Contacts of the helix formed by residues 1047 - 1061 (chain A) in PDB entry 3LJ1
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 LYS1047 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A ASP* 3.3 29.2 - - + +
1016A SER* 3.8 4.7 - - - -
1020A ILE* 4.1 0.9 - - - -
1025A TRP* 3.2 22.5 + - - -
1044A HIS* 3.0 58.8 + - + +
1046A SER* 1.3 85.8 + - - +
1048A LEU* 1.3 64.4 + - - +
1049A MET* 3.3 9.2 - - + +
1050A ASP* 3.7 11.4 + - - +
1051A LEU 3.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1048 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A PHE* 4.0 26.7 - - + +
1013A ASP* 4.7 1.4 + - - +
1015A GLY 4.0 11.0 - - - +
1016A SER* 3.0 22.6 + - - +
1019A VAL* 3.8 45.1 - - + -
1020A ILE* 4.1 4.7 - - + -
1046A SER 3.8 0.2 + - - -
1047A LYS* 1.3 70.8 - - - +
1049A MET* 1.3 66.1 + - - +
1050A ASP 3.2 0.7 - - - -
1051A LEU* 3.5 11.4 + - + -
1052A LEU* 3.1 25.0 + - + +
1091A LEU* 4.0 16.6 - - + -
1095A VAL* 4.5 11.0 - - + +
1098A ILE* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A SER* 5.1 0.5 + - - -
997A LEU* 4.7 15.4 - - + +
1009A LEU* 4.5 22.9 - - + +
1012A PHE* 5.3 7.4 - - + +
1013A ASP* 5.9 0.8 - - - +
1047A LYS* 3.3 8.9 - - + +
1048A LEU* 1.3 79.0 - - - +
1050A ASP* 1.3 65.7 + - - +
1052A LEU* 3.4 6.6 + - - +
1053A ARG* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A TRP* 3.7 9.7 - - + -
1041A ARG* 2.8 26.6 + - - -
1042A LYS 3.4 13.2 - - - +
1043A TYR* 3.4 10.4 - - + -
1044A HIS* 3.5 46.2 + - - +
1047A LYS* 3.7 7.4 + - - +
1048A LEU 3.2 0.4 - - - -
1049A MET* 1.3 80.3 - - - +
1051A LEU* 1.3 57.8 + - - +
1052A LEU 3.2 1.3 - - - -
1053A ARG* 3.8 6.3 - - - +
1054A ALA* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A VAL* 4.2 3.8 - - + -
1020A ILE* 4.0 22.0 - - + -
1025A TRP* 3.5 40.9 - - + +
1029A PHE* 4.3 9.0 - - + -
1047A LYS 3.6 4.8 + - - +
1048A LEU* 3.5 19.9 + - + +
1050A ASP* 1.3 76.1 - - - +
1052A LEU* 1.3 57.8 + - - +
1054A ALA* 3.3 3.6 + - + +
1055A LEU* 3.0 25.0 + - + +
1084A PHE* 4.7 9.9 - - + -
1088A PHE* 4.0 44.0 - - + -
1091A LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1052 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A LEU* 4.0 27.4 - - + +
993A VAL* 3.7 29.8 - - + -
994A SER* 3.6 20.2 + - - +
997A LEU* 4.2 13.5 - - + -
1012A PHE* 4.8 3.6 - - + -
1048A LEU* 3.1 19.2 + - + +
1049A MET 3.5 5.2 - - - +
1051A LEU* 1.3 75.7 - - - +
1053A ARG* 1.3 64.4 + - - +
1055A LEU* 3.3 11.9 + - + +
1056A ARG* 3.1 17.0 + - - +
1091A LEU* 4.0 28.7 - - + -
1095A VAL* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1053 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A SER* 3.5 16.3 + - - +
995A ASP* 3.1 26.5 + - - +
998A GLU* 3.3 49.4 + - - +
1041A ARG* 3.6 34.6 - - - +
1043A TYR* 4.3 1.8 - - + +
1049A MET 3.0 16.8 + - - +
1050A ASP 3.4 4.7 + - - +
1052A LEU* 1.3 72.0 - - - +
1054A ALA* 1.3 59.9 + - - +
1056A ARG* 3.1 33.8 + - - +
1057A ASN* 2.9 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1054 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A TRP* 3.8 25.1 - - + -
1029A PHE* 6.2 0.2 - - + -
1033A PHE* 5.1 10.5 - - + -
