Contacts of the helix formed by residues 921 - 938 (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 ASN 921 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D LYS* 4.4 8.3 - - - +
918D GLU* 2.5 33.6 + - + +
920D SER* 1.3 74.4 + - - +
922D GLU* 1.3 62.4 + - - +
923D ASN* 2.8 38.2 + - - +
924D ASP* 3.0 28.1 + - + +
925D ARG* 3.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 922 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810D GLU* 5.6 0.2 - - - -
881D ARG* 3.4 41.7 + - - +
920D SER 3.6 3.0 + - - +
921D ASN* 1.3 72.4 + - - +
923D ASN* 1.3 73.6 + - - +
925D ARG* 3.0 24.7 + - - +
926D LEU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 923 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D LYS* 5.5 6.3 - - - +
921D ASN* 2.8 14.4 + - - +
922D GLU* 1.3 76.5 + - - +
924D ASP* 1.3 70.1 + - - +
925D ARG 2.9 1.6 - - - -
926D LEU* 2.8 25.1 + - - +
927D LEU* 3.0 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 924 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D LYS* 3.0 44.3 + - - +
916D GLY 4.0 2.6 - - - +
917D ILE* 3.4 21.4 - - + +
918D GLU* 2.8 36.1 + - - +
921D ASN* 3.0 29.7 + - + -
923D ASN* 1.3 80.2 - - - +
925D ARG* 1.3 60.0 + - - +
927D LEU* 3.6 6.5 + - - +
928D VAL* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 925 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784D ILE* 5.8 4.4 - - - +
805D ASN 3.7 18.9 + - - +
806D ILE* 4.2 10.9 - - + +
807D PRO* 4.0 11.8 - - - +
810D GLU* 2.7 50.6 + - - +
881D ARG* 4.5 0.4 - - - +
917D ILE* 5.1 0.4 - - - -
919D TRP* 2.6 30.4 + - + +
920D SER* 2.8 30.5 + - - +
921D ASN 3.2 10.9 + - - +
922D GLU* 3.0 35.9 + - - +
923D ASN 2.8 1.8 + - - -
924D ASP* 1.3 76.9 - - - +
926D LEU* 1.3 65.0 + - - +
928D VAL* 3.4 7.5 + - - +
929D CYS* 3.1 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 926 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810D GLU* 5.8 0.4 - - - -
884D PHE* 4.6 9.9 - - + -
885D LEU* 4.4 26.9 - - + +
888D GLU* 3.5 46.0 - - + +
889D ALA* 6.1 0.7 - - + -
922D GLU 3.0 9.9 + - - +
923D ASN* 2.8 21.3 + - - +
925D ARG* 1.3 72.2 - - - +
927D LEU* 1.3 55.4 + - - +
929D CYS* 3.1 12.0 + - + +
930D GLN* 2.8 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 927 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D PHE* 4.2 15.5 - - + +
904D GLU* 3.9 28.9 - - + +
905D PHE* 3.4 38.4 - - + +
908D LYS* 4.1 22.2 - - + -
923D ASN 3.0 10.2 + - - +
924D ASP* 3.7 10.8 - - - +
926D LEU* 1.3 74.4 - - - +
928D VAL* 1.3 65.4 + - + +
930D GLN* 3.1 18.9 + - - +
931D VAL* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 928 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802D LEU* 4.8 9.9 - - + -
806D ILE* 4.7 9.0 - - + -
905D PHE* 4.3 16.8 - - + -
917D ILE* 3.5 28.0 - - + -
919D TRP* 4.1 16.8 - - + -
924D ASP 3.2 15.8 + - - +
925D ARG* 3.7 7.9 - - - +
927D LEU* 1.3 77.1 - - + +
929D CYS* 1.3 57.5 + - - +
931D VAL* 3.9 2.1 - - - +
932D CYS* 3.0 27.1 + - + +
1003D TYR* 4.2 4.3 - - + +
1008D LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 929 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806D ILE* 4.1 32.3 - - - -
810D GLU* 5.1 10.1 - - - -
811D LEU* 4.7 7.0 - - - -
814D LEU* 3.6 23.4 - - + +
889D ALA* 6.2 2.0 - - + -
925D ARG 3.1 24.6 + - - -
926D LEU* 3.1 16.2 + - + +
928D VAL* 1.3 75.6 - - - +
930D GLN* 1.3 66.6 + - + +
932D CYS* 3.1 8.7 + - - +
933D ILE* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 930 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888D GLU* 2.9 50.9 + - - +
889D ALA* 4.8 2.7 - - - +
892D ALA* 4.0 9.9 - - + -
901D PHE* 3.4 31.2 - - + -
926D LEU* 2.8 26.5 + - + +
927D LEU* 3.1 33.2 + - + +
929D CYS* 1.3 77.4 - - + +
931D VAL* 1.3 63.4 + - - +
