Contacts of the helix formed by residues 937 - 946 (chain A) in PDB entry 1FO4
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 PRO 937 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A GLY 4.8 0.4 - - - +
936A LEU* 1.3 90.6 - - + +
938A ALA* 1.3 67.6 + - - +
939A GLU* 3.3 28.5 - - - +
940A GLU* 2.9 37.2 + - + +
941A VAL* 3.1 11.1 + - - +
981A LYS* 4.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 938 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A SER* 6.0 1.8 - - - -
931A ALA* 3.9 21.5 - - + +
936A LEU 3.2 3.8 + - - -
937A PRO* 1.3 70.0 - - - +
939A GLU* 1.3 67.4 + - - +
941A VAL* 3.0 4.0 + - - +
942A ARG* 2.9 50.1 + - - +
977A TYR* 5.3 3.6 - - - +
999A CYS* 5.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 939 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A PRO* 3.3 25.0 - - - +
938A ALA* 1.3 80.6 + - - +
940A GLU* 1.3 62.3 + - + +
942A ARG* 3.5 1.7 + - - +
943A TRP* 3.0 30.7 + - - +
968A TRP* 3.5 27.8 - - + +
972A LEU* 5.1 2.5 - - + -
977A TYR* 2.8 36.0 + - + +
978A TYR* 3.6 30.5 - - - +
981A LYS* 4.1 10.0 - - - +
1000A ILE* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 940 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936A LEU* 3.9 20.3 - - - +
937A PRO* 2.9 38.1 + - + +
939A GLU* 1.3 84.0 - - - +
941A VAL* 1.3 64.9 + - - +
943A TRP* 3.5 6.6 + - + +
944A LYS* 3.3 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A THR 4.9 0.4 - - - +
854A GLY* 3.7 18.2 - - - +
927A MET* 3.8 16.4 - - - -
930A VAL* 4.1 11.9 - - + +
931A ALA* 3.9 26.9 - - + +
934A CYS* 5.3 0.2 - - + -
936A LEU* 3.9 25.6 - - + -
937A PRO 3.1 12.7 + - - +
938A ALA 3.0 6.8 + - - +
940A GLU* 1.3 75.9 - - - +
942A ARG* 1.3 61.5 + - - +
944A LYS* 3.6 7.2 - - - +
945A ASN* 2.6 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A TYR* 3.2 33.7 - - + +
924A GLU* 2.7 44.2 + - - +
927A MET* 3.8 17.2 - - + +
928A SER* 4.1 16.3 - - - +
931A ALA* 6.1 0.2 - - - +
938A ALA* 2.9 44.9 + - - +
939A GLU* 3.9 4.0 - - - +
941A VAL* 1.3 76.1 - - + +
943A TRP* 1.3 65.8 + - - +
945A ASN 3.3 1.4 + - - -
946A MET* 3.0 21.4 + - + +
968A TRP* 4.0 12.8 - - + -
999A CYS* 3.9 13.3 - - - -
1000A ILE 4.0 15.8 + - - -
1001A ILE* 3.3 21.2 - - - +
1002A PRO* 4.2 6.3 - - - -
1272A PHE* 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A GLU 3.0 18.8 + - - +
940A GLU* 3.9 7.2 - - + +
941A VAL 3.4 0.2 - - - -
942A ARG* 1.3 76.5 - - - +
944A LYS* 1.3 70.2 + - + +
945A ASN 3.2 0.9 + - - -
946A MET* 3.3 35.6 + - + +
965A PRO* 4.2 34.5 - - + -
968A TRP* 3.8 31.3 - + - +
969A ASP* 4.6 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A THR* 2.7 39.4 + - - +
854A GLY 4.6 0.7 - - - -
855A THR* 4.2 20.7 + - - +
936A LEU* 4.4 2.4 - - - +
940A GLU* 3.3 40.5 + - - +
941A VAL* 3.6 14.4 - - - +
943A TRP* 1.3 87.0 - - + +
945A ASN* 1.3 66.9 + - - +
946A MET 3.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A GLY 3.0 24.5 + - - -
855A THR* 3.3 11.0 - - - +
856A ILE* 2.8 42.0 + - + +
889A TYR* 3.3 16.5 - - + -
890A LYS* 2.9 35.3 + - - +
927A MET* 3.9 5.1 - - + +
941A VAL* 2.6 29.2 + - - +
942A ARG 3.3 3.9 + - - +
943A TRP 3.1 0.6 - - - -
944A LYS* 1.3 79.3 - - - +
946A MET* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A CYS* 3.1 21.5 - - + +
889A TYR* 3.8 1.8 - - + -
890A LYS* 4.4 2.8 - - - +
942A ARG 3.0 17.2 + - - +
943A TRP* 3.3 40.3 + - + +
944A LYS 4.5 3.1 - - - +
945A ASN* 1.3 81.0 - - - +
947A TYR* 1.3 73.6 + - - +
948A LYS* 5.1 1.4 - - - +
951A ASP* 5.0 0.2 - - - +
962A PHE* 4.1 6.3 - - + -
964A VAL* 3.6 27.4 - - + -
965A PRO* 4.5 7.9 - - - -
968A TRP* 3.8 38.1 - - + -
1002A PRO* 4.5 9.0 - - + -
----------------------------------------------------------
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