Contacts of the helix formed by residues 1825 - 1830 (chain A) in PDB entry 4M6W
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 HIS1825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1823A GLY* 4.0 4.9 - - - -
1824A GLY* 1.3 73.9 - - - +
1826A GLU* 1.3 69.6 + - - +
1827A ILE 3.3 0.7 - - - -
1828A THR* 3.4 14.1 - - + +
1829A SER* 3.3 29.2 + - - -
1850A LEU 4.8 0.4 - - - -
1851A ASN 6.0 0.4 - - - -
1853A CYS* 3.4 29.2 - - - -
1854A ASP* 2.9 27.7 + - - -
2101A SO4 2.9 35.7 + - - +
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Residues in contact with GLU1826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1822A VAL* 3.7 14.6 - - + -
1823A GLY 2.9 17.3 + - - +
1825A HIS* 1.3 100.8 + - - +
1827A ILE* 1.3 60.3 + - - +
1828A THR 3.3 1.6 - - - -
1829A SER* 4.0 5.7 + - - -
1830A GLY* 2.7 35.9 + - - +
1834A ILE* 3.4 5.3 - - + +
1854A ASP* 3.5 14.8 - - + +
1855A TYR* 3.1 36.3 + - + +
1865A ARG* 2.7 38.0 + - - +
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Residues in contact with ILE1827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1823A GLY 4.8 0.4 - - - +
1824A GLY* 3.1 19.0 + - - +
1826A GLU* 1.3 79.9 - - - +
1828A THR* 1.3 57.8 + - + +
1831A LEU* 3.4 37.4 - - + +
1834A ILE* 3.9 17.0 - - + -
1847A VAL* 3.7 34.3 - - + -
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Residues in contact with THR1828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824A GLY 4.8 1.8 - - - +
1825A HIS* 3.4 24.5 - - - +
1827A ILE* 1.3 79.1 - - + +
1829A SER* 1.3 62.5 + - - +
1830A GLY 3.6 0.2 - - - -
1831A LEU* 4.7 2.9 + - - +
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Residues in contact with SER1829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1825A HIS* 3.3 22.9 + - - -
1826A GLU* 4.0 9.3 + - - -
1828A THR* 1.3 84.7 + - - +
1830A GLY* 1.3 57.4 + - - +
1831A LEU 3.9 0.6 + - - -
1865A ARG* 3.4 19.7 + - - -
1938A GLN* 4.1 10.4 + - - -
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Residues in contact with GLY1830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1826A GLU* 2.7 21.5 + - - -
1829A SER* 1.3 75.2 - - - +
1831A LEU* 1.3 64.0 + - - +
1832A GLU 3.3 2.7 - - - -
1833A VAL* 3.2 14.9 + - - +
1834A ILE* 3.2 16.5 + - - +
1855A TYR* 4.2 0.9 + - - -
1865A ARG* 3.6 16.3 - - - +
1938A GLN* 3.3 13.5 - - - -
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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