Contacts of the helix formed by residues 1665 - 1678 (chain D) 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 THR1665 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1525C LYS* 3.7 36.2 + - + +
1652D THR* 3.2 6.8 - - - +
1664D GLY* 1.3 73.8 - - - +
1666D LEU* 1.4 68.5 + - + +
1667D GLY 3.9 7.6 - - - +
1668D GLU* 3.5 22.6 + - - +
1669D SER* 3.1 29.8 + - - -
1801D PX4 4.0 24.3 + - - +
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Residues in contact with LEU1666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521C MET 5.6 0.4 - - - +
1522C MET* 3.6 53.1 + - + +
1524C GLU 4.5 4.7 + - - +
1525C LYS* 5.2 0.2 - - - +
1645D TYR* 4.6 3.1 - - + +
1648D ALA* 3.9 19.1 - - + -
1649D ILE* 3.7 34.8 - - + +
1652D THR* 3.7 11.8 - - + +
1665D THR* 1.4 76.9 - - + +
1667D GLY* 1.3 54.1 + - - +
1669D SER* 3.2 5.0 + - - -
1670D PHE* 2.8 47.8 + - + +
1801D PX4 5.0 7.0 - - - +
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Residues in contact with GLY1667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1665D THR* 3.4 4.2 - - - +
1666D LEU* 1.3 78.4 - - - +
1668D GLU* 1.4 57.6 + - - +
1670D PHE* 3.4 10.0 - - - +
1671D TYR* 3.0 27.5 + - - +
1801D PX4 3.2 52.2 + - - +
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Residues in contact with GLU1668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1688A ARG* 3.9 8.1 + - - -
1660D PRO 3.3 17.4 - - - +
1661D GLU* 2.9 25.5 - - - +
1662D TRP 2.7 33.3 - - - +
1663D PHE 3.7 1.6 - - - +
1664D GLY 3.7 2.2 - - - +
1665D THR* 3.5 28.7 + - - +
1667D GLY* 1.4 74.5 - - - +
1669D SER* 1.4 55.5 + - - +
1671D TYR* 3.6 4.3 + - - +
1672D THR* 3.1 15.2 + - - -
1801D PX4 3.1 52.5 + - - -
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Residues in contact with SER1669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648D ALA* 3.7 20.4 - - - -
1651D ALA* 4.0 3.6 - - - -
1652D THR* 3.1 10.4 + - - +
1662D TRP 3.5 6.5 + - - -
1663D PHE* 3.0 43.8 + - - +
1665D THR 3.1 6.4 + - - -
1666D LEU 3.3 8.7 - - - -
1668D GLU* 1.4 73.9 - - - +
1670D PHE* 1.4 63.1 + - - +
1672D THR* 3.2 3.8 + - - -
1673D LEU* 3.0 28.6 + - - +
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Residues in contact with PHE1670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641D THR* 4.8 2.9 - - + -
1644D PHE* 3.7 27.6 - + + -
1645D TYR* 3.6 60.6 - + - -
1648D ALA* 3.5 26.4 - - + +
1666D LEU* 2.8 27.3 + - + +
1667D GLY* 3.3 12.3 + - - +
1669D SER* 1.4 71.8 - - - +
1671D TYR* 1.4 61.2 + - - +
1673D LEU* 3.4 10.7 + - - +
1674D PHE* 3.1 22.3 + - - +
1801D PX4 3.7 47.1 - - + +
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Residues in contact with TYR1671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682A TRP* 3.6 6.6 - + - -
1683A SER* 2.7 35.5 + - - -
1687A VAL* 3.4 20.7 - - + +
1688A ARG* 3.3 40.7 + - + -
1691A MET* 4.2 17.3 - - + -
1698A TRP* 4.0 26.9 - + + -
1702A ILE* 4.3 20.9 - - + -
1667D GLY 3.0 16.1 + - - +
1668D GLU 3.6 6.3 - - - +
1670D PHE* 1.4 73.4 - - - +
1672D THR* 1.3 57.8 - - - +
1674D PHE* 3.1 6.2 + - - +
1675D GLN* 2.9 26.1 + - + +
1801D PX4 4.0 27.7 - - + +
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Residues in contact with THR1672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1688A ARG* 2.8 27.2 + - - +
