Contacts of the strand formed by residues 1803 - 1808 (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 LEU1803 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1755X LEU* 5.1 4.3 - - + -
1781X LYS* 2.7 37.7 + - + -
1785X LEU* 3.8 34.1 - - + -
1789X TYR* 5.0 2.7 - - - +
1798X PRO* 3.9 21.5 - - + +
1799X ASP 4.4 3.8 - - - +
1800X PRO* 3.1 7.1 + - + +
1801X ARG 3.3 1.8 - - - +
1802X THR* 1.3 93.3 - - - +
1804X ASP* 1.3 63.0 + - - +
1849X LEU* 4.0 17.3 - - + +
1850X VAL* 3.2 20.4 - - - +
1851X PRO* 4.3 6.1 - - + -
1852X CYS* 4.4 2.0 - - - -
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Residues in contact with ASP1804 (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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1781X LYS* 4.8 1.0 + - - +
1803X LEU* 1.3 74.5 - - - +
1805X VAL* 1.3 62.4 + - - +
1816X ILE* 3.9 31.3 - - + +
1817X LEU 5.2 1.6 - - - +
1849X LEU* 3.5 7.2 - - - +
1850X VAL* 2.5 46.9 + - + +
1851X PRO 4.4 2.6 - - - +
1852X CYS* 3.3 31.3 - - - +
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Residues in contact with VAL1805 (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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6X UNX 4.2 2.5 - - - -
1777X ILE* 3.7 28.7 - - + +
1780X ALA* 6.3 2.5 - - + -
1781X LYS* 3.8 31.4 - - + +
1784X MET* 4.8 7.0 - - - -
1804X ASP* 1.3 71.9 - - - +
1806X GLU* 1.3 60.0 + - - +
1816X ILE* 3.3 6.8 - - - +
1817X LEU* 2.8 58.6 + - + +
1836X LEU* 6.1 1.6 - - + -
1847X VAL* 4.6 14.1 - - + -
1848X ALA 3.6 7.4 - - - +
1849X LEU* 3.8 11.0 - - + -
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Residues in contact with GLU1806 (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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1804X ASP 4.0 0.8 + - - -
1805X VAL* 1.3 74.5 - - - +
1807X TRP* 1.3 63.0 + - - +
1808X ARG* 3.1 32.7 + - - +
1814X HIS* 3.5 36.5 - - + +
1815X LEU 3.5 5.6 - - - +
1816X ILE* 3.3 23.7 - - + +
1847X VAL* 3.2 2.8 - - - -
1848X ALA* 2.6 43.7 + - + +
1850X VAL* 3.8 23.4 - - + +
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Residues in contact with TRP1807 (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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1805X VAL 4.2 0.8 - - - -
1806X GLU* 1.3 70.5 - - - +
1808X ARG* 1.3 64.0 + - - +
1809X SER* 4.0 24.5 + - - +
1813X GLY 4.0 2.1 - - - +
1814X HIS* 3.5 2.1 - - - -
1815X LEU* 2.7 73.8 + - + +
1817X LEU* 4.0 20.5 - - + +
1839X TYR* 3.6 25.8 - - + -
1840X LYS 4.0 7.9 - - - -
1841X VAL* 4.0 17.9 - - + -
1842X PRO* 3.7 23.8 - - + +
1845X ALA* 4.0 21.3 - - + +
1846X THR 3.6 11.2 - - - +
1847X VAL* 4.3 4.9 - - + +
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Residues in contact with ARG1808 (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* 3.4 22.7 - - - +
1756X ALA* 3.6 20.2 - - - +
1806X GLU* 3.1 39.4 + - + +
1807X TRP* 1.3 74.6 - - - +
1809X SER* 1.3 64.0 + - - +
1814X HIS* 3.6 40.8 + - + +
1846X THR* 2.8 52.2 + - + +
1848X ALA* 3.2 26.2 - - - +
1850X VAL* 4.3 2.6 - - - +
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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