Contacts of the helix formed by residues 2131 - 2138 (chain F) in PDB entry 6X34
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 GLY2131 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1955F ARG* 5.6 4.9 + - - -
2043F CYS* 3.6 26.0 + - - -
2127F ARG 4.7 2.5 - - - -
2128F GLN 4.7 2.9 + - - -
2129F TYR 4.0 2.0 + - - -
2130F ASP* 1.3 74.1 - - - +
2132F LEU* 1.3 61.8 + - - +
2133F GLY 3.4 0.4 - - - -
2134F GLU* 3.3 6.8 + - - +
2135F LEU* 2.9 32.4 + - - +
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Residues in contact with LEU2132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2039F LEU* 5.6 2.0 - - + -
2040F LEU* 5.3 13.7 - - + -
2043F CYS* 3.8 15.9 - - + -
2045F ILE* 5.3 8.5 - - + -
2130F ASP* 4.6 0.6 - - - +
2131F GLY* 1.3 77.2 - - - +
2133F GLY* 1.3 57.1 + - - +
2135F LEU* 3.2 25.4 - - + +
2136F LEU* 2.9 30.2 + - - +
3658F ILE* 4.8 11.3 - - + +
3661F GLU* 4.0 17.7 - - + +
3662F ASP* 5.1 1.3 - - - -
3663F HIS* 3.8 36.8 - - + +
3665F PHE* 5.9 6.5 - - + -
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Residues in contact with GLY2133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2130F ASP* 4.7 8.2 - - - +
2131F GLY 3.4 1.4 - - - +
2132F LEU* 1.3 78.6 - - - +
2134F GLU* 1.3 57.2 + - - +
2136F LEU* 3.3 13.2 + - - +
2137F ARG* 2.9 29.5 + - - +
3665F PHE* 6.0 1.8 - - - -
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Residues in contact with GLU2134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952F LEU* 3.6 25.9 - - + +
2127F ARG* 5.1 14.1 - - + +
2130F ASP* 3.9 16.0 + - - +
2131F GLY* 3.3 11.5 + - - +
2132F LEU 3.2 0.6 - - - -
2133F GLY* 1.3 76.8 - - - +
2135F LEU* 1.3 58.5 + - - +
2137F ARG* 3.3 6.2 + - - +
2138F ALA* 2.9 28.9 + - - +
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Residues in contact with LEU2135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952F LEU* 4.7 4.7 - - + +
1955F ARG* 4.6 17.5 - - - +
1956F VAL* 5.8 5.3 - - + +
1959F LEU* 5.7 9.2 - - + -
2039F LEU* 4.4 17.3 - - + -
2043F CYS* 3.7 18.4 - - - -
2131F GLY 2.9 20.2 + - - +
2132F LEU* 3.2 27.6 - - + +
2134F GLU* 1.3 76.1 - - - +
2136F LEU* 1.3 63.9 + - - +
2138F ALA* 3.5 13.9 + - - +
2139F LEU* 3.2 27.0 + - + +
3653F TYR* 6.0 0.2 - - + -
3658F ILE* 4.1 33.0 - - + -
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Residues in contact with LEU2136 (chain F).
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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2132F LEU 2.9 19.2 + - - +
2133F GLY* 3.6 11.0 - - - +
2134F GLU 3.2 0.2 - - - -
2135F LEU* 1.3 79.2 - - - +
2137F ARG* 1.3 67.8 + - + +
2139F LEU* 3.4 25.4 + - + +
2140F PRO* 3.6 9.2 - - - +
3654F LYS* 6.1 3.6 - - + -
3658F ILE* 4.0 19.7 - - + +
3659F LEU* 3.8 29.4 - - + -
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Residues in contact with ARG2137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2133F GLY 2.9 17.2 + - - +
2134F GLU* 3.8 5.4 - - - +
2136F LEU* 1.3 84.0 - - + +
2138F ALA* 1.3 60.8 + - - +
2139F LEU 3.2 0.4 - - - -
2140F PRO* 3.4 13.6 - - - +
2141F ARG* 4.6 5.0 + - - +
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Residues in contact with ALA2138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734F TYR* 4.5 11.2 - - + -
1952F LEU* 4.1 24.2 - - + -
1956F VAL* 4.1 15.7 - - + +
2134F GLU 2.9 17.1 + - - +
2135F LEU* 3.9 8.7 - - - +
2136F LEU 3.2 1.0 - - - -
2137F ARG* 1.3 75.7 - - - +
2139F LEU* 1.3 62.5 + - - +
2140F PRO 3.6 0.2 - - - -
2141F ARG* 3.7 9.6 + - - +
2142F ALA* 3.3 21.8 + - - +
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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