Contacts of the helix formed by residues 116 - 126 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 4.2 3.1 - - - +
112D ALA 3.1 11.3 + - - -
113D VAL 3.2 12.9 + - - +
114D ALA 4.3 4.0 - - - +
115D ARG* 1.3 80.3 - - - +
117D VAL* 1.3 60.1 + - - +
118D VAL 3.5 2.0 - - - -
119D GLU* 2.6 51.5 + - + +
120D GLY* 2.8 25.1 + - - -
137D LEU* 3.7 26.9 - - + +
138D LEU* 3.0 42.4 + - - +
139D GLY* 4.3 1.6 - - - -
248D PHE* 4.8 9.6 - - + -
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.1 17.9 - - + -
108B ALA* 3.8 28.7 - - + +
109B LEU* 4.6 4.3 - - + +
112B ALA* 4.4 22.9 - - + -
118B VAL* 4.6 4.7 - - + -
273B VAL* 4.4 8.5 - - + -
275B THR* 3.9 22.1 - - + +
278B ILE* 5.0 0.7 - - + -
111D LEU 4.0 12.3 - - - +
112D ALA* 3.0 14.7 + - + -
115D ARG* 4.1 3.1 - - + +
116D ARG* 1.3 75.3 - - - +
118D VAL* 1.3 62.0 + - + +
120D GLY* 3.7 0.2 - - - -
121D ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 4.5 8.3 - - + -
118B VAL* 4.4 30.3 - - + +
121B ALA* 4.3 7.9 - - + -
125B ARG* 3.7 27.1 - - - +
112D ALA* 4.2 13.3 + - + +
116D ARG 3.5 0.4 - - - -
117D VAL* 1.3 76.2 - - + +
119D GLU* 1.3 63.7 + - - +
121D ALA* 3.4 2.9 + - - +
122D ALA* 3.2 22.8 + - + +
273D VAL* 4.0 37.5 - - + -
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Residues in contact with GLU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ARG* 2.6 58.0 + - + +
117D VAL 3.3 0.2 - - - -
118D VAL* 1.3 79.6 - - - +
120D GLY* 1.3 57.6 + - - +
122D ALA* 3.4 8.1 + - + +
123D TYR* 3.0 27.1 + - - +
137D LEU* 3.7 9.9 - - + +
270D PRO* 4.0 41.5 - - + +
271D ASN* 5.4 0.7 - - - -
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Residues in contact with GLY 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B THR* 4.7 0.7 - - - -
276B PRO* 3.2 22.0 - - - +
278B ILE* 4.9 2.5 - - - -
116D ARG 2.8 19.8 + - - -
117D VAL* 3.7 1.8 - - - -
118D VAL 3.3 0.2 - - - -
119D GLU* 1.3 75.2 - - - +
121D ALA* 1.3 62.1 + - - +
123D TYR* 3.2 2.1 + - - +
124D ALA* 3.2 18.2 + - - +
137D LEU* 3.7 23.3 - - - +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 4.3 25.8 - - + -
267B TYR* 5.3 1.0 - - - -
273B VAL* 4.7 10.1 - - + -
274B ILE 3.5 20.6 + - - +
275B THR* 4.5 1.4 - - + +
117D VAL 2.9 17.9 + - - +
118D VAL 3.7 4.9 - - - +
120D GLY* 1.3 75.4 - - - +
122D ALA* 1.3 58.8 + - - +
124D ALA* 3.4 3.3 + - - +
125D ARG* 3.0 38.1 + - - +
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 3.2 16.4 + - + +
119D GLU* 3.7 7.2 - - - +
121D ALA* 1.3 76.9 - - - +
123D TYR* 1.3 59.1 + - - +
125D ARG* 3.7 9.8 - - - +
126D ASP* 2.8 46.3 + - - +
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 6.0 2.4 - - - +
276B PRO* 4.1 15.7 - - + -
119D GLU 3.0 13.5 + - - +
120D GLY* 3.3 13.7 - - - +
122D ALA* 1.3 78.4 - - - +
124D ALA* 1.3 60.6 + - - +
126D ASP* 3.5 2.7 + - - -
127D GLY 3.6 0.2 + - - -
128D LEU* 3.1 84.2 + - + +
129D TRP* 3.8 10.5 - - - -
136D LEU* 3.6 36.6 - - + +
137D LEU* 4.4 11.9 - - + -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU 5.2 0.3 - - - +
262B PRO* 4.6 1.9 - - - +
267B TYR* 3.6 38.8 + - + +
274B ILE* 4.0 10.8 - - + +
276B PRO* 4.5 5.6 - - + -
120D GLY 3.2 8.7 + - - +
121D ALA 3.9 5.4 - - - +
123D TYR* 1.3 77.7 - - - +
125D ARG* 1.3 65.4 + - - +
127D GLY* 3.1 13.3 + - - -
129D TRP* 4.1 27.5 - - + +
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.7 26.7 - - - +
262B PRO* 4.5 11.8 - - - +
267B TYR* 2.5 59.0 + - + +
268B ALA 5.3 0.6 - - - -
269B LEU 5.0 5.5 + - - -
272B ALA 5.2 8.7 + - - -
273B VAL* 6.2 1.0 - - - +
28C ARG* 6.3 3.4 - - - +
121D ALA* 3.0 29.7 + - - +
122D ALA* 3.3 9.1 + - - +
124D ALA* 1.3 76.9 - - - +
126D ASP* 1.3 63.7 + - - +
127D GLY* 3.1 3.7 + - - -
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Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PRO* 5.0 0.7 - - - -
122D ALA* 2.8 30.0 + - - +
123D TYR* 3.5 4.1 + - - +
124D ALA 3.2 0.4 - - - -
125D ARG* 1.3 81.3 - - - +
127D GLY* 1.3 62.2 + - - +
128D LEU* 3.4 22.9 + - + +
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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