Contacts of the helix formed by residues 1494 - 1501 (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 LEU1494 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489B PRO* 3.8 37.2 - - + +
1490B SER 3.0 5.9 + - - +
1491B ARG 3.6 2.7 - - - -
1493B GLU* 1.3 80.3 - - - +
1495B PRO* 1.3 68.1 - - - +
1496B GLU* 3.2 24.7 - - - +
1497B TYR* 3.2 34.9 + - + +
1498B TYR* 3.3 13.5 - - - -
1539B PHE* 4.0 24.9 - - + -
1605B 5BW 3.9 28.7 - - + +
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Residues in contact with PRO1495 (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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1491B ARG* 3.2 18.4 - - + +
1492B LYS* 3.8 7.2 - - - +
1493B GLU 3.7 5.2 - - - +
1494B LEU* 1.3 88.7 - - - +
1496B GLU* 1.3 77.4 + - + +
1498B TYR* 3.0 16.3 + - + +
1499B GLU* 2.9 33.0 + - - +
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Residues in contact with GLU1496 (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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1493B GLU 4.9 0.5 - - - +
1494B LEU* 3.4 22.3 - - - +
1495B PRO* 1.3 101.0 - - + +
1497B TYR* 1.3 65.0 + - - +
1499B GLU* 3.2 12.8 + - - +
1500B LEU* 3.1 24.8 + - - +
1539B PHE* 4.3 15.2 - - + -
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Residues in contact with TYR1497 (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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1488B LEU* 3.4 37.5 - - + +
1494B LEU* 3.2 30.3 + - + +
1496B GLU* 1.3 79.1 - - - +
1498B TYR* 1.3 70.9 + + + +
1500B LEU 3.4 0.2 + - - -
1501B ILE* 2.9 59.0 + - + +
1504B PRO* 4.0 7.6 - - + +
1505B VAL 4.8 0.3 + - - -
1535B ASN* 3.5 17.8 + - - +
1539B PHE* 3.5 42.1 - + + -
1605B 5BW 2.9 47.5 + - - -
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Residues in contact with TYR1498 (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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1488B LEU* 3.8 12.8 + - + +
1489B PRO 2.7 29.4 + - - -
1490B SER* 3.8 1.4 - - - -
1491B ARG* 3.6 73.1 + - + +
1494B LEU* 3.3 18.4 - - + -
1495B PRO* 3.0 7.8 + - + +
1497B TYR* 1.3 86.9 - + + +
1499B GLU* 1.3 67.7 + - - +
1501B ILE 3.5 14.1 - - - +
1504B PRO* 3.8 28.7 - - + -
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Residues in contact with GLU1499 (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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1495B PRO* 2.9 43.7 + - - +
1496B GLU* 3.2 11.4 + - - +
1498B TYR* 1.3 82.6 - - - +
1500B LEU* 1.3 61.6 - - - +
1501B ILE 5.0 0.5 - - - +
1502B ARG* 5.5 3.6 - - - +
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Residues in contact with LEU1500 (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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1496B GLU 3.1 14.9 + - - +
1497B TYR 4.1 2.2 - - - +
1499B GLU* 1.3 80.8 - - - +
1501B ILE* 1.3 69.1 + - + +
1502B ARG* 3.8 7.6 + - - +
1538B THR* 3.8 37.0 - - + +
1539B PHE* 3.9 22.4 - - + +
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Residues in contact with ILE1501 (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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1497B TYR* 2.9 52.7 + - + +
1498B TYR 3.5 15.9 - - - +
1500B LEU* 1.3 88.5 - - + +
1502B ARG* 1.3 63.7 + - - +
1503B LYS 4.0 0.4 - - - +
1504B PRO* 3.8 20.6 - - + +
1535B ASN* 3.6 44.2 - - - +
1538B THR* 3.6 37.7 - - + -
1539B PHE* 4.2 3.8 - - + +
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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