Contacts of the helix formed by residues 1474 - 1483 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1376A ASN* 3.7 1.3 - - - -
1395A GLU* 2.6 29.7 + - - -
1468A HIS* 3.4 24.2 + - - -
1469A VAL* 4.1 5.0 + - - +
1472A THR* 3.1 13.6 - - - -
1473A GLY* 1.3 74.1 - - - +
1475A PRO* 1.3 69.2 - - - +
1476A LYS 3.4 3.8 + - - -
1477A GLY* 3.0 18.9 + - - -
1478A LYS* 3.0 23.0 + - - +
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Residues in contact with PRO1475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354A PRO* 4.3 18.6 - - + -
1355A GLU* 4.7 7.2 - - - +
1376A ASN* 4.0 17.0 - - - +
1473A GLY 3.3 9.6 - - - +
1474A SER* 1.3 82.4 - - - +
1476A LYS* 1.3 62.0 + - - +
1478A LYS* 3.5 10.1 + - + +
1479A ALA* 3.1 22.9 + - - +
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Residues in contact with LYS1476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355A GLU* 3.9 33.3 + - + +
1395A GLU* 3.7 21.7 + - - +
1413A LEU* 4.0 24.5 - - + +
1432A LEU* 4.2 5.6 - - - -
1434A GLU* 2.8 33.5 + - - -
1474A SER* 3.2 2.2 + - - +
1475A PRO* 1.3 77.8 - - - +
1477A GLY* 1.3 66.9 + - - +
1479A ALA* 3.1 10.5 + - + +
1480A ILE* 3.0 34.7 + - + +
1487A TYR* 4.4 13.1 + - - -
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Residues in contact with GLY1477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413A LEU* 4.5 6.7 - - - +
1465A ILE* 4.0 13.0 - - - -
1468A HIS* 4.9 0.9 - - - -
1469A VAL* 3.5 20.2 - - - -
1474A SER* 3.0 14.5 + - - -
1476A LYS* 1.3 75.0 - - - +
1478A LYS* 1.3 63.8 + - - +
1480A ILE* 3.1 10.3 + - - +
1481A LEU* 2.9 26.0 + - - +
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Residues in contact with LYS1478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469A VAL* 3.5 24.6 - - + +
1473A GLY* 3.4 33.5 + - - +
1474A SER 3.0 15.1 + - - +
1475A PRO* 3.7 9.2 - - + +
1477A GLY* 1.3 74.7 - - - +
1479A ALA* 1.3 57.3 + - - +
1481A LEU* 3.3 5.8 + - - +
1482A ALA* 2.9 31.6 + - - +
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Residues in contact with ALA1479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A PRO 3.1 13.8 + - - +
1476A LYS* 3.1 14.3 + - + +
1478A LYS* 1.3 76.3 - - - +
1480A ILE* 1.3 62.3 + - - +
1482A ALA* 3.4 6.7 + - - +
1483A ASN* 3.2 21.7 + - - +
1487A TYR* 3.6 23.6 - - + +
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Residues in contact with ILE1480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413A LEU* 3.6 34.3 - - + -
1432A LEU* 3.9 15.3 - - + -
1465A ILE* 4.1 10.8 - - + -
1476A LYS* 3.0 31.5 + - + +
1477A GLY* 3.1 7.2 + - - +
1479A ALA* 1.3 76.2 - - - +
1481A LEU* 1.3 56.6 + - - +
1483A ASN 3.2 4.2 - - - +
1484A TRP* 3.0 58.8 + - + -
1487A TYR* 3.7 39.7 - - + -
1491A PHE* 4.3 5.4 - - + -
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Residues in contact with LEU1481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1462A LYS* 4.2 16.6 - - + -
1465A ILE* 3.9 16.8 - - + +
1466A THR* 3.6 35.4 - - + +
1469A VAL* 3.9 31.0 - - + -
1477A GLY 2.9 14.5 + - - +
1478A LYS* 3.9 4.7 - - - +
1480A ILE* 1.3 76.6 - - - +
1482A ALA* 1.3 61.1 + - - +
1483A ASN 3.5 0.2 + - - -
1484A TRP* 3.8 30.8 + - + +
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Residues in contact with ALA1482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1478A LYS 2.9 17.8 + - - +
1479A ALA* 3.8 7.4 - - - +
1480A ILE 3.3 0.2 - - - -
1481A LEU* 1.3 76.2 - - - +
1483A ASN* 1.3 74.5 + - - +
1484A TRP 3.7 0.4 - - - -
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Residues in contact with ASN1483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A ALA* 3.2 17.6 + - - +
1480A ILE 3.2 3.8 - - - -
1482A ALA* 1.3 89.6 + - - +
1484A TRP* 1.3 64.7 + - - +
1485A SER* 3.2 2.7 - - - -
1486A ASP* 3.1 32.8 + - + +
1487A TYR* 3.2 24.5 + - + -
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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