Contacts of the helix formed by residues 1050 - 1059 (chain B) in PDB entry 3DLS
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 THR1050 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B ILE* 4.8 16.2 - - + -
1040B TRP 5.0 7.2 + - - +
1041B ILE* 4.4 1.6 - - - -
1048B LYS* 5.0 1.6 - - - +
1049B VAL* 1.3 75.9 - - - +
1051B LEU* 1.3 65.2 + - - +
1052B GLU* 3.7 14.4 + - + +
1053B ILE* 3.2 36.7 + - + +
1054B ALA* 2.8 31.9 + - - +
1077B PHE* 4.5 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1051 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040B TRP 5.5 1.2 - - - +
1041B ILE* 3.6 34.9 - - + +
1050B THR* 1.3 74.4 + - - +
1052B GLU* 1.3 60.3 + - - +
1054B ALA* 4.0 6.1 - - + -
1055B ILE* 3.0 50.0 + - + +
1058B ARG* 5.0 0.9 - - - +
1147B PHE 4.6 1.1 - - - -
1150B ALA 3.4 22.9 - - - +
1151B ALA* 4.3 13.0 - - + -
1152B TYR* 4.3 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1052 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B LYS* 2.7 40.6 + - - +
1030B ILE* 4.7 8.8 - - - +
1050B THR* 3.2 12.9 + - + +
1051B LEU* 1.3 78.4 - - - +
1053B ILE* 1.3 56.9 + - + +
1056B LEU* 3.0 36.2 + - + +
1079B LEU* 4.2 19.2 - - + +
1146B ASP* 4.1 1.4 - - - -
1147B PHE* 3.3 41.4 + - + +
1148B GLY* 3.5 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1053 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B ILE* 3.8 17.5 - - + -
1046B LEU* 4.0 4.5 - - + -
1049B VAL* 3.7 13.9 - - + -
1050B THR* 3.2 27.1 + - + +
1052B GLU* 1.3 78.0 - - - +
1054B ALA* 1.3 57.1 + - - +
1056B LEU* 3.5 3.8 + - - +
1057B SER* 2.7 40.4 + - - +
1070B ILE* 3.2 33.9 - - + -
1077B PHE* 3.6 42.4 - - + -
1079B LEU* 4.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1054 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B ILE* 3.7 28.3 - - + -
1043B ASP* 3.8 14.9 - - - +
1046B LEU* 4.1 6.7 - - - -
1049B VAL* 3.9 5.1 - - + +
1050B THR 2.8 19.8 + - - +
1051B LEU* 4.2 6.3 - - + +
1053B ILE* 1.3 75.6 - - - +
1055B ILE* 1.3 60.1 + - - +
1057B SER* 3.4 3.1 + - - -
1058B ARG* 3.2 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1055 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051B LEU* 3.0 36.0 + - + +
1052B GLU* 4.3 1.3 - - - +
1054B ALA* 1.3 73.3 - - - +
1056B LEU* 1.3 58.8 + - - +
1058B ARG* 2.9 25.3 + - - +
1059B VAL* 3.2 14.2 + - + +
1124B ILE* 3.9 25.1 - - + -
1147B PHE* 3.8 27.1 - - + -
1150B ALA* 3.5 35.9 - - + +
1151B ALA* 4.0 7.9 - - - +
1152B TYR* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1056 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B GLU* 3.0 25.0 + - + +
1053B ILE* 3.9 3.8 - - - +
1055B ILE* 1.3 77.0 - - - +
1057B SER* 1.3 59.9 + - - +
1058B ARG 3.5 0.3 + - - -
1059B VAL* 3.9 23.4 + - + +
1064B ILE* 4.4 0.7 - - + -
1065B ILE* 3.7 40.1 - - + +
1067B VAL* 3.8 26.9 - - + +
1079B LEU* 3.9 29.2 - - + -
1081B MET* 4.5 5.8 - - - -
1146B ASP 5.7 2.0 - - - +
1147B PHE* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1057 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ASP* 5.3 0.7 - - - -
1046B LEU* 3.4 32.4 - - - +
1053B ILE* 2.7 30.4 + - - +
1054B ALA 3.5 6.7 - - - -
1055B ILE 3.2 0.2 - - - -
1056B LEU* 1.3 72.7 - - - +
1058B ARG* 1.3 60.4 + - - +
1059B VAL 3.6 1.7 - - - +
1067B VAL* 5.1 8.8 - - - +
1070B ILE* 4.5 7.4 - - - +
1079B LEU* 5.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1058 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B ILE* 4.0 19.2 - - - +
1042B GLU 5.1 1.2 + - - -
1043B ASP* 2.8 37.3 + - - +
1044B PRO* 5.2 3.0 - - - +
1051B LEU* 5.0 2.2 - - - +
1054B ALA* 3.2 22.1 + - - +
1055B ILE* 2.9 9.8 + - - +
1057B SER* 1.3 81.0 - - - +
1059B VAL* 1.3 64.9 + - + +
1060B GLU* 4.1 1.6 + - - +
1118B TYR* 4.2 3.6 + - - -
1122B LYS* 5.2 4.3 - - + +
1124B ILE* 5.7 1.8 - - + -
1152B TYR* 2.6 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055B ILE* 3.6 17.7 - - + +
1056B LEU* 3.9 22.3 - - + +
1057B SER 4.7 1.9 - - - +
1058B ARG* 1.3 82.7 - - + +
1060B GLU* 1.3 65.3 + - - +
1064B ILE* 3.6 30.1 - - + +
1065B ILE 5.6 1.6 - - - +
1118B TYR* 3.4 18.6 - - + +
1119B LEU* 3.9 12.8 - - + -
1122B LYS* 5.0 3.8 - - + -
1124B ILE* 3.7 28.0 - - + -
1147B PHE* 4.8 5.2 - - + -
----------------------------------------------------------
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