Contacts of the helix formed by residues 1563 - 1572 (chain B) in PDB entry 1DDX
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 SER1563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343B ILE* 3.6 6.0 - - - +
1347B ASP* 3.4 14.8 - - - -
1561B THR 4.3 0.2 - - - -
1562B ALA* 1.3 75.3 - - - +
1564B ILE* 1.3 65.3 + - - +
1565B GLN* 2.7 28.8 + - - +
1566B SER* 2.9 14.1 + - - -
1567B LEU* 2.7 21.5 + - - +
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Residues in contact with ILE1564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B MET* 6.0 0.2 - - + -
1201B PHE* 3.6 22.0 - - + -
1301B TYR* 4.1 8.1 - - + +
1343B ILE* 3.5 17.2 - - + +
1347B ASP* 2.7 28.1 + - - +
1563B SER* 1.3 70.2 - - - +
1565B GLN* 1.3 67.0 + - + +
1567B LEU* 3.3 11.1 - - + +
1568B ILE* 2.7 54.9 + - + +
1578B THR* 5.0 7.6 - - + -
1579B SER* 4.8 15.0 - - - +
1580B PHE* 3.4 41.7 - - + -
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Residues in contact with GLN1565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563B SER* 2.7 16.7 + - - +
1564B ILE* 1.3 84.6 - - + +
1566B SER* 1.3 51.7 + - - +
1568B ILE* 2.8 10.8 + - - +
1569B CYS* 2.6 55.2 + - + +
1575B CYS 4.9 1.0 + - - -
1576B PRO 4.2 10.7 + - - -
1577B PHE* 3.7 14.5 - - - +
1578B THR* 3.2 36.9 + - - +
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Residues in contact with SER1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561B THR 4.4 5.1 + - - -
1562B ALA* 4.0 5.2 - - - -
1563B SER* 2.8 37.0 + - - -
1565B GLN* 1.3 71.9 - - - +
1567B LEU* 1.3 66.2 + - - +
1569B CYS* 2.7 12.5 + - - -
1570B ASN* 2.7 42.6 + - - -
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Residues in contact with LEU1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201B PHE* 5.0 0.7 - - + -
1301B TYR* 5.4 2.9 - - + -
1304B ILE* 3.5 15.9 - - + -
1305B TRP* 3.4 46.0 - - + +
1308B GLU* 4.2 15.7 - - + -
1343B ILE* 3.6 16.8 - - + -
1563B SER 2.7 16.0 + - - +
1564B ILE* 3.3 24.5 - - + +
1566B SER* 1.3 73.8 + - - +
1568B ILE* 1.3 64.7 + - + +
1570B ASN* 4.5 3.0 - - - +
1571B ASN* 3.2 43.1 + - - +
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Residues in contact with ILE1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B MET* 4.5 20.0 - - + -
1301B TYR* 4.9 5.2 - - + -
1304B ILE* 4.8 10.3 - - + -
1423B VAL* 3.8 15.5 - - + -
1564B ILE* 2.7 53.7 + - + +
1565B GLN* 2.8 7.1 + - - +
1567B LEU* 1.3 84.2 - - + +
1569B CYS* 1.3 58.6 + - - +
1572B VAL* 2.7 60.1 + - + +
1576B PRO* 3.7 24.4 - - + +
1578B THR* 4.1 7.2 - - + +
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Residues in contact with CYS1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565B GLN* 2.6 25.8 + - - +
1566B SER* 2.7 25.5 + - - +
1568B ILE* 1.3 71.5 - - - +
1570B ASN* 1.3 60.2 + - - +
1572B VAL 3.0 18.7 - - - +
1575B CYS* 2.0 65.9 - - - +
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Residues in contact with ASN1570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308B GLU* 5.2 0.7 - - - +
1311B ARG* 3.9 46.0 + - - +
1566B SER* 2.7 38.4 + - - +
1567B LEU* 4.5 2.9 - - - +
1569B CYS* 1.3 77.4 - - - +
1571B ASN* 1.3 63.0 + - - +
1572B VAL 3.4 3.1 + - - +
1575B CYS* 5.0 0.8 - - - -
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Residues in contact with ASN1571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304B ILE* 2.6 42.2 + - + +
1307B ARG* 3.3 35.7 + - + +
1308B GLU* 2.8 49.0 + - - +
1311B ARG* 4.1 6.9 - - - +
1567B LEU* 3.2 25.6 + - - +
1570B ASN* 1.3 80.7 - - - +
1572B VAL* 1.3 58.9 + - - +
1573B LYS 4.3 0.5 + - - -
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Residues in contact with VAL1572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260B GLU* 6.2 0.2 - - - +
1304B ILE* 4.7 12.3 - - + -
1307B ARG* 5.9 0.9 - - - -
1419B LEU* 4.1 12.1 - - + -
1420B THR* 3.7 38.1 - - + +
1423B VAL* 3.9 14.1 - - + -
1568B ILE* 2.7 49.7 + - + +
1569B CYS 3.0 18.9 - - - +
1570B ASN 4.0 2.1 - - - +
1571B ASN* 1.3 82.1 - - + +
1573B LYS* 1.3 69.2 + - - +
1574B GLY 3.7 0.3 + - - -
1575B CYS 3.4 3.5 + - - -
1576B PRO* 3.9 3.6 - - + -
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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