Contacts of the helix formed by residues 1567 - 1583 (chain D) in PDB entry 6AH0
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1565D SER* 3.2 0.4 - - - +
1566D ARG* 1.3 72.3 - - - +
1568D GLN* 1.3 63.6 + - - +
1569D THR 2.9 7.3 + - - -
1570D ARG* 3.1 12.6 + - - -
1571D LEU* 3.6 6.9 + - - -
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Residues in contact with GLN1568 (chain D).
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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1563D VAL* 6.1 4.0 - - - +
1565D SER* 3.3 17.0 + - - +
1567D LYS* 1.3 75.7 - - - +
1569D THR* 1.3 56.6 + - - +
1570D ARG 3.4 0.2 - - - -
1571D LEU* 3.9 2.9 - - - +
1572D THR* 2.9 27.5 + - - -
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Residues in contact with THR1569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563D VAL* 6.1 2.6 - - - +
1565D SER 3.7 8.1 + - - -
1566D ARG 3.9 5.1 + - - -
1567D LYS 2.9 2.0 + - - -
1568D GLN* 1.3 76.0 - - - +
1570D ARG* 1.3 63.7 + - - +
1572D THR* 3.9 0.9 - - - -
1573D ALA* 3.0 19.4 + - - -
1619D TYR* 5.4 6.6 - - - +
1620D LEU 6.0 0.9 - - - +
1645D VAL* 5.0 21.8 - - - +
1646D ALA 5.5 6.3 - - - +
1647D SER* 5.6 1.1 - - - +
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Residues in contact with ARG1570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566D ARG 4.9 1.4 + - - -
1567D LYS 3.1 7.9 + - - -
1569D THR* 1.3 73.5 - - - +
1571D LEU* 1.3 63.0 + - - +
1573D ALA* 2.8 14.7 + - - -
1574D ILE* 2.9 11.1 + - - -
1619D TYR* 6.4 0.4 - - - +
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Residues in contact with LEU1571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567D LYS 3.6 7.5 + - - -
1568D GLN* 3.5 5.8 + - - +
1569D THR 3.4 0.2 - - - -
1570D ARG* 1.3 73.9 - - - +
1572D THR* 1.3 56.3 + - - +
1574D ILE* 3.3 3.3 + - - +
1575D ASP* 2.9 24.9 + - - -
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Residues in contact with THR1572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568D GLN 2.9 17.4 + - - -
1569D THR 3.9 0.9 - - - -
1571D LEU* 1.3 73.4 - - - +
1573D ALA* 1.3 59.5 + - - +
1575D ASP* 4.4 1.6 - - - +
1576D ILE* 3.0 25.1 + - - -
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Residues in contact with ALA1573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569D THR 3.0 10.5 + - - -
1570D ARG* 2.8 8.3 + - - +
1572D THR* 1.3 72.7 - - - +
1574D ILE* 1.3 64.9 + - - +
1576D ILE* 3.4 2.9 + - - +
1577D LEU* 3.0 17.8 + - - -
1612D THR* 5.9 6.2 - - - -
1617D VAL* 6.3 2.9 - - - +
1618D GLY 5.7 8.5 - - - +
1645D VAL* 6.0 5.0 - - - +
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Residues in contact with ILE1574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570D ARG 2.9 12.1 + - - -
1571D LEU* 3.6 4.0 - - - +
1573D ALA* 1.3 75.2 - - - +
1575D ASP* 1.3 53.4 + - - +
1577D LEU* 2.8 22.7 + - - -
1578D THR* 2.8 12.8 + - - -
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Residues in contact with ASP1575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571D LEU 2.9 18.8 + - - -
1572D THR* 4.0 2.5 - - - +
1574D ILE* 1.3 71.4 - - - +
1576D ILE* 1.3 62.2 + - - +
1578D THR* 4.3 2.7 - - - +
1579D THR* 3.0 21.7 + - - -
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Residues in contact with ILE1576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547D TYR* 6.1 4.9 - - - +
1572D THR 3.0 17.8 + - - -
1573D ALA* 3.8 2.5 - - - +
1574D ILE 3.2 0.4 - - - -
1575D ASP* 1.3 75.4 - - - +
1577D LEU* 1.3 56.9 + - - +
1579D THR 4.0 0.7 - - - -
1580D CYS* 3.1 23.0 + - - -
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Residues in contact with LEU1577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1573D ALA 3.0 9.8 + - - -
1574D ILE* 2.8 10.0 + - - +
1576D ILE* 1.3 76.6 - - - +
1578D THR* 1.3 60.3 + - - +
1580D CYS* 3.3 8.8 + - - +
1581D ALA* 3.3 10.2 + - - -
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Residues in contact with THR1578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D MET* 3.5 22.2 - - - +
642D THR* 6.1 1.1 - - - +
1574D ILE 2.8 16.0 + - - -
1575D ASP* 3.4 3.1 + - - +
1577D LEU* 1.3 72.3 - - - +
1579D THR* 1.3 59.3 + - - +
1580D CYS 3.2 1.7 + - - -
1581D ALA* 3.6 8.8 + - - -
1582D ALA* 3.8 5.0 + - - -
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Residues in contact with THR1579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575D ASP 3.0 14.7 + - - -
1576D ILE 4.0 1.3 - - - -
1578D THR* 1.3 73.3 - - - +
1580D CYS* 1.3 64.1 + - - +
1581D ALA 3.3 0.7 - - - -
1582D ALA* 3.5 11.9 + - - +
1583D ASP* 3.9 6.2 + - - -
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Residues in contact with CYS1580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576D ILE 3.1 18.4 + - - -
1577D LEU* 3.3 5.6 + - - +
1578D THR 3.2 0.6 - - - -
1579D THR* 1.3 77.2 - - - +
1581D ALA* 1.3 62.1 + - - +
1582D ALA 3.5 0.2 + - - -
1583D ASP* 3.5 8.8 + - - -
1585D GLN 2.6 28.6 + - - +
1586D ARG* 5.2 1.1 - - - -
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Residues in contact with ALA1581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1577D LEU 3.3 10.9 + - - -
1578D THR 3.6 5.9 + - - -
1579D THR 3.3 0.6 - - - -
1580D CYS* 1.3 75.6 - - - +
1582D ALA* 1.3 54.5 + - - +
1584D ILE* 2.8 29.3 + - - -
1585D GLN 4.5 4.5 - - - -
1586D ARG* 5.3 4.2 - - - +
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Residues in contact with ALA1582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D MET* 5.4 12.2 + - - +
1578D THR 3.8 5.2 + - - -
1579D THR* 3.5 12.2 + - - +
1580D CYS 3.3 1.4 - - - -
1581D ALA* 1.3 75.7 - - - +
1583D ASP* 1.3 52.0 + - - +
1584D ILE* 2.8 10.7 + - - -
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Residues in contact with ASP1583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579D THR 3.9 5.8 + - - -
1580D CYS 3.5 6.3 + - - -
1581D ALA 3.1 1.8 + - - -
1582D ALA* 1.3 73.5 - - - +
1584D ILE* 1.3 54.2 + - - +
1585D GLN* 2.9 12.6 + - - +
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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