Contacts of the strand formed by residues 1293 - 1300 (chain B) in PDB entry 5FO9
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 ASN1293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291B GLU* 4.1 12.9 - - - +
1292B LEU* 1.3 78.8 - - - +
1294B LEU* 1.3 57.5 + - - +
1311B ILE 3.7 2.2 - - - -
1312B HIS* 2.4 38.7 + - - +
1314B GLU* 5.1 1.7 - - - +
1336B GLY* 3.3 6.9 - - - -
1337B LYS* 2.7 39.8 + - + +
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Residues in contact with LEU1294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B LEU* 5.3 3.6 - - + +
949B PRO* 4.0 25.1 - - + -
984B GLY* 5.2 3.4 - - - -
1292B LEU* 4.3 13.2 - - + -
1293B ASN* 1.3 71.2 - - - +
1295B ASP* 1.3 59.7 + - - +
1296B VAL* 3.9 15.0 - - + -
1309B HIS 3.7 0.5 - - - +
1310B ARG* 3.2 9.2 - - - +
1311B ILE* 2.9 54.9 + - + +
1312B HIS* 4.7 1.6 + - - -
1334B ALA* 5.3 1.6 - - + -
1335B GLU 3.5 16.2 - - - +
1336B GLY 4.0 1.6 - - - +
1337B LYS 3.5 18.6 - - - +
1338B GLY 4.2 3.8 - - - +
1339B GLN 4.3 4.0 - - - +
1340B GLY* 3.9 31.0 - - - +
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Residues in contact with ASP1295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293B ASN 4.2 0.2 + - - -
1294B LEU* 1.3 73.6 - - - +
1296B VAL* 1.3 61.2 + - - +
1297B SER* 5.3 2.9 + - - -
1308B THR* 3.5 20.4 - - - +
1309B HIS 3.9 0.7 - - - -
1310B ARG* 3.3 34.4 + - + +
1333B THR 3.4 4.5 - - - +
1334B ALA 3.6 0.2 - - - -
1335B GLU* 2.9 56.7 + - + +
1336B GLY* 5.9 0.2 - - - -
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Residues in contact with VAL1296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B LEU* 4.7 5.4 - - + -
982B LEU* 3.6 43.5 - - + -
1294B LEU* 4.7 16.4 - - + -
1295B ASP* 1.3 82.5 + - - +
1297B SER* 1.3 64.4 + - - +
1298B LEU* 4.5 4.4 - - + +
1307B ILE 3.7 0.7 - - - +
1308B THR* 3.5 2.9 - - - +
1309B HIS* 2.9 42.8 + - - +
1311B ILE* 5.5 5.4 - - + -
1332B VAL* 3.9 22.4 - - + -
1333B THR 3.4 3.6 - - - +
1334B ALA* 4.3 14.6 - - + -
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Residues in contact with SER1297 (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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1295B ASP* 5.3 4.2 + - - -
1296B VAL* 1.3 75.7 - - - +
1298B LEU* 1.3 69.3 + - - +
1306B LYS* 5.2 8.3 - - - -
1307B ILE 3.1 9.2 - - - -
1308B THR* 4.3 12.8 - - - -
1331B THR 3.8 0.9 - - - +
1332B VAL* 3.7 0.3 - - - -
1333B THR* 2.9 56.4 + - - +
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Residues in contact with LEU1298 (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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980B ILE* 4.5 26.7 - - + -
982B LEU* 5.2 11.2 - - + -
1296B VAL* 4.5 7.9 - - + -
1297B SER* 1.3 85.8 - - - +
1299B GLN* 1.3 61.3 + - - +
1300B LEU* 4.0 11.8 + - + -
1305B SER 3.9 1.0 - - - +
1306B LYS* 3.6 5.5 - - - -
1307B ILE* 2.8 53.7 + - + +
1309B HIS* 5.4 1.8 - - + -
1322B GLU* 4.4 25.6 - - + -
1330B PHE* 4.5 6.5 - - + -
1331B THR 3.8 2.5 - - - +
1332B VAL* 3.7 36.1 - - + -
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Residues in contact with GLN1299 (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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1297B SER 4.3 0.2 - - - -
1298B LEU* 1.3 70.5 - - - +
1300B LEU* 1.3 69.0 + - - +
1301B PRO* 3.9 3.6 - - - +
1303B ARG 3.5 16.6 - - - +
1304B SER* 3.3 18.6 + - - +
1305B SER 4.5 1.6 - - - -
1306B LYS* 3.3 39.7 - - + +
1330B PHE* 3.5 18.1 - - - +
1331B THR* 3.5 22.6 + - - +
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Residues in contact with LEU1300 (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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980B ILE* 4.7 12.3 - - + -
1298B LEU* 4.0 12.0 + - + +
1299B GLN* 1.3 80.1 + - - +
1301B PRO* 1.3 63.1 - - - +
1302B SER 3.0 2.2 - - - -
1303B ARG* 2.6 65.5 + - + +
1304B SER* 4.7 0.2 - - - -
1305B SER 5.0 0.4 + - - -
1307B ILE* 5.2 9.8 - - + +
1322B GLU* 6.5 0.9 - - + -
1323B GLU 5.1 4.3 - - - +
1324B THR* 4.2 25.4 - - + +
1328B GLU* 3.6 17.0 - - - +
1330B PHE* 3.6 35.9 - - + -
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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
------------------------------------------------------------
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