Contacts of the helix formed by residues 1301 - 1309 (chain A) in PDB entry 1FO4
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 THR1301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A SER* 6.3 2.2 - - - -
504A MET* 6.2 1.1 - - - -
1207A THR 3.7 7.4 - - - +
1208A LEU 4.4 9.2 - - - +
1210A GLU* 3.9 24.0 + - + +
1299A PRO* 2.9 34.3 + - + +
1300A ALA* 1.3 75.7 - - - +
1302A PRO* 1.3 77.9 - - + +
1303A GLU* 3.5 10.8 + - - +
1304A LYS* 3.1 25.4 + - - +
1305A ILE* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 3.6 19.5 - - - +
424A ALA 3.4 13.9 - - - +
425A SER* 3.4 32.8 - - - +
507A PHE* 3.6 8.5 - - + -
1169A GLY* 3.4 28.9 - - - +
1170A ASP* 4.8 1.6 - - - -
1171A HIS* 6.2 1.8 - - - +
1207A THR 4.4 7.2 - - - +
1208A LEU* 5.1 2.7 - - + -
1300A ALA 4.7 0.2 - - - +
1301A THR* 1.3 87.7 - - + +
1303A GLU* 1.3 57.4 + - - +
1305A ILE* 4.3 1.6 - - + -
1306A ARG* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A MET* 3.3 53.1 - - + +
506A GLU* 4.5 5.4 - - - +
507A PHE* 3.7 31.0 - - + +
1210A GLU* 4.5 7.1 - - - +
1301A THR* 3.1 9.4 + - - +
1302A PRO* 1.3 80.4 - - - +
1304A LYS* 1.3 67.6 + - + +
1306A ARG* 3.9 0.9 - - - +
1307A ASN* 3.0 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A TYR* 6.5 0.4 - - - -
1210A GLU* 3.0 27.1 + - - -
1296A LEU* 4.2 17.0 - - + +
1297A ASP* 3.6 33.7 - - + +
1298A SER 4.2 1.2 + - - -
1299A PRO* 2.8 33.6 + - - +
1300A ALA* 4.4 0.2 - - - -
1301A THR* 3.1 18.4 + - - +
1303A GLU* 1.3 88.0 + - + +
1305A ILE* 1.3 65.5 + - - +
1307A ASN* 4.3 4.1 - - - +
1308A ALA* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A ILE* 4.4 20.6 - - + -
1165A ASP 5.0 1.6 - - - +
1169A GLY* 3.6 28.5 - - - +
1171A HIS* 4.4 13.2 - - + +
1274A ILE* 3.8 34.3 - - + -
1278A ILE* 4.0 20.6 - - + +
1300A ALA* 3.5 22.9 - - + +
1301A THR 2.9 18.6 + - - +
1302A PRO* 3.8 4.3 - - + +
1304A LYS* 1.3 77.2 - - - +
1306A ARG* 1.3 61.8 + - - +
1308A ALA* 3.3 4.3 + - - +
1309A CYS* 3.2 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A PHE* 3.3 28.7 - - + -
510A THR* 3.4 24.3 - - + +
511A LEU* 4.8 1.6 - - + -
514A SER* 2.8 23.0 + - - -
1166A CYS 3.1 24.3 + - - -
1167A LEU* 2.7 37.3 + - - +
1168A THR* 3.7 7.6 - - - +
1169A GLY* 4.1 2.5 - - - -
1302A PRO 2.9 17.9 + - - +
1305A ILE* 1.3 79.6 - - - +
1307A ASN* 1.3 61.9 + - - +
1309A CYS* 3.1 37.7 + - - +
1311A ASP* 3.1 21.6 + - - -
1313A PHE* 4.0 4.2 - - - -
1314A THR* 3.6 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLU* 3.9 27.8 + - - +
507A PHE* 3.5 27.4 + - - +
510A THR* 4.6 4.9 + - - -
1303A GLU* 3.0 39.1 + - - +
1304A LYS* 4.3 4.2 - - - +
1306A ARG* 1.3 77.4 - - - +
1308A ALA* 1.3 61.1 + - - +
1309A CYS 3.5 0.3 + - - -
1310A VAL* 3.7 17.3 + - - +
1314A THR* 4.6 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278A ILE* 3.7 26.7 - - + -
1282A ARG* 2.6 38.3 + - - +
1294A PHE* 4.4 12.3 - - + -
1295A ARG 6.0 0.2 - - - +
1296A LEU* 5.1 3.1 - - + -
1304A LYS 3.2 19.6 + - - +
1305A ILE 3.5 5.8 - - - +
1306A ARG 3.2 0.6 - - - -
1307A ASN* 1.3 76.8 - - - +
1309A CYS* 1.3 57.5 + - - +
1310A VAL 2.9 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A ILE* 4.1 19.7 - - - -
1166A CYS* 3.8 28.7 - - + +
1278A ILE* 4.6 7.0 - - - -
1281A ALA* 3.8 27.8 - - + -
1282A ARG* 4.8 4.9 - - - +
1286A THR* 4.5 0.2 - - - -
1305A ILE* 3.2 18.8 + - - -
1306A ARG* 3.1 30.6 + - - +
1307A ASN 4.3 0.2 - - - -
1308A ALA* 1.3 72.6 - - - +
1310A VAL* 1.3 66.9 + - - +
1311A ASP* 3.4 5.9 + - - +
1314A THR* 3.8 0.7 - - - +
----------------------------------------------------------
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