6 2.2 - - + -
919B ALA 3.0 12.1 + - - +
920B LEU* 3.4 11.9 - - - +
921B PHE 3.2 0.2 - - - -
922B ILE* 1.3 76.9 - - - +
924B GLU* 1.3 63.4 + - - +
925B ASN 3.2 0.5 + - - -
926B TRP* 3.2 26.7 - - + +
927B MET* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 924 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B ASN* 2.6 26.9 + - - +
889B TYR* 2.7 23.5 + - - -
920B LEU 3.0 11.9 + - - +
921B PHE 4.0 0.4 - - - +
923B ALA* 1.3 77.1 - - - +
925B ASN* 1.3 57.6 + - - +
927B MET* 3.6 6.1 - - - +
928B SER* 2.9 29.1 + - - -
942B ARG* 2.7 34.0 + - - +
1001B ILE* 3.8 11.9 - - + -
1002B PRO* 3.8 3.6 - - - +
1265B PHE* 3.6 27.1 - - + -
1272B PHE* 3.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 925 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B LEU* 3.5 38.6 - - + +
846B TYR* 3.4 30.3 + - - -
921B PHE* 3.0 16.3 + - + +
922B ILE 3.4 9.6 + - - +
923B ALA 3.1 0.4 - - - -
924B GLU* 1.3 76.9 - - - +
926B TRP* 1.3 63.6 + - - +
928B SER* 2.7 21.1 + - - -
929B GLU* 3.2 14.6 + - - +
1271B PHE* 5.6 0.5 - - - -
1272B PHE* 3.7 14.9 - - + -
1275B LYS* 3.4 23.8 + - - -
1296B LEU 4.8 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 926 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B TYR* 3.7 33.7 - + + -
848B VAL* 4.1 19.6 - - + +
856B ILE* 3.7 19.5 - - + -
859B LEU* 3.4 45.9 - - + +
861B VAL* 4.4 5.1 - - + +
885B MET 4.4 3.0 + - - -
886B ASP* 5.6 0.2 - - - -
889B TYR* 4.6 7.6 - + + -
891B ILE* 3.9 19.1 - - + -
922B ILE* 3.3 23.1 + - + +
923B ALA* 3.2 30.0 - - + +
925B ASN* 1.3 80.1 - - - +
927B MET* 1.3 108.3 + - + +
929B GLU* 3.3 13.0 + - - +
930B VAL* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 927 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ILE* 4.3 2.0 - - + -
889B TYR* 3.5 44.4 - - + -
923B ALA 3.1 14.5 + - - +
924B GLU* 3.6 16.8 - - - +
925B ASN 3.1 0.8 - - - -
926B TRP* 1.3 105.1 - - + +
928B SER* 1.3 62.9 + - - +
930B VAL* 3.2 16.5 + - - +
931B ALA* 3.2 13.0 + - - +
941B VAL* 3.8 24.9 - - + -
942B ARG* 3.8 26.6 - - + +
945B ASN* 3.9 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 928 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B GLU 2.9 14.9 + - - -
925B ASN* 2.7 20.6 + - - -
927B MET* 1.3 76.7 - - - +
929B GLU* 1.3 61.0 + - - +
931B ALA* 3.4 7.2 + - - +
932B VAL* 3.2 28.9 + - - +
938B ALA* 5.9 1.1 - - - -
942B ARG* 4.1 15.7 - - - +
1272B PHE* 4.2 13.6 - - - -
1275B LYS* 3.9 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 929 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B VAL* 3.7 18.4 - - + +
846B TYR* 2.7 41.0 + - - -
925B ASN* 3.2 22.3 + - - +
926B TRP* 3.6 7.8 - - + +
927B MET 3.2 0.2 - - - -
928B SER* 1.3 81.5 + - - +
930B VAL* 1.3 59.4 - - - +
932B VAL* 3.5 1.5 + - - +
933B THR* 2.8 35.9 + - - -
1275B LYS* 4.5 11.2 + - - +
1293B LEU* 4.0 37.7 - - + +
1294B PHE 5.0 3.1 - - - +
1295B ARG* 5.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B VAL* 4.2 9.6 - - + -
850B PHE* 3.8 44.6 - - + -
854B GLY* 3.8 27.1 - - - +
856B ILE* 3.9 17.9 - - + -
926B TRP* 2.9 23.1 + - + +
927B MET* 3.2 9.6 + - - +
929B GLU* 1.3 75.1 - - + +
931B ALA* 1.3 65.6 + - - +
933B THR* 3.4 1.2 + - - -
934B CYS* 3.0 24.8 + - - -
941B VAL* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 931 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B MET 3.2 8.8 + - - +
928B SER* 3.8 8.5 - - - +
929B GLU 3.4 0.2 - - - -
930B VAL* 1.3 81.4 - - - +
932B VAL* 1.3 58.5 + - + +
934B CYS* 3.3 0.6 + - - -
935B GLY 2.9 23.7 + - - -
936B LEU 3.0 18.4 + - - +
938B ALA* 3.7 35.4 - - + -
941B VAL* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 932 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B SER* 3.2 18.7 + - - +
929B GLU* 3.8 4.7 - - - +
930B VAL 3.3 0.2 - - - -
931B ALA* 1.3 77.8 - - + +
933B THR* 1.3 65.1 + - - +
935B GLY* 3.0 15.0 + - - -
1279B ARG* 3.9 27.4 - - - +
1290B THR 4.2 7.2 - - - +
1291B LYS* 3.7 23.8 + - - +
1292B GLU 3.7 12.1 - - - +
1293B LEU* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 933 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ASN* 4.6 13.9 + - + +
730B VAL* 4.0 8.1 - - + +
850B PHE* 3.7 24.2 - - + -
929B GLU 2.8 22.6 + - - -
930B VAL 3.8 3.1 - - - -
932B VAL* 1.3 77.5 - - - +
934B CYS* 1.3 56.9 + - - +
1291B LYS* 3.0 31.7 + - + +
1293B LEU* 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 934 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ASN* 4.8 2.5 - - - +
850B PHE* 3.3 36.8 - - - -
851B MET 3.5 13.5 - - - -
852B LYS* 3.6 22.0 - - - +
854B GLY* 3.7 11.0 - - - -
930B VAL 3.0 15.7 + - - +
931B ALA* 3.9 3.4 - - - +
933B THR* 1.3 77.7 - - - +
935B GLY* 1.3 62.6 + - - +
936B LEU* 3.5 20.6 + - + +
1291B LYS* 3.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 935 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B ALA 2.9 5.2 + - - -
932B VAL* 3.0 12.4 + - - -
933B THR 3.2 0.2 - - - -
934B CYS* 1.3 80.6 - - - +
936B LEU* 1.3 63.5 + - - +
937B PRO* 4.7 1.0 - - - +
1291B LYS* 3.5 14.8 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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