Contacts of the helix formed by residues 1700 - 1709 (chain X) in PDB entry 1N5O
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 THR1700 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202X SO4 3.4 21.5 - - - +
1655X SER* 3.0 26.9 + - - +
1656X GLY* 5.6 3.4 - - - +
1689X MET* 3.5 9.0 - - + +
1698X GLU* 3.3 18.5 + - + +
1699X ARG* 1.3 79.1 - - - +
1701X LEU* 1.3 61.1 + - - +
1702X LYS* 3.9 2.1 + - - -
1703X TYR* 3.0 16.6 + - - +
1704X PHE* 2.9 35.0 + - - -
1775X ARG* 5.1 1.3 - - - +
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Residues in contact with LEU1701 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X SO4 2.8 30.8 + - - +
1700X THR* 1.3 72.5 - - - +
1702X LYS* 1.3 59.4 + - + +
1704X PHE* 3.2 7.2 + - + -
1705X LEU* 3.0 53.0 + - + +
1774X ASN 4.7 10.5 - - - +
1775X ARG* 4.7 12.5 - - + +
1776X PRO* 5.0 4.5 - - + -
1779X GLN* 4.1 29.4 - - + +
1783X MET* 3.7 28.5 - - + -
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Residues in contact with LYS1702 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1653X VAL* 3.7 23.8 - - + +
1654X VAL 3.1 28.3 + - - +
1655X SER* 4.1 15.0 - - - +
1677X THR 5.4 0.2 + - - -
1678X ASN* 2.9 29.1 + - - +
1679X LEU* 5.0 0.7 - - - +
1680X ILE* 3.9 24.9 - - + +
1687X VAL* 3.7 23.1 - - + +
1700X THR* 3.3 1.0 + - - -
1701X LEU* 1.3 75.6 - - + +
1703X TYR* 1.3 61.5 + - - +
1705X LEU* 4.6 0.7 - - - -
1706X GLY* 3.0 24.3 + - - -
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Residues in contact with TYR1703 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1687X VAL* 5.0 0.9 - - - -
1689X MET* 3.8 11.6 - - + -
1697X CYS* 3.5 27.6 - - - -
1698X GLU 4.3 2.0 - - - -
1699X ARG* 3.8 24.2 - - + -
1700X THR* 3.0 26.2 + - - +
1702X LYS* 1.3 78.9 - - - +
1704X PHE* 1.3 70.0 + + - +
1706X GLY* 3.3 1.2 + - - -
1707X ILE* 3.1 52.8 + - + +
1713X VAL* 4.1 16.1 - - + +
1736X VAL* 4.0 12.1 - - + -
1738X GLY* 4.0 6.1 + - - -
1739X ASP* 2.6 32.5 + - - -
1742X ASN* 3.9 7.4 + - - -
1749X PRO* 4.5 4.0 - - + +
1843X ALA* 3.8 16.6 + - + -
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Residues in contact with PHE1704 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1699X ARG* 3.7 40.8 - - + -
1700X THR 2.9 35.1 + - - -
1701X LEU* 3.2 7.8 + - + +
1703X TYR* 1.3 80.3 - + - +
1705X LEU* 1.3 53.8 + - - +
1707X ILE* 3.4 2.3 + - - +
1708X ALA* 2.7 35.8 + - - +
1775X ARG* 4.0 19.3 - - - -
1783X MET* 3.5 26.9 - - + -
1839X LEU* 3.5 54.3 - - + -
1842X VAL* 3.5 19.7 - - + +
1843X ALA* 4.3 7.4 - - + -
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Residues in contact with LEU1705 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680X ILE* 3.8 28.4 - - + +
1701X LEU* 3.0 33.3 + - + +
1704X PHE* 1.3 73.8 - - - +
1706X GLY* 1.3 61.3 + - - +
1708X ALA* 3.7 3.1 - - - +
1709X GLY* 3.0 22.7 + - - -
1711X LYS* 4.6 3.3 - - - -
1779X GLN* 3.4 29.6 - - - +
1782X TRP* 3.6 33.2 - - + -
1783X MET* 3.9 34.5 - - + +
1786X LEU* 4.2 10.0 - - + +
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Residues in contact with GLY1706 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680X ILE* 3.8 4.6 - - - +
1687X VAL* 3.8 19.7 - - - -
1702X LYS 3.0 20.8 + - - -
1703X TYR 3.8 0.7 - - - -
1704X PHE 3.3 0.2 - - - -
1705X LEU* 1.3 76.3 - - - +
1707X ILE* 1.3 59.5 - - - +
1709X GLY 3.2 1.9 + - - -
1710X GLY 3.1 4.3 + - - -
1711X LYS* 2.9 32.9 + - - +
1713X VAL* 3.9 7.9 - - - -
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Residues in contact with ILE1707 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703X TYR* 3.1 44.7 + - + +
1704X PHE* 3.6 7.9 - - - +
1706X GLY* 1.3 70.9 - - - +
1708X ALA* 1.3 58.1 + - - +
1709X GLY 3.0 1.6 - - - -
1710X GLY* 2.7 24.3 + - - +
1711X LYS 4.7 1.1 - - - +
1713X VAL* 3.9 6.2 - - + +
1748X GLY 4.5 0.7 - - - +
1749X PRO* 3.9 28.5 - - + -
1752X ALA* 3.4 16.6 - - + +
1842X VAL* 3.2 24.9 - - + +
1843X ALA* 3.4 24.2 - - - +
1845X TYR* 3.8 21.9 - - + -
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Residues in contact with ALA1708 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704X PHE 2.7 21.7 + - - +
1705X LEU* 3.7 10.5 - - - +
1706X GLY 3.3 0.2 - - - -
1707X ILE* 1.3 75.4 - - - +
1709X GLY* 1.3 58.3 + - - +
1710X GLY 3.7 0.2 + - - -
1783X MET* 4.0 17.0 - - + +
1786X LEU* 3.4 46.4 - - + +
1787X CYS* 4.0 15.6 - - - -
1842X VAL* 4.6 1.1 - - + -
1845X TYR* 4.9 5.3 + - - -
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Residues in contact with GLY1709 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705X LEU 3.0 13.4 + - - -
1706X GLY 3.2 3.3 + - - -
1707X ILE 3.0 1.0 - - - -
1708X ALA* 1.3 77.4 - - - +
1710X GLY* 1.3 66.5 + - - +
1711X LYS* 3.4 20.4 - - - +
1786X LEU* 4.4 9.0 - - - -
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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