Contacts of the strand formed by residues 1300 - 1309 (chain A) in PDB entry 1OFD
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 ASN1300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265A THR 3.2 8.0 + - - +
1266A THR* 3.2 27.9 + - - +
1267A ALA 2.9 26.3 + - - +
1297A PHE* 3.9 1.8 - - - -
1299A GLY* 1.3 77.0 - - - +
1301A ILE* 1.3 64.5 + - - +
1302A THR* 3.9 14.7 + - - -
1320A GLY* 3.4 8.2 - - - +
1322A THR* 4.6 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257A ILE* 3.9 16.8 - - + +
1260A ALA* 3.7 29.8 - - + -
1261A ILE* 4.2 12.1 - - + -
1267A ALA* 3.4 6.7 - - + +
1284A LEU* 4.0 35.9 - - + -
1288A ILE* 4.4 4.7 - - + -
1297A PHE* 4.3 13.7 - - + -
1300A ASN* 1.3 77.3 + - - +
1302A THR* 1.3 63.8 + - - +
1303A LEU* 3.7 28.2 - - + +
1320A GLY 2.6 14.4 + - - +
1321A MET* 3.4 5.1 - - + -
1322A THR* 2.8 26.5 + - - +
1323A LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266A THR* 6.2 0.2 - - - +
1267A ALA 2.9 9.4 + - - +
1268A THR* 3.2 19.7 + - + +
1269A LYS 3.1 24.6 + - - +
1300A ASN* 3.9 9.7 + - - -
1301A ILE* 1.3 75.3 + - - +
1303A LEU* 1.3 65.7 + - - +
1304A ASN* 3.9 24.0 - - - +
1322A THR* 3.3 20.5 + - + +
1324A HIS* 4.0 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251A ILE* 4.1 27.6 - - + -
1257A ILE* 4.3 2.7 - - + -
1269A LYS* 3.6 21.3 - - + +
1271A TYR* 4.4 4.0 - - + -
1281A GLY* 4.7 7.9 - - - -
1284A LEU* 3.9 20.4 - - + -
1301A ILE* 3.7 21.8 - - + +
1302A THR* 1.3 80.3 - - - +
1304A ASN* 1.3 60.8 + - - +
1305A PHE* 3.5 29.3 - - + -
1322A THR 2.8 8.7 + - - +
1323A LEU* 3.5 24.4 - - + -
1324A HIS* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268A THR* 3.4 30.5 - - - +
1269A LYS 2.8 9.1 + - - +
1270A THR* 3.2 28.4 + - + +
1271A TYR* 2.8 27.0 + - - -
1302A THR* 3.9 6.0 - - - +
1303A LEU* 1.3 75.0 - - - +
1305A PHE* 1.3 64.0 + - - +
1324A HIS* 3.4 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247A LEU* 4.1 8.7 - - + -
1251A ILE* 4.3 4.3 - - + -
1270A THR* 5.9 0.2 - - - -
1271A TYR* 3.2 34.1 - + + -
1273A LEU* 3.7 32.8 - - + -
1280A VAL* 3.4 29.2 - - + -
1303A LEU* 3.5 42.4 - - + -
1304A ASN* 1.3 78.7 - - - +
1306A GLN* 1.3 67.4 + - - +
1313A PHE* 3.7 19.3 - + - -
1323A LEU* 4.2 7.2 - - + -
1324A HIS 2.7 21.0 + - - +
1325A LEU* 3.5 7.9 - - + -
1326A GLN* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270A THR* 4.8 16.2 - - + +
1271A TYR 3.0 10.8 + - - +
1272A ARG* 3.3 38.0 + - - +
1273A LEU* 2.7 32.8 + - - -
1305A PHE* 1.3 78.9 - - - +
1307A GLY* 1.3 56.4 + - - +
1325A LEU* 4.6 0.7 - - - -
1326A GLN* 3.4 39.6 + - + +
1347A HIS* 4.8 0.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272A ARG* 3.6 15.5 - - - +
1273A LEU* 3.6 8.5 - - - -
1306A GLN* 1.3 74.8 - - - +
1308A ALA* 1.3 59.9 - - - -
1309A ALA 3.9 0.4 - - - -
1325A LEU* 3.7 7.0 - - - +
1326A GLN 2.9 10.2 + - - +
1327A GLY* 3.3 6.0 - - - -
1328A GLU* 3.3 23.0 + - - +
1347A HIS* 3.7 7.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
369A GLY* 3.2 39.9 - - - +
1273A LEU* 3.8 6.2 + - - -
1274A VAL* 2.9 32.3 - - - +
1275A ASN 3.0 3.1 + - - +
1307A GLY* 1.3 71.6 - - - -
1309A ALA* 1.3 62.2 + - - +
1328A GLU* 3.3 23.3 - - + +
1330A ASN* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273A LEU* 3.8 15.7 - - + +
1274A VAL 4.4 0.4 - - - -
1275A ASN* 4.2 0.2 - - - -
1277A ASP 5.0 0.7 - - - +
1307A GLY 3.9 2.2 + - - -
1308A ALA* 1.3 72.3 - - - +
1310A GLY* 1.3 63.3 + - - +
1313A PHE* 3.7 34.5 - - + -
1325A LEU* 3.7 17.9 - - + -
1328A GLU 2.9 8.7 + - - +
1329A ALA* 4.0 3.6 - - + -
1330A ASN* 2.9 31.4 + - - -
----------------------------------------------------------
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