Contacts of the helix formed by residues 2098 - 2108 (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 TYR2098 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1622X THR* 5.9 0.4 - - + -
1623X LEU* 3.4 27.6 - - + -
1626X GLN* 3.5 32.8 - - + -
1628X THR* 3.0 47.5 + - - -
1629X PHE* 3.5 15.3 + + + -
1633X ASP* 4.8 0.7 + - - -
2094X TYR* 3.3 20.6 + + - +
2095X ILE 3.4 3.1 - - - -
2096X ASN 3.3 0.2 - - - -
2097X LYS* 1.3 110.8 + - + +
2099X TYR* 1.3 65.4 + - - +
2101X GLN* 3.2 27.7 + - + +
2102X ILE* 3.0 29.9 + - + +
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Residues in contact with TYR2099 (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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15X UNX 3.5 7.8 - - - -
2092X TYR* 5.7 0.2 - - - -
2095X ILE* 2.8 30.1 + - + +
2096X ASN* 3.2 16.6 + - - +
2097X LYS 3.5 0.6 - - - -
2098X TYR* 1.3 77.6 - - - +
2100X ASP* 1.3 76.7 + - - +
2102X ILE* 3.2 3.3 + - - +
2103X ILE* 3.0 53.4 + - + +
2121X LEU* 4.4 11.7 - - + -
2122X GLN* 3.1 38.1 - - - +
2125X ALA* 4.1 22.9 - - + +
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Residues in contact with ASP2100 (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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15X UNX 3.5 15.7 - - - -
2098X TYR 3.4 0.6 - - - -
2099X TYR* 1.3 91.7 - - - +
2101X GLN* 1.3 62.9 + - - +
2103X ILE* 3.9 4.5 - - - +
2104X THR* 2.7 41.1 + - - +
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Residues in contact with GLN2101 (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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1622X THR* 3.5 8.2 - - + +
1626X GLN* 3.5 39.6 + - - +
2097X LYS 4.2 2.5 + - - +
2098X TYR* 3.2 34.5 - - + +
2099X TYR 4.0 0.2 + - - -
2100X ASP* 1.3 86.8 + - - +
2102X ILE* 1.3 56.1 + - - +
2104X THR* 3.7 5.9 - - - -
2105X ALA* 3.1 27.4 + - - +
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Residues in contact with ILE2102 (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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1615X PHE* 4.6 3.6 - - + -
1618X LYS 5.9 0.4 - - - +
1619X PHE* 3.6 43.7 - - + +
1622X THR* 3.9 22.2 - - + +
1623X LEU* 4.6 3.8 - - + -
2094X TYR 4.3 3.4 - - - +
2095X ILE* 3.9 24.9 - - + +
2098X TYR* 3.0 27.5 + - + +
2099X TYR* 3.8 2.9 - - - +
2101X GLN* 1.3 75.0 - - - +
2103X ILE* 1.3 65.0 + - - +
2105X ALA* 3.4 2.8 + - + +
2106X LEU* 3.0 32.7 + - + +
2121X LEU* 3.5 24.5 - - + -
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Residues in contact with ILE2103 (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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2099X TYR* 3.0 63.0 + - + +
2100X ASP* 3.9 5.4 - - - +
2102X ILE* 1.3 72.7 - - - +
2104X THR* 1.3 67.6 + - - +
2106X LEU* 3.0 7.4 + - - +
2107X GLU* 2.8 47.2 + - + +
2118X GLY* 3.6 26.5 - - - +
2121X LEU* 4.4 12.3 - - + -
2122X GLN* 4.4 10.8 - - + +
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Residues in contact with THR2104 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2100X ASP* 2.7 30.0 + - - +
2101X GLN* 3.7 7.6 - - - +
2103X ILE* 1.3 73.6 - - - +
2105X ALA* 1.3 58.1 + - - +
2107X GLU* 3.4 7.2 + - - +
2108X GLU* 3.0 32.6 + - + +
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Residues in contact with ALA2105 (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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1618X LYS* 4.0 18.1 + - + +
1622X THR* 3.4 26.5 - - + +
2101X GLN 3.1 16.8 + - - +
2102X ILE 3.5 4.9 - - - +
2103X ILE 3.1 1.0 - - - -
2104X THR* 1.3 82.0 - - - +
2106X LEU* 1.3 60.0 + - + +
2108X GLU* 3.8 10.0 + - - +
2109X ASP* 3.9 12.5 + - - +
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Residues in contact with LEU2106 (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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1615X PHE* 4.0 22.2 - - + -
1618X LYS* 4.1 24.2 - - + -
2102X ILE* 3.0 36.0 + - + +
2103X ILE* 3.0 6.0 + - - +
2105X ALA* 1.3 74.2 - - + +
2107X GLU* 1.3 65.3 + - - +
2108X GLU 3.4 0.2 - - - -
2109X ASP* 3.3 8.5 + - - +
2112X ALA* 3.0 31.0 - - + +
2113X GLN 3.9 2.9 + - - -
2117X LEU* 3.9 32.1 - - + +
2118X GLY* 3.9 30.3 - - - +
2121X LEU* 4.2 9.0 - - + -
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Residues in contact with GLU2107 (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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2103X ILE* 2.8 49.0 + - + +
2104X THR* 3.7 7.0 - - - +
2106X LEU* 1.3 68.8 - - + +
2108X GLU* 1.3 56.7 + - - +
2109X ASP 3.1 7.9 + - - -
2113X GLN* 3.0 48.4 + - - +
2118X GLY* 4.3 16.7 + - - -
2119X TYR 5.2 0.3 + - - -
2122X GLN* 5.4 4.9 + - - -
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Residues in contact with GLU2108 (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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1618X LYS* 5.3 1.7 + - - -
2104X THR* 3.0 21.4 + - + +
2105X ALA* 3.8 6.9 + - - +
2106X LEU 3.4 0.6 - - - -
2107X GLU* 1.3 73.2 - - - +
2109X ASP* 1.3 57.3 + - - +
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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