Contacts of the helix formed by residues 1659 - 1664 (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 PHE1659 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1655B PHE* 2.8 16.3 + - + +
1656B GLY 3.8 1.8 - - - -
1658B ARG* 1.3 83.6 - - + +
1660B PRO* 1.3 60.3 - - - +
1661B GLU* 3.1 19.3 - - - +
1662B TRP* 3.6 22.4 - + + -
1663B PHE* 3.0 37.6 + - + -
1664B GLY 3.5 3.1 + - - -
1689B PRO* 3.4 27.1 - - + -
1690B LEU* 3.6 24.7 - - + -
1693B VAL* 3.5 26.7 - - + -
1694B TYR* 3.6 31.6 - + - -
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Residues in contact with PRO1660 (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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1526A GLU* 3.4 40.2 - - + +
1656B GLY 3.6 4.5 - - - +
1657B GLU 4.2 7.6 - - - +
1658B ARG 3.4 9.9 - - - +
1659B PHE* 1.3 85.5 - - - +
1661B GLU* 1.3 77.7 + - + +
1662B TRP 3.1 3.3 - - - -
1663B PHE 3.6 0.2 + - - -
1664B GLY* 2.9 27.6 + - - +
1668B GLU* 3.7 9.9 - - - +
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Residues in contact with GLU1661 (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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1658B ARG 4.6 1.6 - - - +
1659B PHE* 3.1 42.0 - - - +
1660B PRO* 1.3 94.4 - - + +
1662B TRP* 1.3 84.2 + - + +
1668B GLU* 3.0 23.8 - - - +
1688C ARG* 3.9 4.0 + - - -
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Residues in contact with TRP1662 (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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1659B PHE* 3.6 23.8 + + - +
1661B GLU* 1.3 98.5 - - + +
1663B PHE* 1.4 73.6 + + + +
1668B GLU* 2.9 21.9 - - - +
1669B SER 3.5 0.2 + - - -
1672B THR* 2.7 28.4 + - + +
1685B GLY 3.2 26.7 - - - -
1686B ILE* 4.1 11.0 - - + -
1689B PRO* 3.7 16.6 - - + -
1690B LEU* 3.6 32.8 - - + -
1684C MET* 4.4 11.2 - - + +
1688C ARG* 3.4 35.8 - - - +
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Residues in contact with PHE1663 (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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1651B ALA* 3.6 35.2 - - + +
1652B THR* 3.2 22.0 - - - -
1655B PHE* 3.6 15.3 - + + -
1656B GLY* 3.3 8.0 - - - +
1659B PHE* 3.0 17.9 + - + +
1662B TRP* 1.4 94.6 - - + +
1664B GLY* 1.3 61.9 + - - +
1665B THR 3.3 3.5 + - - -
1668B GLU* 4.3 0.2 - - - -
1669B SER* 3.2 18.8 + - - +
1672B THR* 3.5 28.9 - - + -
1673B LEU* 4.8 6.1 - - + -
1686B ILE* 3.7 10.3 - - + -
1690B LEU* 3.7 23.3 - - + -
1701B PHE* 3.6 31.0 - + - -
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Residues in contact with GLY1664 (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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1525A LYS* 3.4 3.6 - - - +
1526A GLU* 2.8 39.8 + - - +
1652B THR* 3.6 4.3 - - - +
1656B GLY* 3.8 10.5 - - - -
1659B PHE 3.5 2.0 + - - -
1660B PRO* 2.9 30.5 + - - -
1662B TRP 3.9 0.2 - - - -
1663B PHE* 1.3 76.2 - - - +
1665B THR* 1.3 59.7 + - - +
1668B GLU* 4.1 0.4 - - - +
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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