Contacts of the helix formed by residues 1567 - 1583 (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 LYS1567 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1565r SER* 3.2 3.0 - - - -
1566r ARG* 1.3 76.3 - - - +
1568r GLN* 1.3 63.4 + - - +
1569r THR 2.9 7.4 + - - -
1570r ARG* 3.1 22.5 + - + +
1571r LEU* 3.6 4.9 + - - +
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Residues in contact with GLN1568 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1563r VAL* 4.2 11.9 - - + -
1564r PRO* 4.9 1.6 - - + -
1565r SER* 3.3 34.5 + - - +
1567r LYS* 1.3 77.7 - - - +
1569r THR* 1.3 57.0 + - - +
1571r LEU* 3.5 9.2 + - - +
1572r THR* 2.9 32.7 + - - -
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Residues in contact with THR1569 (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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1563r VAL* 4.7 4.9 - - - +
1565r SER 3.7 4.9 + - - -
1566r ARG 3.9 12.8 - - - -
1567r LYS 2.9 1.0 + - - -
1568r GLN* 1.3 76.2 - - - +
1570r ARG* 1.3 65.0 + - - +
1572r THR* 4.8 1.1 - - - -
1573r ALA* 3.0 24.3 + - - +
1619r TYR* 4.1 18.6 - - - +
1620r LEU 4.5 5.2 - - - -
1621r HIS* 5.0 2.2 - - - -
1645r VAL* 3.7 22.1 - - - +
1646r ALA 4.6 1.3 - - - -
1647r SER 4.4 16.8 - - - -
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Residues in contact with ARG1570 (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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1566r ARG 4.9 0.4 + - - -
1567r LYS* 3.1 12.7 + - - +
1569r THR* 1.3 77.7 - - - +
1571r LEU* 1.3 56.4 + - - +
1573r ALA* 2.8 28.1 + - - +
1574r ILE* 2.9 12.9 + - - +
1608r THR* 6.1 4.9 - - - -
1619r TYR* 4.6 4.6 - - - +
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Residues in contact with LEU1571 (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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1567r LYS 3.6 6.4 + - - +
1568r GLN* 3.5 11.8 + - - +
1569r THR 3.4 0.2 - - - -
1570r ARG* 1.3 79.8 - - - +
1572r THR* 1.3 57.0 + - - +
1574r ILE* 3.3 9.7 - - - +
1575r ASP* 2.9 29.2 + - - +
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Residues in contact with THR1572 (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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1563r VAL* 5.6 6.3 - - - -
1568r GLN* 2.9 19.2 + - - -
1569r THR* 4.1 4.0 - - - -
1571r LEU* 1.3 73.5 - - - +
1573r ALA* 1.3 60.5 + - - +
1575r ASP* 3.9 6.5 - - - +
1576r ILE* 3.0 28.8 + - - +
1645r VAL* 4.9 8.5 - - - -
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Residues in contact with ALA1573 (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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1569r THR 3.0 13.7 + - - +
1570r ARG* 2.8 11.3 + - - +
1572r THR* 1.3 72.7 - - - +
1574r ILE* 1.3 65.9 + - - +
1576r ILE* 3.4 7.2 + - - +
1577r LEU* 3.0 22.6 + - - +
1612r THR* 4.3 23.4 - - - -
1617r VAL* 4.5 17.2 - - + +
1618r GLY 4.6 6.3 - - - +
1619r TYR* 4.7 3.6 - - + -
1645r VAL* 4.5 12.3 - - + +
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Residues in contact with ILE1574 (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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1570r ARG 2.9 10.4 + - - +
1571r LEU* 3.3 13.9 - - - +
1573r ALA* 1.3 76.9 - - - +
1575r ASP* 1.3 55.0 + - - +
1577r LEU* 2.8 27.3 + - - +
1578r THR* 2.9 15.9 + - - -
1612r THR* 5.5 1.5 - - - -
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Residues in contact with ASP1575 (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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1543r ALA* 4.7 20.0 - - + -
1571r LEU 2.9 19.5 + - - +
1572r THR* 4.0 7.6 - - - +
1574r ILE* 1.3 72.7 - - - +
1576r ILE* 1.3 62.6 + - - +