1662D TRP* 2.7 33.5 + - + +
1663D PHE* 3.7 28.7 - - + -
1668D GLU 3.1 1.4 + - - -
1669D SER 3.2 1.9 + - - -
1671D TYR* 1.3 72.5 - - - +
1673D LEU* 1.3 59.4 + - - +
1675D GLN* 3.2 5.9 + - + +
1676D VAL* 2.8 31.0 + - + +
1686D ILE* 3.8 28.9 - - + -
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Residues in contact with LEU1673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644D PHE* 3.6 21.8 - - + +
1647D PHE* 3.7 5.6 - - + +
1648D ALA* 3.4 42.8 - - + +
1651D ALA* 4.7 4.5 - - + -
1663D PHE* 4.8 4.0 - - + -
1669D SER 3.0 21.4 + - - +
1670D PHE* 3.7 3.4 - - - +
1671D TYR 3.2 0.2 - - - -
1672D THR* 1.3 75.1 - - - +
1674D PHE* 1.4 57.1 + - - +
1676D VAL* 3.6 2.6 + - + -
1677D MET* 3.0 26.7 + - - +
1700D PHE* 4.1 25.6 - - + -
1701D PHE* 4.6 10.1 - - + -
1704D PHE* 3.3 34.4 - - + -
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Residues in contact with PHE1674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682A TRP* 3.6 22.2 - + - -
1702A ILE* 3.6 21.8 - - + -
1705A ILE* 3.6 26.9 - - + -
1706A PHE* 3.4 32.1 - + - -
1644D PHE* 3.6 8.9 - + - -
1670D PHE 3.1 13.1 + - - +
1671D TYR* 3.1 9.8 + - - +
1673D LEU* 1.4 74.8 - - - +
1675D GLN* 1.3 57.5 + - - +
1677D MET* 3.1 19.9 + - + +
1678D THR* 2.9 46.5 + - + +
1801D PX4 3.8 34.3 - - + -
1803D PX4 5.2 3.6 - - + -
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Residues in contact with GLN1675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682A TRP* 3.7 10.3 - - + -
1683A SER* 2.8 38.4 + - - +
1684A MET* 3.3 24.7 - - - +
1688A ARG* 3.0 31.1 - - - +
1671D TYR* 2.9 12.9 + - - +
1672D THR* 3.4 9.2 - - - +
1674D PHE* 1.3 77.3 - - - +
1676D VAL* 1.3 56.0 + - - +
1678D THR* 3.0 19.1 + - - -
1680D GLU* 3.1 41.0 + - + +
1686D ILE* 3.6 16.7 - - - +
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Residues in contact with VAL1676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1672D THR* 2.8 25.1 + - + +
1673D LEU* 3.9 4.9 - - - +
1675D GLN* 1.3 70.3 - - - +
1677D MET* 1.4 59.2 + - - +
1679D LEU* 3.1 18.9 + - - -
1682D TRP* 3.8 29.7 - - + +
1686D ILE* 4.4 22.7 - - + -
1687D VAL* 5.0 0.4 - - + -
1701D PHE* 4.4 22.7 - - + -
1704D PHE* 3.7 20.6 - - + -
1705D ILE* 3.4 31.8 - - + +
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Residues in contact with MET1677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706A PHE* 5.7 1.1 - - + -
1640D MET* 3.7 25.1 - - + -
1644D PHE* 3.4 31.0 - - + -
1673D LEU 3.0 19.0 + - - +
1674D PHE* 3.1 22.6 + - + +
1676D VAL* 1.4 72.0 - - - +
1678D THR* 1.3 58.4 + - + +
1679D LEU* 2.9 23.0 + - - +
1704D PHE* 4.4 3.8 - - + -
1705D ILE* 5.3 2.4 - - - +
1708D VAL* 3.6 22.8 - - + +
1709D THR* 5.6 1.6 + - - -
1712D MET* 4.3 10.8 - - + -
1801D PX4 4.6 10.3 - - + -
1803D PX4 3.8 36.1 - - + +
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Residues in contact with THR1678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679A LEU* 3.9 33.9 - - + +
1682A TRP* 2.8 27.4 + - - +
1705A ILE* 4.4 1.3 - - + -
1674D PHE* 2.9 44.7 + - + +
1675D GLN 3.0 11.4 + - - -
1677D MET* 1.3 72.1 - - - +
1679D LEU* 1.4 63.7 + - - +
1680D GLU* 3.1 7.6 + - - +
1803D PX4 3.9 26.8 - - + +
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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