Contacts of the helix formed by residues 1454 - 1473 (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 ALA1454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1452B ILE* 4.0 2.5 - - - +
1453B THR* 1.3 79.1 - - - +
1455B SER* 1.3 65.5 + - - +
1456B LYS 4.2 0.2 - - - +
1457B GLY* 2.9 12.7 + - - +
1458B GLU* 3.0 12.7 + - - +
1493B GLN* 5.9 0.8 - - - +
1503B PRO 3.4 26.5 - - - +
1504B GLU 3.5 16.3 + - - +
1505B ALA 4.1 2.0 + - - -
1506B ASN 3.8 4.9 - - - +
1507B ASN 3.6 27.6 - - - +
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Residues in contact with SER1455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453B THR 3.6 4.2 + - - -
1454B ALA* 1.3 71.4 - - - +
1456B LYS* 1.3 61.2 + - - +
1458B GLU* 3.3 10.3 + - - +
1459B GLU* 2.8 50.3 + - - +
1507B ASN 4.4 8.8 + - - -
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Residues in contact with LYS1456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1454B ALA* 3.1 1.0 - - - +
1455B SER* 1.3 80.5 + - - +
1457B GLY* 1.3 59.3 + - - +
1459B GLU* 3.4 12.0 + - + +
1460B GLN* 2.9 30.3 + - - +
1503B PRO* 3.6 33.2 - - + +
1504B GLU* 3.9 19.8 - - - +
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Residues in contact with GLY1457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430B TYR* 3.5 20.0 + - - -
1452B ILE* 4.1 7.6 - - - -
1454B ALA 2.9 7.2 + - - -
1456B LYS* 1.3 76.8 - - - +
1458B GLU* 1.3 62.0 + - - +
1460B GLN* 3.3 1.4 + - - -
1461B LEU* 3.1 22.9 + - - +
1493B GLN* 4.3 1.6 - - - -
1504B GLU* 3.1 29.0 + - - +
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Residues in contact with GLU1458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1452B ILE* 3.6 14.8 - - + +
1454B ALA 3.0 11.2 + - - +
1455B SER* 3.5 13.7 - - - +
1457B GLY* 1.3 75.3 - - - +
1459B GLU* 1.3 72.1 + - - +
1461B LEU* 3.5 5.5 + - - +
1462B LYS* 3.0 30.5 + - - +
1484B TRP* 2.7 35.1 + - + +
1488B LEU* 3.6 28.4 - - + +
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Residues in contact with GLU1459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455B SER* 2.8 44.0 + - - +
1456B LYS* 3.9 15.0 - - + +
1458B GLU* 1.3 92.8 - - - +
1460B GLN* 1.3 60.1 + - - +
1462B LYS* 3.9 21.2 + - - +
1463B SER* 3.0 32.9 + - - -
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Residues in contact with GLN1460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391B LYS* 6.1 0.8 - - - +
1409B VAL* 3.5 36.7 - - + +
1428B LEU* 3.8 6.5 - - - +
1430B TYR* 2.7 31.0 + - + +
1456B LYS 2.9 17.9 + - - +
1457B GLY 3.6 4.0 - - - +
1459B GLU* 1.3 72.7 - - - +
1461B LEU* 1.3 66.4 + - - +
1463B SER* 4.0 5.0 - - - -
1464B LEU* 3.2 29.1 + - + +
1504B GLU* 3.7 29.0 + - + +
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Residues in contact with LEU1461 (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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1411B VAL* 3.8 16.4 - - + -
1430B TYR* 3.8 35.6 - - + -
1452B ILE* 3.7 26.5 - - + -
1457B GLY 3.1 16.3 + - - +
1458B GLU* 3.7 3.8 - - - +
1460B GLN* 1.3 77.0 - - - +
1462B LYS* 1.3 64.3 + - - +
1464B LEU* 3.2 5.8 + - - +
1465B ILE* 3.0 45.7 + - + +
1484B TRP* 3.8 14.8 - - + -
1488B LEU* 4.4 4.0 - - + -
1491B PHE* 3.8 28.0 - - + -
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Residues in contact with LYS1462 (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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1458B GLU* 3.0 18.4 + - - +
1459B GLU* 3.9 20.8 + - - +
1460B GLN 3.4 0.2 - - - -
1461B LEU* 1.3 76.0 - - - +
1463B SER* 1.3 58.6 + - - +
1465B ILE* 3.3 2.9 + - - +
1466B THR* 2.8 39.7 + - - +
1481B LEU* 4.3 11.0 - - + -
1484B TRP* 3.7 49.6 - - + +
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Residues in contact with SER1463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459B GLU 3.0 19.0 + - - -
1460B GLN* 4.0 4.9 - - - -
1462B LYS* 1.3 77.0 - - - +
1464B LEU* 1.3 58.3 + - - +
1466B THR* 3.4 7.6 + - - -
1467B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU1464 (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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1372B ASN* 4.3 11.0 - - - +
1374B TYR* 3.9 18.6 - - + +
1391B LYS* 4.4 17.9 - - + -
1392B ALA 5.0 2.9 - - - +
1393B VAL* 3.7 25.5 - - + +
1409B VAL* 3.8 33.9 - - + +
