Contacts of the helix formed by residues 913 - 930 (chain A) in PDB entry 3UGM
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 913 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE 4.6 5.1 + - - -
908A ILE 5.6 0.2 - - - -
911A ASN 3.1 1.5 + - - -
912A ILE* 1.3 77.9 - - - +
914A GLY* 1.3 57.0 + - - +
915A LYS 3.3 1.6 - - - -
916A GLN* 3.0 6.6 + - - +
917A ALA* 2.6 39.8 + - - +
947A GLY 5.7 0.4 - - - -
18B A 4.2 21.5 - - - -
19B C 4.0 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 914 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE 5.7 0.2 + - - -
879A GLY 5.8 0.4 + - - -
883A ALA* 4.4 11.1 - - - +
908A ILE 4.5 0.7 - - - -
909A ALA* 3.9 26.9 - - - -
911A ASN 3.6 5.3 + - - -
913A GLY* 1.3 76.6 - - - +
915A LYS* 1.3 55.1 + - - +
917A ALA* 2.8 8.3 + - - +
918A LEU* 2.7 43.3 + - - +
18B A 5.0 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 915 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A GLN* 3.8 39.7 - - + +
883A ALA* 4.4 7.3 - - - +
886A THR* 3.5 30.7 - - - +
913A GLY 3.3 0.2 - - - -
914A GLY* 1.3 73.9 - - - +
916A GLN* 1.3 83.7 + - - +
919A GLU* 3.0 47.9 + - - +
17B T 5.2 1.2 + - - -
18B A 3.1 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 916 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLY* 3.0 7.4 + - - +
915A LYS* 1.3 115.0 + - - +
917A ALA* 1.3 65.6 + - - +
919A GLU* 4.9 3.4 + - - +
920A THR* 2.9 31.1 + - - -
949A LYS* 3.2 36.6 - - + +
18B A 2.9 33.4 + - - +
19B C 3.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ILE* 3.9 24.9 - - + +
911A ASN* 6.3 0.9 - - + -
913A GLY 2.6 21.7 + - - +
914A GLY* 2.8 9.1 + - - +
916A GLN* 1.3 73.0 - - - +
918A LEU* 1.3 56.5 + - - +
920A THR* 3.8 1.9 - - - -
921A VAL* 2.9 30.4 + - - +
943A ALA* 4.4 15.4 - - - +
945A ASN 5.8 0.7 - - - +
948A GLY* 5.2 2.7 - - - +
949A LYS* 4.2 15.4 - - - +
952A LEU* 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ALA 4.9 1.6 - - - +
886A THR* 3.6 31.2 - - + -
887A VAL* 4.1 13.9 - - + +
890A LEU* 4.9 7.9 - - + -
894A LEU* 4.3 23.6 - - + -
905A VAL* 4.4 13.9 - - + +
908A ILE* 3.4 26.9 - - + -
909A ALA* 3.7 21.1 - - + -
914A GLY 2.7 21.4 + - - +
917A ALA* 1.3 69.3 - - - +
919A GLU* 1.3 54.2 + - - +
920A THR 2.5 6.8 + - - -
921A VAL* 2.4 35.0 + - + -
922A GLN* 2.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 919 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A THR* 4.0 20.3 + - + +
890A LEU* 5.2 12.3 - - + +
915A LYS* 3.0 44.6 + - - +
916A GLN* 3.8 4.1 + - - +
918A LEU* 1.3 72.5 - - - +
920A THR* 1.3 56.6 + - - +
922A GLN* 4.1 6.6 - - - +
923A ARG* 2.7 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 920 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A GLN* 2.9 16.5 + - - -
917A ALA 4.0 1.6 - - - -
918A LEU 2.5 5.8 + - - -
919A GLU* 1.3 77.8 - - - +
921A VAL* 1.3 68.1 + - - +
923A ARG* 3.8 5.9 - - - +
924A LEU* 3.1 33.5 + - + +
949A LYS* 2.8 54.4 + - + +
952A LEU* 4.0 15.4 - - + +
