Contacts of the helix formed by residues 1093 - 1103 (chain B) in PDB entry 2BOA
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 ASP1093 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B ASP* 2.7 38.7 + - - +
1091B GLN 5.0 0.2 - - - -
1092B ARG* 1.3 74.2 - - - +
1094B PRO* 1.3 67.0 - - - +
1095B ALA* 3.3 13.6 + - - +
1096B ILE* 3.4 14.7 + - + +
1097B THR* 2.5 32.1 + - - -
1298B LYS* 3.1 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091B GLN 6.1 0.2 - - - -
1092B ARG 3.3 10.1 - - - +
1093B ASP* 1.3 92.0 - - - +
1095B ALA* 1.3 55.7 + - - +
1097B THR* 3.6 6.6 - - - +
1098B SER* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1095 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B ASP* 3.3 16.7 + - - +
1094B PRO* 1.3 76.0 - - - +
1096B ILE* 1.3 60.1 + - - +
1098B SER* 3.1 18.5 + - - -
1099B ILE* 3.1 23.2 + - - +
1298B LYS* 3.8 15.3 - - + -
1302B GLU* 3.4 27.8 - - + +
1305B ARG* 3.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1096 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086B ILE* 4.4 11.2 - - + +
1089B ASP* 3.4 40.4 - - + +
1090B TYR* 4.1 1.6 - - - +
1093B ASP* 3.4 17.3 + - - +
1095B ALA* 1.3 76.5 - - - +
1097B THR* 1.3 64.5 + - - +
1099B ILE* 3.7 10.4 - - + +
1100B LEU* 3.0 39.6 + - + +
1105B ILE* 4.0 26.0 - - + -
1294B TRP* 3.4 35.4 - - + -
1298B LYS* 4.7 3.5 - - + +
1301B MET* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1097 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B ASP 3.7 0.2 + - - -
1090B TYR* 3.7 21.2 - - + -
1091B GLN* 2.7 42.3 + - + +
1093B ASP 2.5 25.8 + - - -
1094B PRO* 3.6 8.3 - - - -
1096B ILE* 1.3 78.0 - - - +
1098B SER* 1.3 57.3 + - - +
1100B LEU* 3.3 3.8 + - - +
1101B GLU* 3.0 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1098 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B PRO 3.0 16.1 + - - -
1095B ALA* 3.1 5.4 + - - -
1097B THR* 1.3 72.7 - - - +
1099B ILE* 1.3 64.9 + - - +
1101B GLU* 3.3 23.8 - - - +
1102B LYS* 3.5 15.8 - - - +
1305B ARG* 2.5 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1099 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095B ALA 3.1 22.6 + - - +
1096B ILE* 3.7 12.6 - - + +
1097B THR 3.3 0.4 - - - -
1098B SER* 1.3 81.9 + - - +
1100B LEU* 1.3 58.7 + - - +
1102B LYS* 3.2 2.9 + - - +
1103B MET* 2.8 49.5 + - + +
1105B ILE* 4.2 24.9 - - + -
1298B LYS* 3.9 9.9 - - + +
1301B MET* 3.8 31.2 - - + +
1302B GLU* 3.5 22.7 - - + -
1305B ARG* 4.1 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B LEU* 4.0 13.7 - - + -
1052B PHE* 3.6 37.2 - - + +
1053B SER* 4.3 2.5 - - - +
1054B THR* 2.8 33.1 + - + +
1059B ARG* 3.7 2.6 + - - -
1086B ILE* 3.8 24.0 - - + -
1090B TYR* 3.7 26.9 - - + -
1096B ILE* 3.0 21.3 + - + +
1097B THR 3.8 3.4 - - - +
1099B ILE* 1.3 76.0 - - - +
1101B GLU* 1.3 56.1 - - - +
1103B MET 2.9 20.6 - - - +
1105B ILE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054B THR* 3.6 7.0 + - - +
1059B ARG* 3.0 23.6 + - - -
1090B TYR* 3.8 18.4 + - - -
1097B THR* 3.0 35.2 + - - +
1098B SER* 3.3 18.6 - - - +
1100B LEU* 1.3 77.4 - - - +
1102B LYS* 1.3 76.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B ARG* 3.8 11.6 - - - +
1060B PRO* 3.3 25.5 - - - +
1098B SER* 3.5 15.9 - - - +
1099B ILE 3.2 3.7 + - - +
1101B GLU* 1.3 94.9 - - + +
1103B MET* 1.3 66.3 + - + +
1305B ARG* 4.4 15.5 - - + +
1308B LEU* 5.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B PHE 4.2 0.2 - - - +
1059B ARG* 4.5 2.7 - - - -
1060B PRO* 3.2 15.7 - - + +
1061B ALA 5.0 0.9 - - - -
1062B VAL* 3.7 26.5 - - + -
1099B ILE* 2.8 30.4 + - + +
1100B LEU* 2.9 31.0 - - - +
1101B GLU 3.7 0.2 - - - -
1102B LYS* 1.3 88.6 - - + +
1104B ASP* 1.3 70.4 + - - +
1105B ILE* 5.4 0.2 - - + -
1190B LYS* 5.1 0.4 - - - -
1301B MET* 3.4 26.5 - - - +
1304B VAL* 3.7 20.9 - - + -
1305B ARG* 3.8 14.6 - - - +
1308B LEU* 4.2 18.4 - - + -
----------------------------------------------------------
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