Contacts of the helix formed by residues 938 - 951 (chain B) in PDB entry 3LMG
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 THR 938 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B TYR* 6.3 0.2 - - - -
807B GLU* 4.7 10.8 - - - +
875B VAL* 4.9 2.9 - - - -
936B ARG 3.7 2.8 + - - +
937B PRO* 1.3 76.2 - - - +
939B PHE* 1.3 63.8 + - - +
940B LYS* 3.4 11.3 + - - +
941B GLU* 2.9 44.6 + - - +
942B LEU* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 939 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ALA* 4.0 9.7 - - - +
803B MET* 3.4 49.6 - - + -
804B TYR* 3.8 22.2 - - + +
807B GLU* 3.9 21.4 + - + +
871B HIS* 3.6 21.1 - - - -
874B ASP* 3.7 15.5 - - + -
875B VAL* 3.6 28.0 - - + -
878B TYR* 3.7 27.8 - + + -
938B THR* 1.3 74.1 - - - +
940B LYS* 1.3 57.1 + - - +
942B LEU* 3.2 15.4 + - + +
943B ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 940 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B TYR* 3.7 34.8 - - + -
938B THR* 3.1 10.5 - - - +
939B PHE* 1.3 79.4 - - - +
941B GLU* 1.3 61.1 + - + +
943B ALA* 3.4 6.4 - - - +
944B ASN* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 941 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B PRO* 3.2 17.9 - - + +
938B THR* 2.9 47.3 + - - +
940B LYS* 1.3 73.3 - - + +
942B LEU* 1.3 60.9 + - - +
944B ASN* 3.0 10.5 + - - +
945B GLU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 942 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ALA* 4.3 4.5 - - + -
875B VAL* 4.1 9.6 - - + -
878B TYR* 3.7 40.2 - - + +
924B VAL* 3.7 28.0 - - + -
927B LYS* 5.8 0.2 - - - +
928B CYS* 3.9 7.4 - - - -
937B PRO* 3.7 29.6 - - + +
938B THR 3.2 16.5 + - - +
939B PHE* 3.2 25.5 + - + +
941B GLU* 1.3 79.5 - - - +
943B ALA* 1.3 60.4 + - - +
945B GLU* 3.4 3.9 + - - +
946B PHE* 3.3 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B VAL* 4.1 7.1 - - + +
800B ALA* 3.8 18.2 - - + +
801B LYS* 4.7 20.0 - - + +
804B TYR* 5.8 2.0 - - + -
939B PHE 2.8 13.6 + - - +
940B LYS* 3.4 13.5 - - - +
941B GLU 3.2 0.2 - - - -
942B LEU* 1.3 76.0 - - - +
944B ASN* 1.3 57.6 + - - +
946B PHE* 4.2 0.3 - - - -
947B THR* 2.4 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940B LYS* 3.2 18.2 + - - +
941B GLU* 3.0 12.9 + - - +
943B ALA* 1.3 80.2 - - - +
945B GLU* 1.3 61.9 + - - +
947B THR* 4.0 8.3 + - - -
948B ARG* 3.6 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 945 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920B ASP* 5.1 4.8 - - - +
924B VAL* 3.2 35.0 - - + +
927B LYS* 4.7 13.4 + - - +
941B GLU 2.9 14.4 + - - +
942B LEU* 4.2 5.2 - - - +
943B ALA 3.4 0.2 - - - -
944B ASN* 1.3 75.1 - - - +
946B PHE* 1.3 62.9 + - + +
948B ARG* 3.4 34.4 + - - +
949B MET* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 946 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B LEU* 3.7 40.1 - - + +
796B GLY* 3.9 11.7 - - - -
797B VAL* 3.6 22.2 - - + +
878B TYR* 3.5 22.7 - + - -
882B VAL* 3.9 22.2 - - + -
886B MET* 4.1 15.5 - - + -
921B VAL* 4.9 6.7 - - + -
924B VAL* 3.7 35.2 - - + -
942B LEU* 3.3 26.0 + - + +
943B ALA 4.2 0.4 - - - +
945B GLU* 1.3 76.0 - - + +
947B THR* 1.3 56.1 + - - +
949B MET* 3.5 8.3 - - + +
950B ALA* 2.6 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 947 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B VAL* 3.5 22.6 - - + +
801B LYS* 5.2 2.7 - - - -
943B ALA* 2.4 29.0 + - - +
944B ASN* 4.0 9.7 + - - -
945B GLU 3.3 0.2 - - - -
946B PHE* 1.3 78.3 - - - +
948B ARG* 1.3 61.2 + - - +
950B ALA* 3.4 11.3 + - - +
951B ARG* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 948 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920B ASP* 6.3 2.0 - - - +
944B ASN 3.6 11.2 + - - +
945B GLU* 3.4 44.3 + - - +
946B PHE 3.3 0.2 - - - -
947B THR* 1.3 76.7 - - - +
949B MET* 1.3 68.8 + - - +
950B ALA 3.3 0.2 - - - -
951B ARG* 3.4 20.0 - - - +
952B ASP* 4.2 2.1 + - - +
956B TYR* 4.3 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 949 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B LEU* 3.6 22.6 - - + +
920B ASP* 5.0 4.3 - - - +
921B VAL* 3.3 41.5 - - + -
924B VAL* 4.5 11.7 - - + -
945B GLU* 3.0 41.5 + - + +
946B PHE* 3.2 11.4 + - + +
948B ARG* 1.3 79.0 - - + +
950B ALA* 1.3 65.5 + - - +
951B ARG 3.1 0.9 - - - -
952B ASP 3.1 15.2 + - - +
956B TYR* 3.2 57.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 950 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B GLN* 3.9 15.5 + - + +
793B LEU* 4.3 19.9 - - + +
794B ASN* 4.2 19.1 - - - +
797B VAL* 4.6 5.4 - - + -
946B PHE 2.6 22.5 + - - +
947B THR* 3.5 10.1 - - - +
948B ARG 3.3 0.2 - - - -
949B MET* 1.3 67.4 - - - +
951B ARG* 1.3 61.1 + - - +
952B ASP 3.1 6.5 + - - -
953B PRO* 3.3 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 951 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B THR 3.4 7.4 + - - +
948B ARG* 3.4 18.8 - - - +
949B MET 3.1 0.6 - - - -
950B ALA* 1.3 78.1 - - - +
952B ASP* 1.3 59.8 + - + +
953B PRO* 3.8 2.5 - - - +
----------------------------------------------------------
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