1411B VAL* 4.0 14.1 - - + -
1460B GLN* 3.2 26.3 + - + +
1461B LEU* 3.2 7.6 + - - +
1463B SER* 1.3 77.0 + - - +
1465B ILE* 1.3 59.2 + - - +
1467B ALA* 3.3 4.9 + - + +
1468B HIS* 2.9 27.7 + - - +
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Residues in contact with ILE1465 (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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1393B VAL* 5.0 0.9 - - + -
1411B VAL* 4.2 5.4 - - + -
1413B LEU* 3.8 31.0 - - + -
1461B LEU* 3.0 42.4 + - + +
1462B LYS 3.8 3.1 - - - +
1464B LEU* 1.3 73.6 - - - +
1466B THR* 1.3 68.0 + - - +
1468B HIS* 3.2 8.2 + - + +
1469B VAL* 3.0 22.2 + - - +
1477B GLY* 4.1 21.8 - - - +
1480B ILE* 4.2 6.3 - - + -
1481B LEU* 3.7 26.0 - - + -
1484B TRP* 4.0 15.7 - - + -
1491B PHE* 4.0 6.7 - - + -
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Residues in contact with THR1466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462B LYS* 2.8 29.3 + - - +
1463B SER* 3.6 8.0 - - - -
1465B ILE* 1.3 77.0 - - - +
1467B ALA* 1.3 57.2 + - - +
1469B VAL* 3.3 2.9 + - - +
1470B GLU* 3.0 36.5 + - + +
1481B LEU* 4.0 24.7 - - + +
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Residues in contact with ALA1467 (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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1374B TYR* 3.6 22.9 - - + +
1463B SER* 2.9 17.4 + - - +
1464B LEU* 3.6 6.3 - - + +
1465B ILE 3.3 0.2 - - - -
1466B THR* 1.3 75.2 - - - +
1468B HIS* 1.3 57.2 + - - +
1470B GLU* 3.2 8.1 + - - +
1471B HIS* 2.9 41.7 + - + +
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Residues in contact with HIS1468 (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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1374B TYR* 3.5 28.1 - - + +
1375B ALA 3.4 32.3 - - - -
1376B ASN 4.0 0.4 - - - -
1393B VAL* 3.5 35.7 - - + +
1395B GLU* 2.9 24.1 + - + +
1413B LEU* 4.1 8.7 - - + -
1464B LEU 2.9 18.1 + - - +
1465B ILE* 3.2 7.4 + - - +
1467B ALA* 1.3 76.8 - - - +
1469B VAL* 1.3 53.2 + - - +
1471B HIS* 3.5 0.5 + - - +
1472B THR* 2.8 49.0 + - + +
1474B SER* 3.5 25.4 - - - -
1477B GLY* 5.1 2.2 - - - -
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Residues in contact with VAL1469 (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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1465B ILE 3.0 16.3 + - - +
1466B THR 3.7 7.4 - - - +
1468B HIS* 1.3 72.2 - - + +
1470B GLU* 1.3 67.7 + - + +
1473B GLY* 2.8 28.8 + - - +
1474B SER* 4.1 7.6 - - - +
1477B GLY* 3.6 36.3 - - - -
1478B LYS* 3.6 31.4 - - + +
1481B LEU* 3.8 16.2 - - + -
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Residues in contact with GLU1470 (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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1466B THR* 3.0 27.3 + - + +
1467B ALA* 3.2 11.6 + - - +
1469B VAL* 1.3 81.7 - - + +
1471B HIS* 1.3 63.0 + - + +
1473B GLY 4.8 0.3 + - - -
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Residues in contact with HIS1471 (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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1322B THR* 6.0 2.0 - - + -
1324B HIS* 4.6 13.9 + + - -
1341B GLU* 3.0 35.7 + - + -
1343B VAL* 3.6 38.6 - - + +
1345B VAL* 4.7 1.9 - - - +
1374B TYR* 3.4 30.1 + + + -
1467B ALA* 2.9 29.1 + - + +
1468B HIS 4.0 3.4 - - - +
1470B GLU* 1.3 78.6 - - + +
1472B THR* 1.3 61.6 + - - +
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Residues in contact with THR1472 (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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1343B VAL* 4.0 8.1 - - - +
1345B VAL* 3.8 24.7 - - + +
1374B TYR* 4.1 9.4 + - - +
1376B ASN* 3.3 35.6 + - + +
1468B HIS* 2.8 29.9 + - - +
1471B HIS* 1.3 80.3 - - - +
1473B GLY* 1.3 59.0 + - - +
1474B SER* 3.2 24.0 + - - +
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Residues in contact with GLY1473 (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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1469B VAL* 2.8 22.9 + - - -
1470B GLU 4.8 0.4 + - - -
1471B HIS 3.9 0.4 - - - -
1472B THR* 1.3 72.5 - - - +
1474B SER* 1.3 64.9 + - - +
1475B PRO* 3.0 11.0 - - - +
1478B LYS* 3.5 27.4 + - - +
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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