Contacts of the strand formed by residues 1846 - 1851 (chain X) in PDB entry 3HM6
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 THR1846 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752X ASN* 3.1 33.1 + - - +
1754X LEU* 5.0 13.9 - - + -
1807X TRP* 3.6 5.8 - - - +
1808X ARG* 2.8 69.6 + - + +
1844X GLY 3.8 1.6 + - - -
1845X ALA* 1.3 69.5 - - - +
1847X VAL* 1.3 59.1 + - - +
1848X ALA 5.0 0.2 - - - +
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Residues in contact with VAL1847 (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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1751X LEU* 4.3 18.2 - - + -
1752X ASN 3.2 5.6 + - - +
1753X ALA* 3.5 2.1 - - - -
1754X LEU 3.2 15.3 + - - -
1784X MET* 3.1 33.5 - - + +
1805X VAL* 4.6 12.1 - - + -
1806X GLU 3.2 9.2 - - - +
1807X TRP* 4.3 5.8 - - + +
1817X LEU* 5.8 2.2 - - + -
1836X LEU* 6.5 0.4 - - + -
1841X VAL* 6.0 3.8 - - + -
1845X ALA 3.5 3.1 + - - +
1846X THR* 1.3 74.7 - - - +
1848X ALA* 1.3 60.0 + - - +
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Residues in contact with ALA1848 (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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1754X LEU* 3.5 16.4 - - + +
1756X ALA* 4.3 8.5 - - + -
1784X MET* 4.3 0.4 - - - +
1805X VAL* 3.6 6.2 - - - +
1806X GLU* 2.6 40.3 + - + +
1808X ARG* 3.2 40.3 - - - +
1846X THR 4.1 0.8 + - - -
1847X VAL* 1.3 74.3 - - - +
1849X LEU* 1.3 65.7 + - - +
1850X VAL* 4.1 0.9 - - + -
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Residues in contact with LEU1849 (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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1754X LEU 3.1 9.6 + - - +
1755X LEU* 3.6 22.5 - - + +
1756X ALA 3.0 26.0 + - - -
1781X LYS* 4.1 13.5 - - + +
1784X MET* 4.0 21.1 - - + -
1785X LEU* 3.7 44.6 - - + +
1788X LEU* 5.3 2.2 - - + -
1803X LEU* 4.0 18.2 - - + +
1804X ASP 3.5 11.2 - - - +
1805X VAL* 3.8 20.0 - - + -
1848X ALA* 1.3 82.3 - - - +
1850X VAL* 1.3 61.4 + - - +
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Residues in contact with VAL1850 (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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1756X ALA* 3.4 34.5 - - + -
1803X LEU* 3.2 7.7 - - - +
1804X ASP* 2.5 55.0 + - + +
1806X GLU* 3.8 37.9 - - + +
1808X ARG* 4.3 2.9 - - - +
1816X ILE* 4.3 6.5 - - + -
1848X ALA* 4.7 2.5 - - + -
1849X LEU* 1.3 72.3 - - - +
1851X PRO* 1.3 70.8 - - + +
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Residues in contact with PRO1851 (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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1756X ALA 4.5 11.2 - - - +
1802X THR 3.3 12.8 - - - +
1803X LEU* 4.3 8.0 - - + -
1804X ASP* 4.4 3.5 - - - +
1850X VAL* 1.3 100.4 - - + +
1852X CYS* 1.3 64.2 + - - +
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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