933D ILE* 2.9 15.0 + - - +
934D LYS* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 931 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D PHE* 5.1 9.9 - - + +
902D LEU* 5.9 1.3 - - + -
905D PHE* 3.3 41.7 - - + -
927D LEU* 2.9 21.8 + - + +
928D VAL 3.9 3.8 - - - +
930D GLN* 1.3 75.1 - - + +
932D CYS* 1.3 61.6 + - - +
934D LYS* 3.6 10.7 - - + +
935D LEU* 3.0 23.3 + - + +
999D LEU* 4.2 21.4 - - + +
1002D SER* 6.4 0.2 - - - -
1003D TYR* 3.4 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 932 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749D VAL* 4.1 13.2 - - - -
752D LEU* 4.0 19.8 - - - +
753D THR* 4.0 26.2 - - - -
802D LEU* 5.3 0.7 - - + -
814D LEU* 4.2 2.7 - - + -
928D VAL* 3.0 21.0 + - + +
929D CYS* 3.3 10.1 - - - +
930D GLN 3.0 0.2 - - - -
931D VAL* 1.3 77.8 - - - +
933D ILE* 1.3 57.8 + - - +
935D LEU* 3.2 6.7 + - - +
936D ALA* 3.1 24.1 + - - +
1003D TYR* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 933 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745D VAL* 4.4 12.3 - - + -
749D VAL* 4.0 11.0 - - + +
814D LEU* 3.8 19.5 - - + -
817D ALA* 4.2 13.7 - - + -
818D ALA* 3.9 32.5 - - + +
821D HIS* 4.8 5.2 - - + -
889D ALA* 3.9 22.9 - - + +
892D ALA* 4.7 2.5 - - + -
893D THR* 4.2 19.6 - - + +
929D CYS 2.9 12.8 + - - +
930D GLN* 2.9 23.3 + - - +
932D CYS* 1.3 73.6 - - - +
934D LYS* 1.3 65.3 + - - +
936D ALA* 3.7 0.8 - - - +
937D ASP* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 934 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892D ALA* 3.5 33.1 + - + +
893D THR* 4.7 4.9 - - - +
895D LEU* 3.7 16.7 - - - +
898D HIS* 3.3 56.0 + - - +
901D PHE* 4.1 21.3 - - + -
902D LEU 5.5 0.4 - - - +
930D GLN 2.8 19.0 + - - +
931D VAL* 3.6 12.8 - - + +
933D ILE* 1.3 75.5 - - + +
935D LEU* 1.3 66.0 + - - +
937D ASP* 3.4 11.8 + - - +
938D ILE* 3.3 21.9 + - - +
999D LEU* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752D LEU* 4.6 13.7 - - + -
931D VAL* 3.0 13.4 + - + +
932D CYS* 3.4 9.9 - - - +
934D LYS* 1.3 78.0 - - - +
936D ALA* 1.3 60.8 + - - +
938D ILE* 3.2 9.9 + - + +
939D ASN* 3.2 23.6 + - + +
996D VAL* 5.0 2.2 - - + +
999D LEU* 3.4 27.3 - - + +
1000D CYS* 3.3 35.9 - - - +
1003D TYR* 4.1 34.8 - - + -
1009D LEU* 4.9 8.3 - - + -
1061D LEU* 5.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 936 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745D VAL* 3.5 30.9 - - + +
748D ALA* 3.5 28.9 - - + -
749D VAL* 3.8 11.4 - - + +
752D LEU* 4.8 4.4 - - + +
932D CYS 3.1 14.8 + - - +
933D ILE 3.8 3.1 - - - +
934D LYS 3.3 0.2 - - - -
935D LEU* 1.3 77.9 - - - +
937D ASP* 1.3 59.0 + - - +
938D ILE 3.2 0.2 - - - -
939D ASN* 2.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 937 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 5.6 0.2 - - - -
477D MG 1.9 33.0 - - - -
478D MG 4.3 2.8 - - - -
736D TYR* 3.6 7.6 + - - -
741D HIS* 2.8 23.1 + - - -
745D VAL* 3.9 5.4 - - + -
821D HIS* 2.7 21.7 + - + +
893D THR* 3.8 25.5 - - + +
895D LEU* 6.2 0.2 - - - +
933D ILE 3.0 16.7 + - - +
934D LYS* 3.8 7.2 - - - +
935D LEU 3.3 0.4 - - - -
936D ALA* 1.3 76.9 - - - +
938D ILE* 1.3 66.3 + - + +
939D ASN 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 938 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 3.5 23.7 - - + +
895D LEU* 4.8 17.7 - - + -
898D HIS* 5.3 0.4 - - + -
934D LYS* 3.3 15.5 - - - +
935D LEU* 3.4 8.9 - - + +
936D ALA 3.2 0.4 - - - -
937D ASP* 1.3 89.5 - - + +
939D ASN* 1.3 59.9 + - - +
940D GLY 3.3 4.1 + - - -
941D PRO* 3.8 7.3 - - - +
991D PHE* 4.1 17.9 - - + -
995D ILE* 3.6 23.8 - - + -
996D VAL* 3.6 37.1 - - + +
999D LEU* 4.0 16.4 - - + -
----------------------------------------------------------
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