Contacts of the helix formed by residues 1403 - 1408 (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 SER1403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1393B ASP 4.6 4.5 - - - -
1394B THR* 4.7 2.0 - - - +
1395B PHE* 4.3 2.2 - - - -
1402B TYR* 1.3 76.6 - - - +
1404B PHE* 1.3 54.2 + - - +
1405B LYS* 3.1 30.9 - - - +
1406B GLN* 2.4 48.6 + - - +
1407B PHE* 2.7 31.7 + - - +
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Residues in contact with PHE1404 (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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1391B LEU* 3.3 40.6 - - + -
1392B PRO 2.9 29.8 - - - -
1393B ASP* 3.7 16.2 - - - -
1395B PHE* 3.6 23.8 - + - -
1403B SER* 1.3 71.8 - - - +
1405B LYS* 1.3 86.7 + - - +
1406B GLN 2.8 1.9 + - - -
1407B PHE* 4.5 1.3 - - - -
1408B LEU* 3.0 38.6 + - + +
1441B PRO* 4.1 10.5 - - + -
1443B ALA* 3.4 29.2 - - + -
1444B VAL* 4.1 7.9 - - + -
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Residues in contact with LYS1405 (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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1393B ASP 4.3 6.1 + - - -
1403B SER* 3.1 21.3 - - - +
1404B PHE* 1.3 112.6 - - - +
1406B GLN* 1.3 61.0 + - + +
1408B LEU* 4.7 9.4 - - - +
1443B ALA* 4.6 11.0 - - - +
1681B NAG 4.4 9.4 - - - +
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Residues in contact with GLN1406 (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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1400B GLN* 5.9 0.4 + - - -
1401B GLU 3.4 7.1 + - - +
1402B TYR* 2.7 32.0 - - + -
1403B SER* 2.4 56.2 + - - +
1405B LYS* 1.3 74.9 - - + +
1407B PHE* 1.3 68.8 + - - +
1408B LEU 3.2 7.4 + - - +
1410B ASN* 3.5 5.2 - - - +
1413B ILE* 4.5 3.1 - - - -
1681B NAG 3.2 26.9 + - - +
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Residues in contact with PHE1407 (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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1200B PHE* 3.6 20.2 - + - -
1295B VAL* 5.4 3.4 - - + -
1296B PRO* 3.4 30.7 - - + +
1297B GLY 4.5 3.1 - - - -
1395B PHE* 3.1 58.6 - + + -
1397B ILE* 4.2 7.6 - - + -
1402B TYR* 4.3 5.1 - + + +
1403B SER 2.7 16.9 + - - +
1404B PHE* 3.9 2.2 - - - +
1406B GLN* 1.3 72.1 - - - +
1408B LEU* 1.3 68.7 + - + +
1409B TYR 3.2 0.5 + - - -
1410B ASN* 2.8 19.2 + - - +
1413B ILE* 3.3 34.3 - - + +
1422B PHE* 4.3 4.3 - + - -
1426B PHE* 3.3 26.9 - + - -
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Residues in contact with LEU1408 (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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1294B LEU* 3.5 16.4 - - + +
1295B VAL* 4.6 9.4 - - + -
1296B PRO* 4.9 0.2 - - - -
1395B PHE* 6.6 0.2 - - + -
1404B PHE* 3.0 27.5 + - + +
1405B LYS* 4.7 7.8 - - - +
1406B GLN 3.2 7.3 + - - +
1407B PHE* 1.3 82.4 - - + +
1409B TYR* 1.3 102.8 + - + +
1410B ASN* 2.9 7.4 + - - +
1681B NAG 5.9 1.6 - - - +
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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