Contacts of the helix formed by residues 1594 - 1602 (chain B) in PDB entry 5EK0
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 SER1594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1593B VAL* 1.4 85.0 - - - +
1595B PRO* 1.4 66.7 - - - +
1596B THR* 2.9 11.7 - - - -
1597B LEU* 2.9 45.2 + - - +
1598B PHE* 3.4 5.9 + - - +
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Residues in contact with PRO1595 (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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1593B VAL 3.7 1.1 - - - +
1594B SER* 1.4 83.3 - - - +
1596B THR* 1.4 57.4 + - - +
1598B PHE* 3.4 12.8 + - + +
1599B ARG* 2.8 52.9 + - - +
1657C GLU* 5.2 3.7 - - - +
1658C ARG* 5.4 7.9 - - - +
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Residues in contact with THR1596 (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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1594B SER* 4.5 8.8 - - - -
1595B PRO* 1.4 78.7 - - - +
1597B LEU* 1.4 60.4 + - - +
1599B ARG* 2.8 30.9 + - - +
1600B VAL* 3.3 28.8 - - - +
1801C PX4 3.3 52.1 - - - +
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Residues in contact with LEU1597 (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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1588B ILE* 3.9 26.5 - - + -
1593B VAL* 3.9 16.8 - - + -
1594B SER* 2.9 26.9 + - - +
1596B THR* 1.4 77.0 - - - +
1598B PHE* 1.3 58.9 + - - +
1600B VAL* 4.2 1.7 - - - +
1601B ILE* 3.0 46.0 + - + +
1801C PX4 4.6 15.7 - - - -
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Residues in contact with PHE1598 (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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1537B TYR* 3.2 28.0 - - - -
1585B ALA* 3.3 37.0 - - + -
1588B ILE* 4.6 11.1 - - + +
1589B GLU* 3.4 33.4 - - + -
1593B VAL 4.9 1.1 - - - +
1594B SER 3.4 7.2 + - - +
1595B PRO* 3.4 13.4 + - + +
1597B LEU* 1.3 77.5 - - - +
1599B ARG* 1.4 62.4 + - + +
1601B ILE* 3.3 7.0 + - - +
1602B ARG* 2.9 55.6 + - - +
1806B 5P2 3.4 14.8 - - - -
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Residues in contact with ARG1599 (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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1595B PRO* 2.8 41.8 + - - +
1596B THR* 2.8 47.7 + - - +
1598B PHE* 1.4 77.3 - - + +
1600B VAL* 1.3 66.1 + - + +
1602B ARG* 4.0 4.1 + - - +
1653C GLN* 3.3 34.5 - - - +
1654C LEU* 3.5 35.6 - - - +
1657C GLU* 3.7 31.9 + - - +
1658C ARG* 4.8 16.8 - - - +
1694C TYR* 3.5 29.8 + - - -
1801C PX4 4.5 6.8 - - - -
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Residues in contact with VAL1600 (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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1596B THR 3.3 20.8 + - - +
1597B LEU* 4.2 2.5 - - - +
1598B PHE 3.3 0.6 - - - -
1599B ARG* 1.3 78.7 - - + +
1601B ILE* 1.4 61.3 + - + +
1603B LEU* 3.0 32.2 - - + +
1654C LEU* 4.4 6.7 - - + -
1801C PX4 4.1 49.8 - - - +
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Residues in contact with ILE1601 (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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1581B GLY* 5.3 3.4 - - - +
1584B LEU* 3.8 33.4 - - + -
1585B ALA* 3.8 22.3 - - + +
1588B ILE* 3.7 19.3 - - + -
1597B LEU* 3.0 35.2 + - + +
1598B PHE* 3.4 11.7 - - - +
1600B VAL* 1.4 73.0 - - + +
1602B ARG* 1.4 60.5 + - - +
1603B LEU 3.1 10.2 + - - -
1604B ALA* 3.5 17.7 + - - +
1806B 5P2 4.6 2.1 + - - -
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Residues in contact with ARG1602 (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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1524B GLU* 2.8 35.0 + - - -
1537B TYR* 3.4 27.0 + - - -
1540B ASN* 5.8 0.4 - - - +
1585B ALA* 4.7 4.3 - - + -
1598B PHE* 2.9 48.3 + - + +
1599B ARG* 4.2 4.1 - - - +
1600B VAL 3.3 0.6 - - - -
1601B ILE* 1.4 72.8 - - - +
1603B LEU* 1.4 54.5 + - - +
1604B ALA 3.0 12.0 + - - -
1605B ARG* 3.2 46.0 + - - +
1806B 5P2 2.8 58.2 + - + +
1653C GLN* 3.4 24.3 - - - +
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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