Contacts of the helix formed by residues 944 - 969 (chain D) in PDB entry 1SO2
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 944 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678D ASN* 2.9 26.1 + - + +
943D LYS* 1.3 76.7 - - - +
945D ARG* 1.3 62.2 + - + +
946D ASP* 3.8 24.9 - - + +
947D LEU* 2.5 59.9 + - + +
948D HIS 2.9 7.7 + - - -
1064D HIS* 3.7 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 945 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943D LYS 3.7 1.8 + - - -
944D VAL* 1.3 74.0 - - + +
946D ASP* 1.3 69.8 + - - +
948D HIS* 3.1 1.7 + - - +
949D LEU* 2.8 61.7 + - + +
1064D HIS* 5.2 1.4 + - - -
1068D ASN* 3.4 24.3 + - - +
1071D ILE* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 946 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944D VAL* 2.8 23.5 + - + +
945D ARG* 1.3 90.1 - - - +
947D LEU* 1.3 63.5 + - + +
949D LEU* 4.4 6.1 - - - +
950D LYS* 3.6 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 947 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678D ASN* 3.6 37.2 - - + +
679D PHE 4.2 12.6 - - - +
680D PRO* 5.1 4.0 - - + -
681D ILE* 4.5 7.0 - - + +
682D PHE* 4.2 27.4 - - + -
943D LYS* 3.7 22.9 - - + +
944D VAL* 2.5 34.1 + - + +
946D ASP* 1.3 74.3 - - + +
948D HIS* 1.3 65.7 + - - +
950D LYS* 3.0 13.8 + - - +
951D TRP* 3.1 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 948 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 2.8 25.2 + - - +
940D GLY* 3.3 21.8 + - - +
941D PRO* 3.6 16.7 - - + +
944D VAL 2.9 6.7 + - - +
945D ARG 3.4 5.6 - - - +
947D LEU* 1.3 77.2 - - - +
949D LEU* 1.3 69.6 + - + +
951D TRP 3.1 2.4 + - - -
952D THR* 2.8 50.0 + - - -
988D GLN* 3.7 15.7 - - - -
992D ILE* 4.8 1.1 - - + +
1068D ASN* 3.5 40.4 - - + +
1071D ILE* 4.5 2.0 - - + -
1072D TRP* 3.3 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 949 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945D ARG* 2.8 63.2 + - + +
946D ASP* 4.4 5.8 - - - +
948D HIS* 1.3 81.3 - - + +
950D LYS* 1.3 62.0 + - - +
952D THR* 3.3 5.0 + - - +
953D GLU* 3.0 24.3 + - - +
1071D ILE* 4.3 9.2 - - + -
1072D TRP* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 950 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682D PHE* 3.4 53.2 - - + -
946D ASP 3.6 12.8 + - - +
947D LEU 3.0 9.3 + - - +
949D LEU* 1.3 80.0 - - - +
951D TRP* 1.3 63.4 + - - +
953D GLU* 3.2 34.8 + - - +
954D GLY* 3.2 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 951 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 3.4 26.9 - + + +
681D ILE* 4.3 4.6 - - + +
682D PHE* 3.7 29.7 - + - -
736D TYR* 3.7 35.1 - + - -
738D ASN* 4.9 2.2 - - - -
740D ILE* 3.6 28.0 - - + -
741D HIS* 3.8 32.8 - - + -
744D ASP* 3.7 33.3 + - + -
939D ASN* 4.8 4.9 - - - +
940D GLY* 4.4 13.5 - - - -
943D LYS* 5.3 1.4 - - + +
947D LEU* 3.1 38.2 + - + +
948D HIS 3.7 0.9 - - - +
950D LYS* 1.3 76.2 - - - +
952D THR* 1.3 61.4 + - - +
954D GLY* 3.3 2.4 + - - +
955D ILE* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 952 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 3.4 7.3 + - - -
948D HIS* 2.8 42.7 + - - -
949D LEU* 3.6 9.9 - - - -
950D LYS 3.2 0.2 - - - -
951D TRP* 1.3 77.1 - - - +
953D GLU* 1.3 65.0 + - - +
955D ILE* 3.0 24.2 - - - +
