Contacts of the helix formed by residues 1693 - 1700 (chain D) in PDB entry 5JH5
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 GLU1693 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1597D MSE 5.4 0.9 - - - -
1645D HIS 4.3 2.6 - - - +
1646D PHE* 3.6 31.2 - - - -
1647D GLU 4.4 2.8 + - - -
1691D ARG* 3.5 44.6 + - + +
1692D TYR* 1.3 82.5 - - - +
1694D PRO* 1.3 78.4 - - + +
1695D ASP* 4.5 9.2 - - - +
1696D LEU* 3.0 25.1 + - + +
1697D LEU* 3.1 16.2 + - - +
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Residues in contact with PRO1694 (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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164C ARG* 4.2 19.1 - - - +
1597D MSE 3.6 23.3 - - + -
1693D GLU* 1.3 88.7 - - + +
1695D ASP* 1.3 62.2 + - - +
1697D LEU* 3.2 12.5 + - + +
1698D ARG* 3.0 53.8 + - - +
1704D VAL* 4.3 8.5 - - + -
1706D PHE* 4.4 9.6 - - + -
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Residues in contact with ASP1695 (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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1646D PHE* 3.9 20.3 - - + -
1693D GLU* 3.2 10.3 - - - +
1694D PRO* 1.3 78.3 - - - +
1696D LEU* 1.3 62.0 + - - +
1698D ARG* 3.5 20.4 + - - +
1699D LEU* 3.1 21.5 + - - +
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Residues in contact with LEU1696 (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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1623D PHE* 3.7 25.1 - - + -
1628D VAL* 3.9 21.1 - - + -
1632D LEU* 4.9 0.4 - - + -
1639D PHE* 4.1 8.5 - - + -
1646D PHE* 3.6 35.7 - - + -
1690D VAL* 3.5 33.7 - - + -
1691D ARG 3.5 16.4 - - - +
1693D GLU* 3.0 9.9 + - + +
1695D ASP* 1.3 76.6 - - - +
1697D LEU* 1.3 61.5 + - - +
1699D LEU* 3.3 8.4 + - + -
1700D LEU* 3.0 31.5 + - + +
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Residues in contact with LEU1697 (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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1597D MSE 4.5 6.3 - - + -
1599D GLU* 3.6 25.4 - - + +
1623D PHE* 3.4 37.0 - - + -
1692D TYR* 3.4 39.3 - - + +
1693D GLU 3.1 14.3 + - - +
1694D PRO* 3.2 9.2 + - + +
1696D LEU* 1.3 73.1 - - - +
1698D ARG* 1.3 65.7 + - - +
1700D LEU* 3.2 12.4 + - + +
1701D GLY 3.4 0.2 + - - -
1702D SER* 3.0 27.1 + - - -
1704D VAL* 4.1 23.8 - - + -
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Residues in contact with ARG1698 (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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1694D PRO* 3.0 34.9 + - - +
1695D ASP* 3.6 25.9 + - - +
1697D LEU* 1.3 75.3 - - - +
1699D LEU* 1.3 61.9 + - - +
1701D GLY* 3.0 14.2 + - - -
1702D SER 3.5 16.3 - - - +
1703D GLU* 5.5 0.7 - - - +
1704D VAL* 4.1 33.0 + - + +
1706D PHE* 4.3 10.3 - - - -
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Residues in contact with LEU1699 (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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1632D LEU* 3.7 32.4 - - + +
1639D PHE* 4.7 0.2 - - + -
1643D PHE* 3.6 44.9 - - + -
1646D PHE* 3.7 25.6 - - + -
1695D ASP 3.1 13.8 + - - +
1696D LEU* 3.5 12.3 - - + +
1697D LEU 3.2 0.2 - - - -
1698D ARG* 1.3 78.1 - - - +
1700D LEU* 1.3 56.7 + - - +
1701D GLY* 3.0 5.9 + - - -
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Residues in contact with LEU1700 (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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1599D GLU* 5.2 3.1 - - - +
1606D LEU* 4.1 21.5 - - + -
1623D PHE* 4.2 26.7 - - + -
1628D VAL* 4.2 13.2 - - + -
1631D ARG* 3.6 47.8 + - + +
1632D LEU* 3.9 21.8 - - + -
1696D LEU* 3.0 27.3 + - + +
1697D LEU* 3.2 11.8 + - + +
1699D LEU* 1.3 73.2 - - - +
1701D GLY* 1.3 58.0 + - - +
1702D SER* 3.5 6.7 + - - +
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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