Contacts of the helix formed by residues 1606 - 1615 (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 ASP1606 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1604D LEU* 4.8 3.5 - - - -
1605D SER* 1.3 74.9 + - - +
1607D SER* 1.3 63.7 + - - +
1608D THR 3.5 1.8 - - - -
1609D LEU* 3.8 7.4 + - - +
1610D LYS* 3.6 14.4 + - - -
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Residues in contact with SER1607 (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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1605D SER 3.2 6.3 + - - -
1606D ASP* 1.3 70.7 - - - +
1608D THR* 1.3 64.4 + - - +
1609D LEU 3.3 0.2 - - - -
1610D LYS* 3.3 10.4 + - - -
1611D GLU 3.5 6.9 + - - -
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Residues in contact with THR1608 (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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1606D ASP 3.5 0.2 - - - -
1607D SER* 1.3 73.2 - - - +
1609D LEU* 1.3 60.9 + - - +
1611D GLU* 3.0 4.3 + - - +
1612D THR* 2.9 25.8 + - - -
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Residues in contact with LEU1609 (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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1606D ASP* 3.8 9.3 + - - +
1607D SER 3.3 0.6 - - - -
1608D THR* 1.3 75.5 - - - +
1610D LYS* 1.3 62.9 + - - +
1612D THR* 4.5 1.8 - - - +
1613D LEU* 2.9 22.9 + - - -
1618D GLY* 5.1 6.5 - - - -
1619D TYR 6.2 0.4 - - - +
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Residues in contact with LYS1610 (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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1601D LEU* 6.4 1.3 - - - +
1606D ASP 3.6 9.4 + - - -
1607D SER 3.3 8.7 + - - -
1608D THR 3.2 1.0 - - - -
1609D LEU* 1.3 77.4 - - - +
1611D GLU* 1.3 55.4 + - - +
1613D LEU* 3.8 1.3 - - - +
1614D LEU* 2.9 25.1 + - - -
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Residues in contact with GLU1611 (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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1607D SER 3.5 7.4 + - - -
1608D THR* 3.0 7.2 + - - +
1610D LYS* 1.3 72.8 - - - +
1612D THR* 1.3 59.6 + - - +
1614D LEU* 2.9 18.3 + - - +
1615D ASN* 3.3 9.0 + - - -
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Residues in contact with THR1612 (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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1573D ALA 5.9 6.5 - - - -
1608D THR 2.9 17.4 + - - -
1609D LEU* 4.0 1.8 - - - +
1611D GLU* 1.3 72.6 - - - +
1613D LEU* 1.3 53.1 + - - +
1615D ASN* 3.5 3.0 + - - +
1616D GLY 3.4 3.5 + - - -
1617D VAL* 2.7 30.3 + - - -
1618D GLY* 3.3 12.2 + - - +
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Residues in contact with LEU1613 (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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1609D LEU 2.9 17.7 + - - -
1610D LYS* 3.8 1.3 - - - +
1612D THR* 1.3 75.7 - - - +
1614D LEU* 1.3 64.2 + - - +
1616D GLY* 3.0 14.2 + - - -
1617D VAL 4.3 2.0 - - - +
1618D GLY* 3.9 12.9 - - - +
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Residues in contact with LEU1614 (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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1590D LEU* 5.9 1.0 - - - -
1610D LYS 2.9 11.7 + - - -
1611D GLU* 2.9 10.1 + - - +
1613D LEU* 1.3 78.0 - - - +
1615D ASN* 1.3 56.1 + - - +
1616D GLY 3.8 0.2 + - - -
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Residues in contact with ASN1615 (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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1587D GLN* 3.9 21.8 - - - +
1589D PHE* 4.1 4.3 + - - -
1590D LEU* 3.8 13.9 + - - -
1611D GLU 3.3 9.4 + - - -
1612D THR 3.5 2.6 + - - -
1613D LEU 3.1 0.6 - - - -
1614D LEU* 1.3 75.3 - - - +
1616D GLY* 1.3 59.4 + - - +
1617D VAL 3.6 2.0 - - - -
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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