Contacts of the helix formed by residues 1482 - 1486 (chain B) in PDB entry 5DKD
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 SER1482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1469B VAL 4.1 4.9 + - - -
1470B ILE* 2.6 44.3 + - - +
1472B TYR 4.8 1.0 + - - -
1480B GLN* 2.9 14.6 + - - +
1481B LEU* 1.3 75.8 - - - +
1483B GLU* 1.3 65.6 + - - +
1484B VAL 3.3 0.7 - - - -
1485B PHE* 2.7 21.9 + - - +
1486B ILE* 3.4 10.5 + - - +
1507B PHE* 4.2 15.3 - - - -
1553B LEU* 4.0 13.7 - - - +
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Residues in contact with GLU1483 (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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1479B ARG* 3.9 18.9 + - - +
1480B GLN* 3.0 49.6 + - + +
1481B LEU 3.1 4.0 + - - -
1482B SER* 1.3 78.5 + - - +
1484B VAL* 1.3 63.1 + - - +
1485B PHE 3.2 0.3 + - - -
1486B ILE* 3.4 20.6 + - - +
1487B GLN 4.9 0.2 + - - -
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Residues in contact with VAL1484 (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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1481B LEU 4.4 2.4 + - - +
1483B GLU* 1.3 78.4 - - - +
1485B PHE* 1.3 80.4 + - + +
1486B ILE 3.4 1.0 + - - -
1487B GLN 4.0 9.8 - - - +
1489B PRO* 5.9 0.2 - - - +
1546B ILE* 3.6 28.3 - - + -
1549B ASP* 5.7 2.5 - - - +
1605B 5BW 3.5 46.8 - - + -
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Residues in contact with PHE1485 (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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1481B LEU 3.7 15.7 - - - -
1482B SER 2.7 12.4 + - - +
1484B VAL* 1.3 79.5 - - + +
1486B ILE* 1.3 64.2 + - - +
1487B GLN 3.3 2.2 - - - -
1506B ASP* 3.5 7.6 - - - +
1507B PHE* 3.0 35.9 + - + -
1532B LEU* 3.8 21.8 - - + -
1536B ALA* 3.8 22.0 - - + -
1546B ILE* 3.5 41.5 - - + -
1549B ASP* 3.9 8.5 - - + -
1550B SER* 3.9 11.2 - - - -
1553B LEU* 3.6 31.6 - - + -
1605B 5BW 3.5 18.8 - + - -
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Residues in contact with ILE1486 (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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1470B ILE* 3.8 43.3 - - + -
1480B GLN* 5.1 2.9 - - - +
1482B SER* 3.7 13.7 - - - +
1483B GLU* 3.4 19.9 + - - +
1484B VAL 3.4 1.6 - - - -
1485B PHE* 1.3 79.2 - - - +
1487B GLN* 1.3 81.7 + - + +
1506B ASP* 3.5 1.7 - - - +
1507B PHE* 3.4 10.0 + - + -
1508B LYS* 2.9 29.5 + - + +
1511B LYS* 4.2 18.2 - - - +
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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