Contacts of the helix formed by residues 1411 - 1419 (chain r) in PDB entry 6FF7
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 GLU1411 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1409r THR* 3.6 3.1 - - - -
1410r GLY* 1.3 74.9 - - - +
1412r THR* 1.3 66.1 + - - +
1413r SER* 4.6 3.1 - - - +
1414r THR* 4.2 18.0 - - - +
1415r ASP* 3.0 26.4 + - - +
2059r LYS 5.9 3.4 - - - +
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Residues in contact with THR1412 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410r GLY 3.5 3.8 + - - -
1411r GLU* 1.3 71.1 - - - +
1413r SER* 1.3 64.5 + - - +
1415r ASP* 3.5 5.2 - - - +
1416r LEU* 2.9 24.1 + - - +
1434r ILE* 6.6 0.2 - - - -
1435r LEU* 5.8 7.6 - - - -
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Residues in contact with SER1413 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411r GLU* 3.4 3.5 - - - +
1412r THR* 1.3 77.3 - - - +
1414r THR* 1.3 65.0 + - - +
1416r LEU* 2.8 19.4 + - - +
1417r LYS* 3.0 13.2 + - - +
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Residues in contact with THR1414 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409r THR* 6.0 5.4 - - - -
1411r GLU* 3.6 17.9 + - - +
1412r THR 3.5 0.4 - - - -
1413r SER* 1.3 79.1 - - - +
1415r ASP* 1.3 56.5 + - - +
1417r LYS* 3.5 7.9 + - - +
1418r LEU* 2.9 27.8 + - - +
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Residues in contact with ASP1415 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408r LEU* 5.1 8.8 - - + +
1409r THR* 4.6 21.7 - - - +
1411r GLU 3.0 21.6 + - - +
1412r THR* 3.5 6.1 - - - +
1414r THR* 1.3 75.8 - - - +
1416r LEU* 1.3 65.4 + - - +
1418r LEU* 3.2 8.6 - - - +
1419r LEU* 3.2 22.0 + - - +
1431r LYS* 6.0 1.3 - - + +
1435r LEU* 5.6 9.0 - - + -
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Residues in contact with LEU1416 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412r THR 2.9 12.4 + - - +
1413r SER* 2.8 11.5 + - - +
1415r ASP* 1.3 76.8 - - - +
1417r LYS* 1.3 60.1 + - - +
1418r LEU 3.2 0.5 + - - -
1419r LEU* 2.9 26.0 + - - +
1444r ASN* 5.6 3.5 - - - +
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Residues in contact with LYS1417 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413r SER 3.0 11.1 + - - +
1414r THR* 3.7 10.8 - - - +
1416r LEU* 1.3 76.1 - - - +
1418r LEU* 1.3 64.5 + - - +
1419r LEU 3.1 7.3 - - - +
1421r LYS* 4.1 11.8 + - - +
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Residues in contact with LEU1418 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406r VAL* 4.5 21.3 - - + +
1407r LEU 5.5 5.8 - - - +
1408r LEU* 5.6 5.4 - - - -
1414r THR 2.9 15.4 + - - +
1415r ASP* 3.2 15.0 - - - +
1416r LEU 3.1 0.4 - - - -
1417r LYS* 1.3 79.1 - - - +
1419r LEU* 1.3 63.3 + - - +
1421r LYS* 3.5 5.1 + - - +
1422r GLY* 3.5 16.6 + - - -
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Residues in contact with LEU1419 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406r VAL* 5.7 1.3 - - - -
1415r ASP 3.2 9.2 + - - +
1416r LEU* 2.9 18.6 - - - +
1417r LYS* 3.1 9.9 - - - +
1418r LEU* 1.3 79.9 - - - +
1420r GLY* 1.3 58.9 + - - +
1421r LYS 3.1 0.9 + - - -
1422r GLY* 4.6 3.4 - - - +
1425r ILE* 4.6 20.9 - - + -
1444r ASN* 5.2 15.0 - - + +
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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