953A GLU* 4.4 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.9 18.6 - - + -
900A LEU* 4.8 8.1 - - + -
908A ILE* 4.3 10.3 - - + -
917A ALA 2.9 15.8 + - - +
918A LEU* 2.4 35.7 + - + +
920A THR* 1.3 68.1 - - - +
922A GLN* 1.3 79.7 + - - +
924A LEU 2.8 4.9 + - - -
925A LEU* 2.8 26.6 + - + -
939A VAL* 3.9 19.1 - - + -
940A VAL* 5.1 4.7 - - + -
943A ALA* 3.9 25.8 - - + -
952A LEU* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A LEU* 3.7 45.9 - - + +
893A VAL* 4.3 22.0 - - + +
894A LEU* 3.8 10.5 - - + -
898A HIS* 4.6 7.9 + - + -
918A LEU 2.9 4.9 + - - +
919A GLU* 4.1 5.9 - - - +
921A VAL* 1.3 83.9 - - - +
923A ARG* 1.3 99.8 + - - +
924A LEU 3.1 0.3 + - - -
925A LEU* 3.2 11.9 + - - +
926A PRO* 3.5 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A GLU* 2.7 62.5 + - - +
920A THR* 3.8 5.5 - - - +
922A GLN* 1.3 93.2 + - - +
924A LEU* 1.3 75.2 + - + +
925A LEU 4.0 0.2 + - - -
926A PRO* 4.9 2.1 - - - +
927A VAL* 4.2 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A THR* 3.1 27.8 + - + +
921A VAL 2.8 10.5 + - - +
923A ARG* 1.3 95.6 - - + +
925A LEU* 1.3 66.1 + - - +
926A PRO* 3.7 0.7 - - - -
927A VAL* 3.8 12.2 + - + +
928A LEU* 3.5 17.2 + - - +
939A VAL* 5.3 0.9 - - - +
952A LEU* 5.0 9.6 - - + -
953A GLU* 4.7 15.7 - - + +
956A GLN* 3.8 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 5.4 2.7 - - + -
898A HIS* 3.8 32.3 - - + -
900A LEU* 4.0 29.2 - - + -
921A VAL* 2.8 21.6 + - + +
922A GLN* 3.2 3.3 + - - +
924A LEU* 1.3 68.7 - - - +
926A PRO* 1.4 82.7 - - + +
928A LEU* 2.7 20.5 + - - +
929A CYS* 3.7 18.7 + - - -
936A GLN* 4.7 11.7 - - + +
939A VAL* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A HIS* 3.5 27.6 - - + +
922A GLN 3.5 8.7 - - - +
923A ARG 4.9 2.7 - - - +
924A LEU 4.1 0.2 - - - -
925A LEU* 1.4 97.4 - - + +
927A VAL* 1.3 63.8 + - + +
928A LEU 2.9 5.2 + - - -
929A CYS* 3.4 12.4 + - + +
930A GLN* 3.2 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A ARG 4.2 17.9 - - - +
924A LEU* 3.9 14.6 - - + +
925A LEU 2.9 3.0 + - - -
926A PRO* 1.3 77.2 - - + +
928A LEU* 1.3 59.3 + - - +
930A GLN* 3.5 23.0 - - - +
956A GLN* 4.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A LEU 3.5 7.5 + - - +
925A LEU 2.7 18.1 + - - +
926A PRO 2.9 0.2 + - - -
927A VAL* 1.3 72.1 - - - +
929A CYS* 1.3 69.9 + - - +
930A GLN 3.1 5.7 + - - -
933A GLY 4.2 3.3 + - - -
934A LEU* 3.3 28.0 + - + +
939A VAL* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A LEU* 3.7 17.7 + - - -
926A PRO* 3.4 7.1 + - + +
928A LEU* 1.3 80.6 - - - +
930A GLN* 1.3 63.2 + - + +
933A GLY* 3.7 9.0 + - - -
934A LEU* 3.1 26.6 + - - +
935A THR* 4.1 2.0 - - - -
936A GLN* 3.8 42.6 - - - -
939A VAL* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A PRO* 3.2 41.2 + - - +
927A VAL* 3.5 23.9 + - - +
928A LEU 3.1 3.6 - - - -
929A CYS* 1.3 83.7 - - + +
933A GLY 5.2 4.9 - - - -
----------------------------------------------------------
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