Contacts of the helix formed by residues 116 - 126 (chain C) in PDB entry 2CUK
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 ARG 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ILE* 4.2 3.3 - - - +
283A ARG* 5.5 2.8 - - - +
112C ALA 3.1 7.9 + - - -
113C VAL* 3.1 15.7 + - - +
114C ALA 4.4 3.6 - - - +
115C ARG* 1.3 80.7 - - - +
117C VAL* 1.3 59.6 + - - +
118C VAL 3.6 2.0 - - - -
119C GLU* 2.8 49.8 + - + +
120C GLY* 2.9 24.8 + - - -
137C LEU* 3.6 26.1 - - + +
138C LEU* 3.0 45.7 + - - +
139C GLY* 4.3 1.8 - - - -
248C PHE* 4.7 9.4 - - + -
271C ASN* 6.6 0.4 - - - -
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Residues in contact with VAL 117 (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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105A LEU* 4.1 15.7 - - + -
108A ALA* 4.0 20.9 - - + +
109A LEU* 4.6 11.2 - - + -
112A ALA* 4.7 8.5 - - + -
118A VAL* 4.6 15.9 - - + -
273A VAL* 4.6 2.2 - - + -
275A THR* 3.9 21.6 - - + +
278A ILE* 5.0 0.7 - - - -
111C LEU 3.9 18.2 - - - +
112C ALA* 3.1 15.2 + - + -
115C ARG* 4.0 8.5 - - + +
116C ARG* 1.3 73.8 - - - +
118C VAL* 1.3 62.6 + - + +
120C GLY* 3.2 0.7 + - - -
121C ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 4.7 3.8 - - + -
118A VAL* 4.5 25.9 - - + +
121A ALA* 4.1 13.7 - - + -
125A ARG* 3.4 29.8 - - - +
112C ALA* 4.3 10.7 + - + -
116C ARG* 3.6 0.4 - - - +
117C VAL* 1.3 76.2 - - + +
119C GLU* 1.3 63.1 + - - +
121C ALA* 3.4 7.5 + - - +
122C ALA* 3.2 21.3 + - - +
125C ARG* 5.2 1.2 + - - -
273C VAL* 3.8 38.1 - - + -
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Residues in contact with GLU 119 (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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116C ARG* 2.8 59.1 + - + +
117C VAL 3.2 0.2 - - - -
118C VAL* 1.3 81.3 - - - +
120C GLY* 1.3 56.6 + - - +
122C ALA* 3.3 8.8 + - + +
123C TYR* 3.0 27.0 + - + +
137C LEU* 3.9 11.0 - - + +
270C PRO* 4.1 40.7 + - + +
271C ASN* 5.5 1.0 - - - -
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Residues in contact with GLY 120 (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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275A THR* 4.8 0.4 - - - -
276A PRO* 3.2 28.1 - - - +
278A ILE* 4.6 3.6 - - - -
116C ARG 2.9 19.2 + - - -
117C VAL 3.2 2.2 + - - -
119C GLU* 1.3 74.7 - - - +
121C ALA* 1.3 63.8 + - - +
123C TYR* 3.1 2.3 + - - +
124C ALA 3.1 18.7 + - - -
137C LEU* 4.0 17.0 - - - -
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Residues in contact with ALA 121 (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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118A VAL* 4.4 15.0 - - + -
267A TYR* 5.0 0.9 - - - -
273A VAL* 4.9 7.0 - - + -
274A ILE 3.4 21.8 - - - +
275A THR* 4.5 1.4 - - + +
117C VAL 2.9 16.7 + - - +
118C VAL* 3.6 6.5 - - - +
120C GLY* 1.3 75.3 - - - +
122C ALA* 1.3 56.4 + - - +
124C ALA* 3.4 2.3 + - - +
125C ARG* 2.9 52.6 + - - +
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Residues in contact with ALA 122 (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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125A ARG* 6.4 0.9 - - - +
118C VAL* 3.2 12.8 + - + +
119C GLU* 3.5 11.7 - - - +
120C GLY 3.2 0.2 - - - -
121C ALA* 1.3 75.8 - - - +
123C TYR* 1.3 56.2 + - - +
125C ARG* 3.7 17.6 - - - +
126C ASP* 2.7 51.3 + - - +
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Residues in contact with TYR 123 (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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30A LEU* 4.7 12.1 - - - +
276A PRO* 3.8 17.3 - - + -
119C GLU* 3.0 13.3 + - + +
120C GLY* 3.3 13.0 - - - +
122C ALA* 1.3 79.0 - - - +
124C ALA* 1.3 60.1 + - - +
126C ASP* 4.1 1.0 - - - -
127C GLY 3.6 1.7 + - - -
128C LEU* 3.0 74.8 + - + +
129C TRP* 3.5 23.2 + - + -
130C LYS 4.7 0.7 + - - -
131C ALA 5.4 0.7 + - - -
136C LEU* 3.5 40.7 - - + +
137C LEU* 4.1 13.2 - - + -
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Residues in contact with ALA 124 (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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260A LEU 4.8 0.9 - - - +
262A PRO* 4.7 2.4 - - - +
267A TYR* 3.5 36.0 + - + +
274A ILE* 4.1 11.0 - - + +
276A PRO* 4.3 7.6 - - + -
120C GLY 3.1 12.5 + - - +
121C ALA 3.8 5.6 - - - +
123C TYR* 1.3 73.6 - - - +
125C ARG* 1.3 66.6 + - - +
127C GLY* 3.2 13.2 + - - -
129C TRP* 3.8 28.3 - - + +
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Residues in contact with ARG 125 (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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118A VAL* 3.7 20.0 - - - +
122A ALA* 6.4 0.6 - - - +
125A ARG* 5.6 5.7 - - - +
262A PRO* 4.3 15.1 - - - +
267A TYR* 3.7 39.5 + - + +
273A VAL* 6.2 1.6 - - - +
274A ILE 6.1 0.2 - - - +
118C VAL 5.2 0.8 + - - -
121C ALA* 2.9 39.7 + - - +
122C ALA* 3.7 28.8 - - - +
124C ALA* 1.3 78.5 - - - +
126C ASP* 1.3 65.9 + - - +
127C GLY 3.3 0.9 + - - -
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Residues in contact with ASP 126 (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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262A PRO* 4.9 2.2 - - - +
122C ALA* 2.7 35.0 + - - +
123C TYR* 4.3 3.3 - - - +
125C ARG* 1.3 80.8 - - - +
127C GLY* 1.3 61.1 + - - +
128C LEU* 3.5 19.2 - - + +
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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