Contacts of the helix formed by residues 1456 - 1461 (chain F) in PDB entry 1IV4
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 ASP1456 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309E ARG* 3.1 23.1 + - - -
1330E THR* 3.6 15.5 - - + -
1331E PHE* 3.1 23.1 + - - +
1446F ASP* 3.3 16.2 - - - +
1449F LEU* 3.7 8.0 - - - +
1455F GLY* 1.3 76.3 - - - +
1457F ILE* 1.3 66.1 + - - +
1458F GLY 3.1 1.2 + - - -
1459F LEU* 3.0 16.1 + - - +
1460F LEU* 3.0 23.2 + - - +
1606F C5P 2.9 31.7 + - - +
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Residues in contact with ILE1457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332E LYS* 3.8 14.4 - - - +
1442F HIS* 3.7 43.5 - - + +
1445F THR* 3.4 36.1 - - + -
1446F ASP* 2.8 29.1 + - - +
1449F LEU* 4.3 0.7 - - + -
1456F ASP* 1.3 76.5 - - - +
1458F GLY* 1.3 61.2 + - - +
1461F PHE* 2.7 48.5 + - + +
1476F PHE* 5.4 4.7 - - + -
1566F MG 4.5 0.7 - - - -
1606F C5P 3.7 12.3 - - - +
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Residues in contact with GLY1458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456F ASP* 3.8 0.2 - - - -
1457F ILE* 1.3 78.0 - - - +
1459F LEU* 1.3 62.4 + - - +
1461F PHE 5.1 0.7 - - - -
1462F PRO* 3.6 22.5 - - - +
1606F C5P 2.9 39.4 + - - -
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Residues in contact with LEU1459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309E ARG* 3.9 33.7 - - - +
1454F LEU 3.8 22.0 - - - +
1455F GLY* 3.9 9.9 - - - -
1456F ASP* 3.0 20.3 + - - +
1458F GLY* 1.3 81.2 - - - +
1460F LEU* 1.3 69.6 + - + +
1462F PRO* 3.5 10.2 - - - +
1606F C5P 3.9 0.8 + - - -
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Residues in contact with LEU1460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449F LEU* 3.3 37.7 - - + -
1454F LEU* 3.8 24.7 - - + +
1456F ASP 3.0 16.3 + - - +
1459F LEU* 1.3 89.2 - - + +
1461F PHE* 1.3 82.3 + - + +
1462F PRO* 3.3 6.4 - - - +
1465F ASP* 5.3 0.2 - - - +
1467F ARG* 5.6 0.7 + - - -
1468F TRP* 3.4 12.3 + - - -
1483F LEU* 3.8 19.7 - - + -
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Residues in contact with PHE1461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1445F THR* 3.9 13.5 - - + -
1449F LEU* 4.2 7.2 - - + -
1457F ILE* 2.7 36.2 + - + +
1458F GLY* 5.2 0.3 - - - -
1460F LEU* 1.3 101.4 - - + +
1462F PRO* 1.3 65.4 - - - +
1463F ASP* 5.5 0.2 - - - -
1468F TRP* 3.7 30.1 - + + +
1476F PHE* 3.4 70.4 - + + -
1479F GLU* 3.6 32.8 - - + -
1480F ALA* 4.2 4.9 - - - -
1483F LEU* 5.2 0.2 - - + -
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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