Contacts of the helix formed by residues 106 - 112 (chain C) in PDB entry 4K2S
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 PRO 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C GLY 4.6 1.8 - - - +
105C MET* 1.3 90.7 - - + +
107C LEU* 1.3 67.2 + - - +
108C TYR* 3.6 20.6 - - + -
109C GLN* 3.0 29.5 + - + +
110C LEU* 3.7 1.6 + - - +
330C HIS* 3.6 5.6 - - + -
368C GLY 3.6 19.5 - - - +
369C GLU* 3.7 26.2 - - - +
370C SER 3.3 21.9 - - - +
371C PRO 4.8 0.2 - - - -
372C GLY 3.5 0.4 - - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TRP* 4.1 44.9 - - + +
100C ALA* 4.1 5.4 - - + -
105C MET 3.6 0.2 + - - -
106C PRO* 1.3 72.4 - - - +
108C TYR* 1.3 63.5 + - - +
110C LEU* 3.0 20.6 + - + +
111C LEU* 3.2 25.7 + - + +
295C ILE* 3.9 28.3 - - + -
327C ALA* 4.4 5.4 - - + +
330C HIS* 3.6 24.1 - - + -
372C GLY 2.9 20.4 + - - +
373C HIS* 4.1 20.6 - - + -
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PRO* 3.1 11.1 + - + -
107C LEU* 1.3 76.2 - - - +
109C GLN* 1.3 91.5 + - + +
111C LEU* 3.5 12.2 + - - +
112C GLY 3.5 1.2 + - - -
113C GLY* 2.9 23.9 + - - +
114C LYS* 3.7 46.7 - - + -
330C HIS* 3.1 57.4 + + - +
333C THR* 4.2 9.4 - - + -
334C TRP* 4.1 3.3 - - + +
367C ALA* 4.0 12.6 - - + -
368C GLY 3.6 11.7 - - - -
369C GLU* 2.7 33.6 + - - -
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C MET* 4.0 22.8 - - + +
106C PRO* 3.0 28.1 + - + +
108C TYR* 1.3 104.0 + - + +
110C LEU* 1.3 63.7 + - - +
112C GLY* 3.3 11.1 + - - -
113C GLY* 3.5 18.3 + - - +
114C LYS 5.3 0.2 - - - -
369C GLU* 5.6 0.4 + - - -
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP* 3.6 36.6 - - + -
99C LYS* 3.8 20.6 - - + -
100C ALA* 3.8 21.3 - - + +
103C ALA* 3.6 29.2 - - + -
105C MET* 3.8 14.4 - - + -
106C PRO 3.7 2.9 + - - +
107C LEU* 3.0 17.1 + - + +
109C GLN* 1.3 80.0 - - - +
111C LEU* 1.3 60.9 + - - +
112C GLY* 3.4 0.7 + - - -
299C ARG* 4.8 1.2 + - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP* 4.8 10.5 - - + -
107C LEU* 3.2 34.0 + - + +
108C TYR* 3.8 7.0 - - - +
109C GLN 3.2 0.4 - - - -
110C LEU* 1.3 78.4 - - - +
112C GLY* 1.3 57.4 + - - +
295C ILE* 4.0 23.8 - - + -
299C ARG* 3.1 37.2 + - + +
330C HIS 4.3 5.2 - - - +
331C PHE* 3.9 38.1 - - + +
334C TRP* 3.2 34.1 + - + -
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Residues in contact with GLY 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLN 3.3 4.7 + - - -
110C LEU 3.2 4.6 + - - -
111C LEU* 1.3 80.5 - - - +
113C GLY* 1.3 65.7 + - - +
334C TRP* 3.8 8.6 - - - -
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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