Contacts of the strand formed by residues 1321 - 1329 (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 MET1321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1281B GLY 4.5 2.5 - - - +
1284B LEU* 4.5 12.3 - - + -
1285B SER* 2.8 42.0 - - - +
1288B ILE* 3.9 21.8 - - + -
1301B ILE* 3.4 7.2 - - + +
1317B ASN* 3.0 41.8 + - - +
1318B LEU* 2.4 46.0 + - + +
1319B ASP 4.5 0.9 - - - +
1320B GLY* 1.3 82.0 - - - +
1322B THR* 1.3 63.1 + - - +
1323B LEU* 4.7 7.9 - - + -
1340B GLY* 3.4 2.3 - - - -
1341B GLU 3.1 12.5 + - - -
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Residues in contact with THR1322 (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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1300B ASN* 3.8 13.3 + - - -
1301B ILE 2.8 12.0 + - - +
1302B THR* 3.3 16.0 - - + +
1303B LEU 2.8 27.7 + - - +
1320B GLY 5.1 0.5 - - - -
1321B MET* 1.3 75.1 + - - +
1323B LEU* 1.3 61.0 + - - +
1324B HIS* 3.7 27.8 - - + +
1341B GLU* 3.5 31.3 + - + +
1343B VAL* 5.5 1.8 - - + -
1471B HIS* 6.0 1.8 - - + -
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Residues in contact with LEU1323 (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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1280B VAL 4.2 9.0 - - - +
1281B GLY* 4.5 7.9 - - - -
1284B LEU* 5.8 0.7 - - + -
1303B LEU* 3.5 35.4 - - + +
1305B PHE* 4.4 3.6 - - + -
1313B PHE* 4.2 21.8 - - + -
1314B GLY* 3.5 28.5 - - - +
1317B ASN* 3.4 29.6 - - - +
1321B MET* 4.7 6.7 - - + -
1322B THR* 1.3 81.8 - - - +
1324B HIS* 1.3 60.1 + - - +
1341B GLU 2.8 13.3 + - - +
1342B ILE* 3.4 9.1 - - + +
1343B VAL* 2.9 27.9 + - - +
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Residues in contact with HIS1324 (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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1302B THR* 4.2 10.8 - - + +
1303B LEU 2.8 7.6 + - - +
1304B ASN* 3.4 29.2 - - + +
1305B PHE* 2.7 37.1 + - - -
1313B PHE* 4.7 0.2 - - - -
1322B THR* 3.7 30.0 - - + +
1323B LEU* 1.3 74.3 - - - +
1325B LEU* 1.3 56.2 + - - +
1326B GLN 4.2 0.2 - - - -
1343B VAL* 3.4 35.6 - - + +
1471B HIS* 4.6 15.0 + - - -
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Residues in contact with LEU1325 (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* 4.2 13.0 - - + -
1305B PHE* 3.5 23.3 - - + +
1307B GLY 3.7 21.1 - - - +
1309B ALA* 3.7 16.4 - - + -
1313B PHE* 3.8 18.4 - - + -
1323B LEU 4.2 0.2 + - - -
1324B HIS* 1.3 74.5 - - - +
1326B GLN* 1.3 63.1 + - - +
1327B GLY 4.6 0.7 - - - +
1328B GLU 3.4 25.1 - - - +
1329B ALA* 3.8 13.5 - - + -
1343B VAL 2.8 13.1 + - - +
1344B ILE* 3.3 18.8 - - + +
1345B VAL* 2.9 29.6 + - - +
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Residues in contact with GLN1326 (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* 5.7 0.6 - - - +
1305B PHE 2.9 14.8 + - - +
1306B GLN* 3.3 31.7 + - + +
1307B GLY 2.9 27.3 + - - +
1324B HIS 4.2 0.2 - - - -
1325B LEU* 1.3 73.0 - - - +
1327B GLY* 1.3 57.5 + - - +
1345B VAL* 3.3 15.2 - - + +
1346B PRO 3.8 14.4 - - - +
1347B HIS* 3.2 26.6 + - - +
1348B PRO* 3.4 27.0 - - + +
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Residues in contact with GLY1327 (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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381B LYS* 4.7 4.5 + - - -
1307B GLY 3.4 3.6 - - - -
1325B LEU* 3.9 1.7 - - - -
1326B GLN* 1.3 75.2 - - - +
1328B GLU* 1.3 66.1 + - - +
1344B ILE* 5.1 0.9 - - - -
1345B VAL 2.8 19.9 + - - +
1346B PRO* 3.7 6.4 - - - +
1347B HIS* 3.3 30.1 + - - +
1359B ILE* 3.5 13.2 - - - +
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Residues in contact with GLU1328 (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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353B ARG* 4.2 5.4 + - - +
368B ALA* 3.4 37.6 - - + +
375B GLU* 4.4 2.4 - - - +
381B LYS* 2.9 42.0 + - + +
1307B GLY 3.3 4.6 + - - -
1308B ALA* 3.3 20.4 - - + +
1309B ALA 2.9 22.9 + - - -
1325B LEU* 3.4 11.3 - - - +
1326B GLN 4.4 0.2 - - - -
1327B GLY* 1.3 74.8 - - - +
1329B ALA* 1.3 62.2 + - - +
1330B ASN* 5.8 0.2 - - - +
1344B ILE* 4.8 1.1 - - - -
1347B HIS* 5.8 1.0 + - - -
1358B VAL 4.9 2.5 - - - +
1359B ILE* 3.6 22.4 - - + +
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Residues in contact with ALA1329 (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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353B ARG* 2.5 33.5 + - - -
1309B ALA* 3.7 12.8 - - + -
1310B GLY 5.1 0.2 - - - +
1313B PHE* 4.5 4.0 - - + -
1325B LEU* 3.8 17.0 - - + -
1328B GLU* 1.3 76.3 - - - +
1330B ASN* 1.3 58.4 + - - +
1333B VAL* 3.5 27.8 - - + -
1344B ILE* 4.3 2.0 - - + +
1359B ILE 2.9 11.2 + - - +
1360B ILE* 3.7 8.1 - - + -
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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