Contacts of the helix formed by residues 1593 - 1602 (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 THR1593 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1592r CYS* 1.3 79.5 - - - +
1594r GLU* 1.3 65.3 + - - +
1595r LYS* 3.1 10.8 - - - -
1596r ASP* 3.1 20.6 + - - +
1597r LEU* 3.9 4.7 + - - +
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Residues in contact with GLU1594 (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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1592r CYS 3.9 0.6 + - - -
1593r THR* 1.3 74.4 - - - +
1595r LYS* 1.3 61.1 + - - +
1596r ASP 3.3 0.5 + - - -
1597r LEU* 3.4 16.5 + - - +
1598r ILE* 3.6 10.9 + - - +
1614r LEU 6.0 2.5 - - - +
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Residues in contact with LYS1595 (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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1593r THR* 3.1 8.1 - - - -
1594r GLU* 1.3 78.3 - - - +
1596r ASP* 1.3 60.3 + - - +
1597r LEU 3.7 0.2 + - - -
1598r ILE* 3.8 16.7 + - - +
1599r PRO 4.9 0.7 - - - -
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Residues in contact with ASP1596 (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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1592r CYS* 4.3 17.0 - - + -
1593r THR* 3.1 14.9 + - - +
1595r LYS* 1.3 80.0 - - - +
1597r LEU* 1.3 59.2 + - - +
1598r ILE 3.3 0.8 + - - -
1599r PRO* 4.1 12.4 - - - +
1600r TYR* 4.9 1.4 + - - +
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Residues in contact with LEU1597 (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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1593r THR 3.9 4.3 + - - +
1594r GLU* 3.4 13.0 + - - +
1596r ASP* 1.3 78.3 - - - +
1598r ILE* 1.3 65.7 + - - +
1599r PRO 3.4 0.4 - - - -
1600r TYR* 3.0 13.6 + - + +
1601r LEU* 2.9 23.6 + - + +
1613r LEU 5.8 4.5 - - - +
1614r LEU* 6.1 4.3 - - - -
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Residues in contact with ILE1598 (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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1594r GLU 3.6 9.1 + - - +
1595r LYS* 3.9 14.6 - - - +
1596r ASP 3.3 0.8 - - - -
1597r LEU* 1.3 77.6 - - - +
1599r PRO* 1.4 65.1 - - - +
1601r LEU* 3.1 16.8 + - - +
1602r GLU* 3.2 14.4 + - - +
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Residues in contact with PRO1599 (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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1595r LYS 4.9 1.0 - - - -
1596r ASP 4.1 9.9 - - - +
1597r LEU 3.4 0.6 - - - -
1598r ILE* 1.4 76.7 - - - +
1600r TYR* 1.3 59.6 + - - +
1602r GLU* 3.9 14.1 - - + +
1603r LYS* 4.7 3.1 + - - +
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Residues in contact with TYR1600 (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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1596r ASP 4.9 0.6 + - - +
1597r LEU* 3.0 15.9 + - + +
1599r PRO* 1.3 77.6 - - - +
1601r LEU* 1.3 64.1 + - - +
1602r GLU 3.2 1.1 + - - -
1603r LYS* 3.4 19.0 + - - +
1604r LEU* 5.2 1.0 - - - +
1631r LEU* 5.2 17.3 - - + +
1635r LEU* 6.3 3.4 - - + -
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Residues in contact with LEU1601 (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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1597r LEU* 2.9 16.9 + - + +
1598r ILE* 3.1 8.5 + - - +
1600r TYR* 1.3 72.6 - - - +
1602r GLU* 1.3 59.4 + - - +
1603r LYS 3.1 7.0 + - - -
1604r LEU* 3.3 22.7 + - + +
1610r LYS* 5.5 13.3 - - + +
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Residues in contact with GLU1602 (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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1598r ILE 3.2 14.2 + - - +
1599r PRO* 3.9 11.2 - - + +
1600r TYR 3.2 0.6 - - - -
1601r LEU* 1.3 76.6 - - - +
1603r LYS* 1.3 56.8 + - + +
1604r LEU 3.3 5.9 + - - +
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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