1037A LEU* 5.8 7.0 - - + -
1043A TYR* 4.2 11.8 - - + -
1050A ASP 2.7 22.9 + - - +
1051A LEU* 3.3 8.1 - - + +
1053A ARG* 1.3 74.1 - - - +
1055A LEU* 1.3 61.3 + - - +
1057A ASN* 3.5 4.3 + - - +
1058A LYS* 3.2 31.5 + - - +
1084A PHE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1055 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A LEU* 3.9 17.5 - - + -
990A LEU* 4.3 21.3 - - + -
991A LEU* 3.5 25.8 - - + +
1051A LEU 3.0 12.5 + - - +
1052A LEU* 3.4 13.9 - - + +
1053A ARG 3.2 0.2 - - - -
1054A ALA* 1.3 75.9 - - - +
1056A ARG* 1.3 62.3 + - + +
1058A LYS 3.7 0.3 + - - -
1059A TYR* 3.3 15.8 + - - +
1080A PHE* 3.5 9.2 - - + -
1081A TYR* 6.2 1.6 - - + -
1084A PHE* 3.5 55.8 - - + -
1091A LEU* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1056 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A LEU* 3.8 21.3 - - + +
994A SER* 3.7 21.3 - - - +
995A ASP* 3.1 32.3 + - - +
1052A LEU 3.1 6.4 + - - +
1053A ARG* 3.1 30.4 + - - +
1055A LEU* 1.3 74.3 - - - +
1057A ASN* 1.3 82.2 - - - +
1059A TYR* 3.0 4.9 + - - +
1060A HIS* 2.9 65.7 + - + +
1061A HIS* 5.2 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1057 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A LEU* 6.3 2.5 - - + -
1041A ARG* 5.1 1.6 + - - -
1043A TYR* 2.6 28.6 + - - +
1053A ARG* 2.9 34.2 + - - +
1054A ALA* 3.9 4.7 - - - +
1056A ARG* 1.3 102.0 - - - +
1058A LYS* 1.3 59.5 + - + +
1060A HIS* 4.5 0.9 - - - +
1061A HIS* 2.9 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1058 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033A PHE* 3.1 52.2 + - + +
1036A ASN* 2.6 42.2 + - - +
1037A LEU* 4.2 13.2 - - - -
1054A ALA* 3.2 18.4 + - - +
1055A LEU 3.8 4.9 - - - +
1057A ASN* 1.3 78.4 - - - +
1059A TYR* 1.3 56.6 + - - +
1061A HIS* 3.7 1.9 - - - -
1062A PHE* 3.2 32.9 + - - +
1065A LEU* 4.1 21.0 - - + +
1069A ILE* 6.3 0.2 - - - +
1073A MET* 3.8 22.0 - - + -
1080A PHE* 3.9 3.6 - - + -
1084A PHE* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1059 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A LEU* 4.1 23.1 - - + -
988A GLU* 4.5 9.4 + - - -
991A LEU* 3.7 37.6 - - + +
1055A LEU 3.3 11.6 + - - +
1056A ARG 3.0 8.5 + - - +
1058A LYS* 1.3 76.8 - - - +
1060A HIS* 1.3 85.8 + + - +
1062A PHE* 3.2 18.8 + - - +
1076A VAL* 5.0 17.3 - - + -
1077A PRO* 5.6 2.4 - - + +
1080A PHE* 3.5 19.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1060 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A LEU* 5.7 5.4 - - + -
995A ASP* 4.6 8.5 - - - -
1056A ARG* 2.9 64.7 + - + +
1057A ASN 4.2 2.0 - - - +
1059A TYR* 1.3 97.5 - + - +
1061A HIS* 1.3 68.4 + - + +
1062A PHE 3.4 1.7 + - - -
1063A MET* 5.0 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1061 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A ARG* 5.2 4.5 - - - -
1057A ASN* 2.9 39.6 + - + +
1058A LYS* 3.7 4.5 - - - -
1060A HIS* 1.3 85.2 - - + +
1062A PHE* 1.3 62.2 + - - +
1063A MET* 3.1 3.4 - - - +
1064A ASP* 3.0 42.8 + - + +
1065A LEU* 3.5 9.5 + - - +
----------------------------------------------------------
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