Contacts of the helix formed by residues 1238 - 1249 (chain E) in PDB entry 3F5P
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 PRO1238 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106E PRO* 4.8 8.1 - - + -
1107E PRO 5.9 0.9 - - - +
1109E LEU* 4.0 40.4 - - + +
1112E MET* 5.3 8.7 - - - -
1206E ALA* 6.0 0.4 - - + -
1236E ASN 3.3 10.1 - - - +
1237E CYS* 1.3 99.1 - - - +
1239E ASP* 1.3 67.4 + - - +
1240E MET* 3.2 4.7 + - + +
1241E LEU* 3.3 12.2 + - + +
1242E PHE* 3.4 0.9 + - - +
1036S ASN* 3.9 18.8 - - + +
1037S GLU* 5.2 10.8 - - + +
1038S ALA* 4.3 8.7 - - - +
1073S GLN* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233E LYS* 3.2 31.5 + - - +
1237E CYS 4.0 2.3 - - - +
1238E PRO* 1.3 72.3 - - - +
1240E MET* 1.3 59.8 + - - +
1242E PHE* 3.2 4.3 + - - +
1243E GLU* 2.8 38.3 + - + +
1037S GLU* 5.5 9.1 + - - +
1038S ALA* 5.3 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109E LEU* 3.9 24.9 - - + -
1113E ILE* 3.4 35.0 - - + -
1238E PRO* 3.2 2.1 - - + +
1239E ASP* 1.3 79.1 - - - +
1241E LEU* 1.3 63.9 + - + +
1243E GLU* 3.0 14.0 + - - +
1244E LEU* 3.1 38.8 + - + +
1266E ILE* 3.8 14.8 - - + -
981F PHE* 3.4 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109E LEU* 4.5 7.2 - - + -
1112E MET* 3.6 37.5 - - + -
1113E ILE* 3.6 31.0 - - + -
1116E ALA* 5.0 2.0 - - + -
1202E LEU* 4.4 29.2 - - + +
1205E ILE* 5.5 1.3 - - + -
1206E ALA* 4.4 6.7 - - + -
1237E CYS* 4.3 6.5 - - - -
1238E PRO* 3.3 12.1 + - + +
1240E MET* 1.3 87.2 - - + +
1242E PHE* 1.3 62.3 + - - +
1244E LEU* 3.2 10.1 + - + +
1245E MET* 3.1 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203E TRP* 5.3 0.2 - + - -
1230E LEU* 6.2 3.4 - - + -
1231E LEU 3.7 15.0 - - - -
1232E ASP 4.0 1.1 - - - -
1233E LYS* 3.3 63.5 - - + -
1234E PRO* 4.0 7.0 - - + -
1237E CYS* 4.0 15.1 - - - -
1238E PRO 3.4 3.7 + - - +
1239E ASP 3.2 7.0 + - - +
1241E LEU* 1.3 76.2 - - - +
1243E GLU* 1.3 68.8 + - - +
1245E MET* 3.9 16.4 - - + -
1246E ARG* 2.9 62.1 + - + +
1249E TRP* 4.2 12.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233E LYS* 5.5 2.8 + - - -
1239E ASP* 2.8 24.0 + - + +
1240E MET* 3.0 12.5 + - - +
1242E PHE* 1.3 83.0 - - - +
1244E LEU* 1.3 66.9 + - - +
1246E ARG* 3.2 32.9 + - - +
1247E MET* 3.2 30.8 + - + +
981F PHE* 4.0 24.0 - - + +
982F SER* 5.1 2.6 - - - -
1041F MET* 2.9 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113E ILE* 5.3 0.9 - - + -
1116E ALA* 5.5 4.5 - - + -
1198E PHE* 5.3 0.2 - - + -
1202E LEU* 3.9 20.2 - - + -
1240E MET* 3.1 29.6 + - + +
1241E LEU* 3.4 14.1 - - + +
1243E GLU* 1.3 75.8 - - - +
1245E MET* 1.3 63.5 + - - +
1247E MET* 2.9 23.2 + - + +
1248E CYS* 3.0 22.3 + - - -
1257E PRO* 5.4 1.1 - - + -
1262E ILE* 4.4 33.7 - - + -
1265E SER* 4.6 5.4 - - - +
1266E ILE* 4.5 11.4 - - + -
981F PHE* 3.9 21.3 - - + -
986F VAL* 4.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199E GLY* 3.9 5.8 - - - +
1202E LEU* 3.6 28.2 - - + +
1203E TRP* 3.5 48.5 - - - +
1206E ALA* 3.9 16.8 - - + -
1234E PRO* 4.7 1.1 - - + -
1237E CYS* 4.2 7.6 - - - -
1241E LEU* 3.1 28.2 + - + +
1242E PHE* 3.8 17.9 - - + +
1243E GLU 3.4 0.2 - - - -
1244E LEU* 1.3 76.3 - - - +
1246E ARG* 1.3 62.7 + - - +
1248E CYS* 3.2 9.2 + - - +
1249E TRP* 3.0 49.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230E LEU* 5.1 17.1 - - + +
1242E PHE* 2.9 56.0 - - + +
1243E GLU* 3.2 21.9 + - - +
1244E LEU 3.1 1.0 - - - -
1245E MET* 1.3 76.9 - - - +
1247E MET* 1.3 55.0 + - - +
1249E TRP* 3.4 16.7 + - + +
1250E GLN* 2.6 27.0 + - - +
1040F SER* 5.8 1.0 - - - +
1041F MET* 3.4 48.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243E GLU* 3.4 30.3 - - + +
1244E LEU* 2.9 13.4 + - + +
1246E ARG* 1.3 73.1 - - - +
1248E CYS* 1.3 60.7 + - - +
1249E TRP 3.1 5.5 + - - -
1250E GLN* 3.3 21.5 + - - +
1256E ARG* 3.6 1.0 - - - +
1257E PRO* 3.5 12.7 - - + +
981F PHE* 4.3 4.9 - - + -
982F SER 3.6 9.4 - - - +
983F ALA* 3.5 27.1 - - - +
986F VAL* 3.3 29.6 - - + -
987F TYR* 3.3 38.7 + - + +
1041F MET* 3.9 19.7 - - + -
1045F ILE* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195E VAL* 3.7 29.2 - - - +
1196E TRP* 3.4 13.7 + - - -
1198E PHE* 3.9 25.4 - - - -
1199E GLY* 3.9 13.5 - - - -
1202E LEU* 5.2 1.1 - - - -
1244E LEU* 3.0 22.2 + - - +
1245E MET* 3.2 8.2 + - - +
1247E MET* 1.3 75.1 - - - +
1249E TRP* 1.3 58.6 + - - +
1250E GLN 3.4 0.4 - - - -
1256E ARG* 3.2 20.7 + - - -
1257E PRO* 4.0 11.9 - - - -
1262E ILE* 4.1 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196E TRP* 3.3 50.7 + + + -
1199E GLY* 3.4 39.2 - - - -
1200E VAL* 3.6 5.8 - - + +
1203E TRP* 3.9 13.2 - + + -
1213E TYR* 5.7 0.9 - - - -
1230E LEU* 3.8 33.9 - - + +
1231E LEU* 3.8 56.5 - - + -
1242E PHE* 4.2 9.6 - + - -
1245E MET* 3.0 36.6 + - + +
1246E ARG* 3.4 12.5 + - + +
1247E MET 3.1 0.8 - - - -
1248E CYS* 1.3 84.7 - - - +
1250E GLN* 1.3 69.2 + - - +
1251E TYR* 3.1 3.6 + - - -
----------------------------------------------------------
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