Contacts of the helix formed by residues 1474 - 1483 (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 SER1474 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376B ASN* 3.6 2.0 + - - -
1395B GLU* 2.7 28.2 + - - -
1468B HIS* 3.5 16.2 + - - -
1469B VAL* 4.1 6.2 - - - +
1472B THR* 3.2 20.8 - - - -
1473B GLY* 1.3 73.0 - - - +
1475B PRO* 1.3 64.2 - - - +
1476B LYS 3.5 2.9 + - - -
1477B GLY* 3.0 20.5 + - - -
1478B LYS* 2.8 30.7 + - - +
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Residues in contact with PRO1475 (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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1354B PRO* 4.4 19.3 - - + -
1355B GLU* 4.7 8.1 - - - +
1376B ASN* 4.0 16.8 - - - +
1473B GLY 3.3 10.3 - - - +
1474B SER* 1.3 81.7 - - - +
1476B LYS* 1.3 56.8 + - - +
1478B LYS* 3.3 10.8 + - + +
1479B ALA* 2.9 28.6 + - - +
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Residues in contact with LYS1476 (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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1355B GLU* 4.0 32.2 + - + +
1395B GLU* 3.9 20.4 - - - +
1413B LEU* 4.0 21.5 - - + +
1432B LEU* 4.0 14.1 - - - -
1434B GLU* 2.7 36.3 + - - -
1474B SER* 3.3 2.0 + - - +
1475B PRO* 1.3 75.2 - - - +
1477B GLY* 1.3 67.5 + - - +
1479B ALA* 3.1 12.1 + - + +
1480B ILE* 2.9 37.5 + - + +
1487B TYR* 4.2 12.2 + - - +
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Residues in contact with GLY1477 (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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1413B LEU* 4.4 6.3 - - - +
1465B ILE* 4.1 13.9 - - - -
1468B HIS* 5.1 0.2 - - - -
1469B VAL* 3.6 16.2 - - - -
1474B SER* 3.0 17.7 + - - -
1476B LYS* 1.3 76.7 - - - +
1478B LYS* 1.3 61.7 + - - +
1480B ILE* 3.2 8.7 + - - +
1481B LEU* 2.9 28.8 + - - +
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Residues in contact with LYS1478 (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* 3.6 24.0 - - + +
1473B GLY* 3.5 30.8 + - - +
1474B SER 2.8 21.2 + - - +
1475B PRO* 3.5 8.7 - - + +
1476B LYS 3.2 0.2 - - - -
1477B GLY* 1.3 72.2 - - - +
1479B ALA* 1.3 57.5 + - - +
1481B LEU* 3.5 5.1 + - - +
1482B ALA* 3.0 29.8 + - - +
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Residues in contact with ALA1479 (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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1475B PRO 2.9 14.4 + - - +
1476B LYS* 3.1 14.3 + - + +
1478B LYS* 1.3 73.7 - - - +
1480B ILE* 1.3 64.5 + - - +
1482B ALA* 3.3 6.8 + - - +
1483B ASN* 3.2 21.6 + - - +
1487B TYR* 3.6 23.8 - - + +
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Residues in contact with ILE1480 (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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1413B LEU* 3.8 33.2 - - + -
1432B LEU* 4.0 17.5 - - + -
1465B ILE* 4.2 11.4 - - + -
1476B LYS* 2.9 30.9 + - + +
1477B GLY* 3.2 7.4 + - - +
1479B ALA* 1.3 75.2 - - - +
1481B LEU* 1.3 64.3 + - - +
1483B ASN 3.2 5.5 + - - +
1484B TRP* 3.1 50.5 + - + -
1487B TYR* 3.6 40.4 - - + -
1491B PHE* 4.3 5.8 - - + -
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Residues in contact with LEU1481 (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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1462B LYS* 4.3 9.9 - - + -
1465B ILE* 3.7 18.4 - - + -
1466B THR* 4.0 33.0 - - + +
1469B VAL* 3.8 30.7 - - + -
1477B GLY 2.9 15.2 + - - +
1478B LYS* 3.9 4.9 - - - +
1480B ILE* 1.3 76.6 - - - +
1482B ALA* 1.3 61.3 + - - +
1483B ASN 3.4 0.7 + - - -
1484B TRP* 3.7 32.7 + - + +
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Residues in contact with ALA1482 (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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1478B LYS 3.0 18.5 + - - +
1479B ALA* 3.8 7.0 - - - +
1480B ILE 3.3 0.4 - - - -
1481B LEU* 1.3 75.9 - - - +
1483B ASN* 1.3 73.4 + - - +
1484B TRP 3.7 0.4 + - - -
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Residues in contact with ASN1483 (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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1479B ALA* 3.2 10.6 + - - +
1480B ILE 3.2 6.6 + - - -
1482B ALA* 1.3 89.7 + - - +
1484B TRP* 1.3 62.6 + - - +
1485B SER* 3.3 3.1 - - - -
1486B ASP* 3.0 34.4 + - - +
1487B TYR* 3.2 24.0 + - + -
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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