Contacts of the helix formed by residues 112 - 118 (chain Y) in PDB entry 3FKS
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 ASP 112 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78Y THR 3.9 23.0 + - - -
109Y THR* 5.0 3.1 + - - -
110Y ILE* 4.2 13.6 + - - -
113Y LYS* 1.3 64.4 + - - +
114Y ILE* 3.3 7.0 - - - +
115Y LYS* 3.6 37.1 + - - +
116Y MET* 4.1 16.8 + - - +
131Y ASN* 2.8 54.2 - - - +
132Y GLY* 4.3 2.0 - - - +
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Residues in contact with LYS 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396X LEU 5.9 1.0 + - - -
398X GLU* 5.3 7.3 + - - +
78Y THR 5.0 3.7 + - - +
112Y ASP* 1.3 77.0 - - - +
114Y ILE* 1.3 62.9 + - - +
115Y LYS 3.3 0.9 - - - -
116Y MET* 3.8 12.8 + - + +
117Y GLN* 3.5 26.0 + - + +
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Residues in contact with ILE 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Y ILE* 4.7 4.7 - - + -
78Y THR* 3.6 40.4 - - + -
91Y LEU* 4.5 24.2 - - + +
109Y THR* 3.4 32.3 - - + +
112Y ASP 4.5 3.1 - - - +
113Y LYS* 1.3 78.5 - - - +
115Y LYS* 1.3 64.9 + - - +
116Y MET 3.3 0.7 - - - -
117Y GLN* 3.6 26.7 - - + +
118Y LEU* 3.1 42.2 + - + +
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Residues in contact with LYS 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y THR* 4.0 29.1 + - + +
110Y ILE* 5.2 13.8 - - - +
112Y ASP* 3.6 29.9 + - - +
113Y LYS 3.3 0.6 - - - -
114Y ILE* 1.3 85.0 - - - +
116Y MET* 1.3 72.7 + - + +
118Y LEU* 4.0 2.6 - - - +
119Y LEU* 3.7 24.7 + - + +
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Residues in contact with MET 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398X GLU* 5.4 6.1 - - - +
112Y ASP* 4.1 18.4 - - - +
113Y LYS* 3.8 16.9 + - + +
114Y ILE 3.3 0.4 - - - -
115Y LYS* 1.3 91.2 - - + +
117Y GLN* 1.3 61.8 + - - +
118Y LEU 3.4 0.2 - - - -
119Y LEU* 3.6 30.4 - - - +
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Residues in contact with GLN 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398X GLU* 4.6 23.1 - - - +
91Y LEU 5.4 4.6 + - - -
92Y ALA* 5.9 1.4 - - - +
96Y ARG* 3.2 19.9 + - - +
113Y LYS* 3.5 24.7 + - + +
114Y ILE* 3.3 19.6 + - + +
115Y LYS 3.3 0.4 - - - -
116Y MET* 1.3 81.4 - - - +
118Y LEU* 1.3 81.4 + - - +
119Y LEU 3.3 2.2 + - - -
120Y ARG* 5.0 5.9 + - - -
121Y THR* 3.5 7.8 + - - -
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Residues in contact with LEU 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Y ILE* 6.2 1.1 - - + -
91Y LEU 5.5 1.6 - - - +
95Y VAL* 3.9 31.4 - - + -
96Y ARG* 3.7 15.9 - - - +
114Y ILE* 3.1 33.2 + - + +
115Y LYS* 3.8 5.4 + - - +
116Y MET 3.4 0.2 - - - -
117Y GLN* 1.3 97.6 - - - +
119Y LEU* 1.3 61.7 + - - +
120Y ARG 3.5 1.6 - - - -
121Y THR* 3.3 25.1 - - + +
122Y HIS* 3.4 27.2 + - + +
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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