Contacts of the strand formed by residues 1300 - 1309 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1265B THR 3.0 7.7 + - - -
1266B THR* 3.3 22.2 + - - +
1267B ALA 3.0 24.9 + - - +
1297B PHE* 3.9 1.2 - - - -
1298B GLU 5.3 0.4 - - - +
1299B GLY* 1.3 76.3 - - - +
1301B ILE* 1.3 61.2 + - - +
1302B THR* 3.8 16.1 + - - -
1320B GLY* 3.4 7.4 - - - +
1322B THR* 3.8 13.7 + - - -
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Residues in contact with ILE1301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257B ILE* 4.0 16.6 - - + +
1260B ALA* 3.7 30.1 - - + -
1261B ILE* 4.1 12.6 - - + -
1267B ALA* 3.5 7.2 - - + +
1284B LEU* 4.1 33.4 - - + -
1288B ILE* 4.2 12.3 - - + -
1297B PHE* 4.3 7.6 - - + -
1300B ASN* 1.3 75.8 - - - +
1302B THR* 1.3 58.4 + - - +
1303B LEU* 3.8 29.4 + - + +
1320B GLY 2.7 13.6 + - - +
1321B MET* 3.4 5.7 - - + +
1322B THR* 2.8 32.1 + - - +
1323B LEU* 5.5 0.2 - - - +
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Residues in contact with THR1302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267B ALA 2.8 14.2 + - - +
1268B THR* 3.3 15.4 + - + +
1269B LYS 3.0 24.6 + - - +
1300B ASN* 3.8 13.5 + - - -
1301B ILE* 1.3 74.5 - - - +
1303B LEU* 1.3 66.4 + - - +
1304B ASN* 4.1 24.2 - - - +
1322B THR* 3.3 18.7 - - + +
1324B HIS* 4.2 12.8 - - + +
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Residues in contact with LEU1303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251B ILE* 4.2 14.6 - - + -
1257B ILE* 4.2 9.6 - - + -
1269B LYS* 3.6 22.4 - - + +
1271B TYR* 4.3 8.5 - - + -
1281B GLY* 4.9 6.1 - - - -
1284B LEU* 3.9 22.2 - - + -
1301B ILE* 3.8 20.0 - - + -
1302B THR* 1.3 80.6 - - - +
1304B ASN* 1.3 58.6 + - - +
1305B PHE* 3.4 30.6 - - + -
1322B THR 2.8 9.3 + - - -
1323B LEU* 3.5 23.8 - - + -
1324B HIS 2.8 32.9 + - - +
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Residues in contact with ASN1304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268B THR* 3.7 21.4 - - - +
1269B LYS 2.8 13.1 + - - -
1270B THR* 3.1 29.3 + - + +
1271B TYR* 2.8 26.7 + - - -
1302B THR* 4.1 8.3 - - - +
1303B LEU* 1.3 73.4 - - - +
1305B PHE* 1.3 61.8 + - - +
1306B GLN* 6.2 0.7 - - + -
1324B HIS* 3.4 32.8 - - + +
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Residues in contact with PHE1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247B LEU* 4.1 9.2 - - + -
1251B ILE* 4.2 5.2 - - + -
1271B TYR* 3.2 35.0 - + + -
1273B LEU* 3.6 34.8 - - + -
1280B VAL* 3.4 28.5 - - + -
1303B LEU* 3.4 45.8 - - + -
1304B ASN* 1.3 73.1 - - - +
1306B GLN* 1.3 66.9 + - - +
1313B PHE* 3.6 17.5 - + - -
1323B LEU* 4.4 7.0 - - + -
1324B HIS 2.7 21.1 + - - +
1325B LEU* 3.5 8.3 - - + -
1326B GLN* 2.9 26.1 + - - +
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Residues in contact with GLN1306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B THR* 4.3 21.1 - - + +
1271B TYR 3.1 10.4 + - - +
1272B ARG* 3.1 40.6 + - - +
1273B LEU* 2.9 24.7 + - - -
1304B ASN* 5.5 0.7 - - + -
1305B PHE* 1.3 81.8 - - - +
1307B GLY* 1.3 57.5 + - - +
1325B LEU* 4.7 0.4 - - - -
1326B GLN* 3.3 35.5 + - + +
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Residues in contact with GLY1307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272B ARG* 3.8 13.2 - - - -
1273B LEU* 3.6 10.1 - - - -
1305B PHE 4.3 0.2 - - - -
1306B GLN* 1.3 75.6 - - - +
1308B ALA* 1.3 59.5 + - - -
1309B ALA 3.9 0.2 - - - -
1325B LEU* 3.7 7.9 - - - +
1326B GLN 2.9 8.8 + - - +
1327B GLY* 3.4 7.0 - - - -
1328B GLU* 3.3 21.2 + - - +
1347B HIS* 3.8 8.7 - - - -
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Residues in contact with ALA1308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ALA 4.5 0.2 - - - +
369B GLY* 3.3 38.4 - - - +
1273B LEU* 3.8 6.0 + - - -
1274B VAL* 3.0 30.9 - - - +
1275B ASN* 3.0 3.3 + - - +
1307B GLY* 1.3 71.6 - - - -
1309B ALA* 1.3 61.3 + - - +
1328B GLU* 3.3 26.0 - - + +
1330B ASN* 4.9 0.2 - - - +
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Residues in contact with ALA1309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1273B LEU* 3.8 14.5 - - + +
1274B VAL 4.5 0.4 - - - -
1277B ASP 4.5 0.9 - - - +
1307B GLY 3.8 2.2 + - - -
1308B ALA* 1.3 72.4 - - - +
1310B GLY* 1.3 60.1 + - - +
1313B PHE* 3.6 39.7 - - + -
1325B LEU* 3.7 18.4 - - + -
1328B GLU 2.9 8.4 + - - +
1329B ALA* 3.7 2.9 - - + -
1330B ASN* 2.9 32.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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