Contacts of the helix formed by residues 1085 - 1096 (chain B) in PDB entry 4G0U
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 SER1085 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A LYS* 4.1 14.0 - - - +
1152A GLU* 3.2 19.5 - - - -
1084B ARG* 1.3 75.5 - - - +
1086B LYS* 1.3 66.6 + - - +
1087B LYS* 3.8 9.8 + - - +
1088B ASP* 3.0 32.3 + - - +
1089B LEU* 2.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A TRP* 3.6 38.6 - - + -
1150A THR* 5.2 1.3 - - - -
1152A GLU* 3.1 25.4 + - - +
1084B ARG 3.7 0.8 + - - -
1085B SER* 1.3 71.1 - - - +
1087B LYS* 1.3 57.4 + - - +
1089B LEU* 3.7 5.5 - - - -
1090B ILE* 2.8 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A GLU* 5.0 0.2 + - - -
1085B SER* 3.9 9.6 - - - +
1086B LYS* 1.3 80.6 - - - +
1088B ASP* 1.3 70.5 + - - +
1090B ILE* 3.8 5.4 - - - +
1091B GLN* 3.2 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B ARG* 4.3 17.2 + - + +
1085B SER* 3.0 25.9 + - - +
1087B LYS* 1.3 88.3 + - - +
1089B LEU* 1.3 59.1 + - - +
1091B GLN* 3.4 23.0 + - - +
1092B MET* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A TRP* 4.7 1.1 - - + -
1150A THR* 4.1 14.8 - - + -
1070B PHE* 6.0 0.4 - - + -
1080B THR 4.2 1.8 - - - +
1081B ILE* 3.7 39.3 - - + -
1084B ARG* 3.7 33.2 - - + +
1085B SER 2.8 16.1 + - - +
1086B LYS* 3.8 6.3 - - - +
1088B ASP* 1.3 76.1 - - - +
1090B ILE* 1.3 70.1 + - + +
1092B MET* 3.2 10.0 + - + +
1093B LEU* 2.9 34.9 + - + +
1142B LEU* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A TRP* 4.1 25.4 - - + -
1086B LYS* 2.8 33.7 + - + +
1087B LYS* 3.4 5.4 + - - +
1089B LEU* 1.3 77.9 - - + +
1091B GLN* 1.3 65.1 + - - +
1093B LEU* 3.1 6.0 + - + +
1094B VAL* 3.1 23.2 + - + +
1136B PRO* 4.0 33.0 - - + +
1138B PHE* 4.2 22.7 - - + +
1142B LEU* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087B LYS* 3.2 24.5 + - - +
1088B ASP* 3.4 24.5 + - - +
1090B ILE* 1.3 81.2 - - - +
1092B MET* 1.3 66.2 + - - +
1094B VAL* 3.3 7.4 + - - +
1095B GLN* 2.7 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B PHE* 5.6 0.4 - - + -
1079B ILE* 3.4 35.0 - - + -
1080B THR 4.7 6.1 - - - +
1081B ILE* 6.1 0.7 - - + -
1084B ARG* 3.6 26.5 - - - +
1088B ASP 3.0 21.5 + - - +
1089B LEU* 3.5 11.9 - - + +
1091B GLN* 1.3 80.3 - - + +
1093B LEU* 1.3 86.0 + - + +
1095B GLN* 3.6 10.5 + - - +
1096B ARG* 3.1 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B PHE* 4.0 23.1 - - + -
1089B LEU* 2.9 24.1 + - + +
1090B ILE* 3.5 7.6 - - + +
1092B MET* 1.3 90.4 - - + +
1094B VAL* 1.3 66.3 + - - +
1096B ARG 3.1 7.3 + - - -
1098B TYR* 3.1 52.7 + - + -
1138B PHE* 3.5 44.6 - - + -
1141B ILE* 5.1 4.7 - - + -
1142B LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1094 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B ILE* 3.1 16.4 + - + +
1091B GLN* 3.7 10.1 - - - +
1093B LEU* 1.3 76.1 - - - +
1095B GLN* 1.3 61.7 + - + +
1097B GLY* 2.8 21.1 + - - -
1098B TYR 4.7 4.7 - - - +
1136B PRO* 3.9 18.8 - - + -
1138B PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1095 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091B GLN* 2.7 45.7 + - + +
1092B MET* 4.0 8.7 - - - +
1094B VAL* 1.3 81.1 - - + +
1096B ARG* 1.3 58.8 + - + +
1097B GLY* 3.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1096 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B ARG* 2.5 36.2 + - - +
1073B GLU* 3.0 36.8 + - - -
1078B LYS* 3.8 30.4 + - - +
1079B ILE* 4.0 8.3 - - - -
1092B MET* 3.1 42.1 + - + +
1093B LEU 3.1 6.3 + - - +
1095B GLN* 1.3 76.7 - - + +
1097B GLY* 1.3 56.9 + - - +
1098B TYR* 3.4 11.9 - - + -
----------------------------------------------------------
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