956D VAL* 3.1 12.2 - - + +
984D LEU* 3.5 25.1 - - + -
988D GLN* 3.4 24.0 - - + +
1072D TRP* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 953 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949D LEU 3.0 13.8 + - - +
950D LYS* 3.2 30.8 + - - +
952D THR* 1.3 78.2 - - - +
954D GLY* 1.3 57.1 + - - +
956D VAL* 2.9 24.5 - - + +
957D ASN* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 954 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735D PRO* 3.5 29.2 - - - +
736D TYR* 3.7 10.2 - - - +
950D LYS 3.2 9.3 + - - -
951D TRP* 3.3 4.7 + - - -
952D THR 3.3 0.4 - - - -
953D GLU* 1.3 77.3 - - - +
955D ILE* 1.3 64.1 + - - +
957D ASN* 3.4 1.2 + - - -
958D GLU* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 955 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 4.2 30.7 - - + -
736D TYR* 3.5 35.9 - - + -
737D HIS* 4.5 11.9 - - + -
951D TRP 3.2 10.4 + - - +
952D THR* 3.0 18.6 - - - +
954D GLY* 1.3 72.5 - - - +
956D VAL* 1.3 84.5 + - + +
958D GLU* 2.9 7.6 + - + +
959D PHE* 2.8 58.8 + - + +
987D LEU* 5.0 1.8 - - + -
988D GLN* 4.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 956 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D THR* 3.1 15.3 - - + +
953D GLU* 2.9 30.3 - - + +
955D ILE* 1.3 87.3 - - + +
957D ASN* 1.3 76.7 + - - +
959D PHE* 3.0 11.9 + - - +
960D TYR* 3.0 42.7 + - + +
976D PHE 5.9 0.4 - - - -
984D LEU* 3.3 36.3 - - + -
987D LEU* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 957 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735D PRO* 4.0 13.9 - - + -
953D GLU* 3.0 37.2 + - - +
954D GLY* 3.9 4.0 - - - +
955D ILE 3.2 0.2 - - - -
956D VAL* 1.3 87.4 - - - +
958D GLU* 1.3 60.6 + - - +
960D TYR* 3.5 16.4 + - - +
961D GLU* 3.3 25.8 + - - +
979D ARG* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 958 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734D ILE* 3.2 17.5 - - + +
735D PRO* 3.5 13.6 - - + +
736D TYR* 2.7 33.4 + - + -
737D HIS* 2.6 41.4 + - - -
827D GLY* 3.5 30.8 - - - +
828D ARG* 5.6 0.9 - - - +
954D GLY 3.0 11.3 + - - +
955D ILE* 2.9 13.7 + - + +
957D ASN* 1.3 76.5 - - - +
959D PHE* 1.3 65.7 + - + +
961D GLU* 3.1 17.6 + - + +
962D GLN* 3.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 959 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 4.1 49.6 - + + -
829D THR* 4.9 3.8 - - + -
955D ILE* 2.8 41.2 + - + +
956D VAL* 3.3 11.2 - - - +
958D GLU* 1.3 81.0 - - + +
960D TYR* 1.3 55.3 + - - +
962D GLN* 3.2 5.7 + - + +
963D GLY 3.0 22.5 + - - -
976D PHE* 4.0 20.9 - - + +
977D MET* 3.3 46.9 - - + +
987D LEU* 4.0 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 960 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D VAL* 3.0 35.1 + - + +
957D ASN* 3.9 14.8 - - - +
958D GLU 3.2 0.2 - - - -
959D PHE* 1.3 74.9 - - - +
961D GLU* 1.3 60.1 + - - +
963D GLY* 3.7 0.2 - - - -
964D ASP* 2.8 36.0 + - - +
976D PHE 3.8 16.2 - - - -
977D MET* 3.7 10.5 - - - +
978D ASP 3.7 6.7 - - - -
979D ARG* 3.1 74.0 - - + +
982D PRO* 3.1 26.3 - - + +
983D GLN 5.0 0.3 + - - -
984D LEU* 5.3 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 961 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734D ILE* 5.8 2.4 - - - +
735D PRO* 3.4 33.4 - - - +