1578r THR* 4.2 7.1 - - - +
1579r THR* 3.0 27.7 + - - -
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Residues in contact with ILE1576 (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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1546r VAL* 6.4 1.8 - - + -
1547r TYR* 5.4 11.7 - - + +
1572r THR 3.0 20.4 + - - +
1573r ALA* 3.5 7.4 - - - +
1574r ILE 3.2 0.2 - - - -
1575r ASP* 1.3 75.4 - - - +
1577r LEU* 1.3 58.1 + - - +
1579r THR* 4.0 2.6 - - - -
1580r CYS* 3.1 26.3 + - - +
1617r VAL* 5.7 5.4 - - + -
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Residues in contact with LEU1577 (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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1573r ALA 3.0 11.8 + - - +
1574r ILE* 2.8 13.0 + - - +
1576r ILE* 1.3 77.7 - - - +
1578r THR* 1.3 58.3 + - - +
1580r CYS* 3.1 20.9 + - - +
1581r ALA* 3.3 8.7 + - - +
1612r THR* 6.1 4.7 - - - -
1615r ASN* 5.1 15.5 - - + -
1617r VAL* 6.0 3.6 - - + -
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Residues in contact with THR1578 (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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641r MET* 3.5 24.3 - - - +
642r THR* 5.3 10.3 - - - -
1574r ILE 2.9 17.0 + - - -
1575r ASP* 3.4 7.8 + - - -
1577r LEU* 1.3 71.6 - - - +
1579r THR* 1.3 59.5 + - - +
1580r CYS 3.2 2.0 + - - -
1581r ALA* 3.6 15.1 - - - +
1582r ALA* 3.8 2.9 + - - +
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Residues in contact with THR1579 (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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641r MET* 6.0 1.8 - - - -
1543r ALA 6.4 0.2 - - - -
1544r LYS* 5.6 9.9 - - - -
1547r TYR* 4.9 19.5 - - - +
1575r ASP 3.0 16.3 + - - -
1576r ILE 4.0 1.3 - - - -
1578r THR* 1.3 74.5 - - - +
1580r CYS* 1.3 62.1 + - - +
1581r ALA 3.3 0.9 - - - -
1582r ALA* 3.4 23.4 - - - +
1583r ASP* 3.9 5.9 + - - +
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Residues in contact with CYS1580 (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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1547r TYR* 6.4 0.4 - - - -
1576r ILE 3.1 21.2 + - - +
1577r LEU* 3.1 15.3 - - - +
1578r THR 3.2 0.2 - - - -
1579r THR* 1.3 76.5 - - - +
1581r ALA* 1.3 60.0 + - - +
1582r ALA 3.5 0.2 + - - -
1583r ASP* 3.5 12.3 + - - +
1585r GLN 2.6 30.1 - - - +
1586r ARG* 5.2 0.7 - - - -
1587r GLN 5.5 6.5 - - - +
1588r ARG* 6.1 1.6 - - + +
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Residues in contact with ALA1581 (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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641r MET* 4.9 5.6 - - - +
1577r LEU 3.3 7.9 + - - +
1578r THR* 3.6 13.0 - - - +
1580r CYS* 1.3 77.1 - - - +
1582r ALA* 1.3 55.3 + - - +
1584r ILE* 2.8 29.0 + - - -
1585r GLN 4.5 4.0 - - - -
1586r ARG* 5.3 6.0 - - + +
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Residues in contact with ALA1582 (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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641r MET* 4.7 19.9 + - + +
1578r THR 3.8 2.7 + - - +
1579r THR* 3.4 23.8 + - - +
1580r CYS 3.3 0.2 - - - -
1581r ALA* 1.3 78.5 - - - +
1583r ASP* 1.3 54.3 + - - +
1584r ILE* 2.8 12.5 + - - +
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Residues in contact with ASP1583 (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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1579r THR 3.9 4.6 + - - +
1580r CYS* 3.5 15.0 + - - +
1581r ALA 3.1 0.6 + - - -
1582r ALA* 1.3 77.5 - - - +
1584r ILE* 1.3 61.8 + - - +
1585r GLN* 2.9 19.3 + - + +
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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