Contacts of the helix formed by residues 1985 - 1992 (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 PHE1985 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1571X TYR* 3.4 27.4 - + - -
1575X ILE* 4.6 1.1 - - + -
1688X THR* 5.4 1.1 - - - +
1691X MET* 4.2 11.0 - - + -
1692X SER* 3.5 31.6 - - - -
1695X LEU* 3.6 30.1 - - + -
1699X VAL* 3.8 15.3 - - + -
1981X LEU* 2.7 24.1 + - + +
1984X ARG* 1.3 74.6 - - - +
1986X TRP* 1.3 105.7 + + - +
1987X ILE 3.4 0.9 - - - -
1988X ASN* 3.2 20.2 - - + +
1989X ILE* 3.2 33.2 + - + +
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Residues in contact with TRP1986 (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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1695X LEU* 4.4 6.7 - - + -
1698X PHE* 3.7 27.1 - + - -
1699X VAL* 4.0 9.4 - - + -
1703X VAL* 3.4 40.8 - - + -
1940X ILE* 3.4 44.7 + - + +
1941X LEU* 6.1 0.2 - - + -
1981X LEU* 3.3 27.5 + - + +
1982X PRO* 3.2 26.4 + - + +
1985X PHE* 1.3 106.8 - + - +
1987X ILE* 1.3 64.3 + - - +
1989X ILE* 3.3 13.1 + - + +
1990X ILE* 3.0 29.0 + - - +
2016X PHE* 3.8 15.7 - + + -
2052X TYR* 4.8 5.8 + + - -
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Residues in contact with ILE1987 (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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1982X PRO 2.8 21.4 + - - +
1983X LEU* 3.2 45.1 - - + +
1984X ARG* 4.4 0.9 - - - +
1986X TRP* 1.3 72.8 - - - +
1988X ASN* 1.3 62.1 + - + +
1990X ILE* 3.4 7.1 + - - +
1991X LYS* 3.0 53.3 + - + +
2013X ALA* 3.3 39.5 - - + +
2014X GLN* 5.1 0.4 - - - -
2016X PHE* 4.7 4.2 - - + -
2017X MET* 3.5 14.4 - - + +
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Residues in contact with ASN1988 (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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8X UNX 2.6 26.7 - - - -
1575X ILE* 4.1 22.8 + - - +
1685X LYS* 6.1 0.2 - - - +
1688X THR* 4.6 7.3 - - - +
1692X SER* 5.3 0.8 + - - -
1984X ARG 3.8 17.5 + - - +
1985X PHE* 3.2 12.8 - - - +
1987X ILE* 1.3 85.1 - - + +
1989X ILE* 1.3 58.6 + - + +
1991X LYS* 4.9 2.6 - - - +
1992X ASN* 2.8 46.9 + - - +
1995X PHE* 3.7 18.6 - - - -
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Residues in contact with ILE1989 (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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1571X TYR* 4.7 0.9 - - + -
1575X ILE* 4.1 18.6 - - + -
1699X VAL* 5.2 4.3 - - + -
1703X VAL* 5.5 0.4 - - + -
1707X LEU* 3.2 33.1 - - + +
1985X PHE* 3.2 37.8 + - + +
1986X TRP* 3.3 21.7 + - + +
1988X ASN* 1.3 78.4 - - + +
1990X ILE* 1.3 66.8 + - + +
1992X ASN 3.5 17.4 - - - +
1993X PRO* 3.7 6.2 - - - +
1995X PHE* 4.1 16.2 - - + -
1996X VAL* 3.5 27.8 - - + -
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Residues in contact with ILE1990 (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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1707X LEU* 4.3 10.1 - - + +
1710X LEU* 5.4 0.4 - - + -
1936X LEU* 4.4 17.0 - - + -
1937X PHE* 4.4 10.3 - - + -
1940X ILE* 4.5 11.9 - - + -
1986X TRP* 3.0 25.4 + - + +
1987X ILE* 3.7 6.5 - - - +
1988X ASN 3.3 0.2 - - - -
1989X ILE* 1.3 80.1 - - + +
1991X LYS* 1.3 61.7 + - - +
1992X ASN 3.4 0.2 + - - -
1993X PRO* 3.9 1.4 - - - +
2009X LEU* 3.5 49.5 - - + +
2012X ILE* 4.4 10.1 - - + -
2013X ALA* 3.8 13.9 - - + +
2016X PHE* 4.0 36.6 - - + -
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Residues in contact with LYS1991 (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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1987X ILE* 3.0 40.3 + - + +
1988X ASN* 5.6 1.5 - - - +
1990X ILE* 1.3 76.0 - - - +
1992X ASN* 1.3 73.7 + - - +
1993X PRO* 3.4 7.9 - - - +
1994X GLN* 4.7 0.5 + - - +
2006X ASP* 4.4 14.3 - - - +
2009X LEU* 4.2 14.1 - - - +
2010X LEU* 3.9 28.6 - - + +
2013X ALA* 3.4 27.4 - - + -
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Residues in contact with ASN1992 (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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7X UNX 3.5 14.7 - - - -
8X UNX 3.8 4.6 - - - -
1988X ASN* 2.8 39.3 + - - +
1989X ILE* 3.5 10.2 - - - +
1990X ILE 3.3 0.2 - - - -
1991X LYS* 1.3 94.3 - - - +
1993X PRO* 1.3 66.2 - - - +
1994X GLN* 3.0 29.3 + - - +
1995X PHE* 3.0 38.4 + - + +
1996X VAL* 4.4 0.7 + - - +
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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