828D ARG* 3.5 26.0 + - - +
957D ASN* 3.3 10.1 + - - +
958D GLU* 3.1 10.8 + - + +
960D TYR* 1.3 79.4 - - - +
962D GLN* 1.3 60.9 + - - +
964D ASP* 3.5 10.8 + - - +
965D GLU* 3.3 15.9 + - - +
979D ARG* 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 962 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827D GLY 4.2 2.4 - - - +
828D ARG* 3.2 33.0 - - - +
829D THR* 2.9 45.4 + - - +
832D PHE* 3.6 20.1 - - + +
958D GLU 3.2 8.6 + - - +
959D PHE* 3.2 10.1 + - - +
960D TYR 3.2 0.6 - - - -
961D GLU* 1.3 76.2 - - - +
963D GLY* 1.3 59.7 + - - +
965D GLU* 3.2 2.6 + - - +
966D GLU* 2.8 52.1 + - + +
974D SER* 4.2 3.2 + - - -
977D MET* 3.3 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 963 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D PHE 3.0 10.9 + - - -
960D TYR 3.2 0.6 + - - -
962D GLN* 1.3 76.2 - - - +
964D ASP* 1.3 63.6 + - - +
966D GLU* 3.3 17.7 + - - +
967D ALA* 3.0 24.4 + - - +
973D ILE* 4.0 12.0 - - - +
977D MET* 3.4 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 964 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960D TYR* 2.8 26.2 + - - +
961D GLU* 3.5 10.6 - - - +
962D GLN 3.2 0.2 - - - -
963D GLY* 1.3 77.9 - - - +
965D GLU* 1.3 58.1 + - - +
967D ALA* 3.3 7.1 + - - +
968D ASN* 3.0 37.4 + - - +
977D MET 5.3 1.0 - - - +
979D ARG* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 965 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828D ARG* 2.8 40.0 + - - +
832D PHE* 3.2 19.4 - - + -
961D GLU 3.3 9.2 + - - +
962D GLN 3.2 7.8 + - - +
964D ASP* 1.3 78.1 - - - +
966D GLU* 1.3 67.4 + - - +
968D ASN* 3.0 13.8 + - + +
969D LEU* 3.0 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 966 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832D PHE* 3.7 27.4 - - + +
962D GLN* 2.8 44.8 + - - +
963D GLY* 3.6 13.5 - - - +
965D GLU* 1.3 72.4 - - - +
967D ALA* 1.3 56.0 + - - +
969D LEU* 3.2 6.4 + - - +
971D LEU* 2.7 55.1 + - + +
972D PRO 4.1 5.1 - - - +
973D ILE* 3.3 5.1 - - - +
974D SER* 2.5 51.8 + - - -
977D MET* 4.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 967 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LEU* 3.9 5.0 - - - +
963D GLY 3.0 13.5 + - - +
964D ASP* 3.3 11.4 - - - +
966D GLU* 1.3 73.5 - - - +
968D ASN* 1.3 55.1 + - - +
969D LEU 2.9 4.0 - - - -
970D GLY* 2.7 26.2 + - - -
971D LEU 4.0 7.9 - - - -
973D ILE* 4.3 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 968 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A PRO* 6.0 1.4 - - - +
719A GLN* 4.7 3.1 + - - -
872A LEU* 3.4 15.9 - - - +
873A HIS* 4.7 12.1 + - - -
964D ASP* 3.0 31.2 + - - +
965D GLU* 3.0 13.8 + - + +
967D ALA* 1.3 75.0 - - - +
969D LEU* 1.3 65.3 + - + +
970D GLY 3.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 969 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A GLN* 4.4 21.5 + - - +
866A PRO* 4.6 9.9 - - - +
869A ASN* 4.7 2.3 + - - +
872A LEU* 4.1 4.0 - - - -
832D PHE* 4.3 9.0 - - + -
836D THR* 3.7 29.2 - - + -
965D GLU* 3.0 38.5 + - + +
966D GLU* 3.7 4.9 - - - +
967D ALA 2.9 1.2 - - - -
968D ASN* 1.3 83.4 - - + +
970D GLY* 1.3 59.7 + - - +
971D LEU* 3.1 20.1 + - + +
----------------------------------------------------------
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