Contacts of the helix formed by residues 254 - 264 (chain C) in PDB entry 2CNW
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 GLY 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C ALA 2.9 24.7 + - - -
42C ASP* 3.7 8.5 - - - +
43C VAL* 3.7 18.3 - - - +
220C ALA 4.9 0.2 + - - -
252C ARG 3.6 1.2 - - - -
253C GLY* 1.3 75.3 - - - +
255C ALA* 1.3 55.9 + - - +
256C ALA 3.0 1.1 - - - -
257C LEU* 2.9 23.7 + - - +
258C SER* 3.3 10.2 + - - -
291C ILE* 4.0 10.2 - - - +
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Residues in contact with ALA 255 (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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42C ASP* 3.6 6.8 + - - +
218C LEU* 3.6 11.4 - - + +
219C ASP 4.7 3.6 - - - +
220C ALA 5.0 1.6 - - - +
222C THR* 3.3 36.0 + - - +
223C GLY 4.3 0.4 - - - +
226C ALA* 3.4 25.8 - - + +
244C LEU* 5.6 1.3 - - + -
253C GLY* 3.2 1.9 + - - -
254C GLY* 1.3 74.8 - - - +
256C ALA* 1.3 55.8 + - - +
257C LEU 3.3 0.2 - - - -
258C SER* 3.4 6.3 + - - -
259C ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 256 (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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86C LEU* 4.0 2.9 - - + +
218C LEU* 4.4 4.9 - - - +
242C LEU* 5.9 1.1 - - - -
244C LEU* 3.6 30.8 - - + +
253C GLY 3.1 15.1 + - - +
254C GLY 3.0 0.6 - - - -
255C ALA* 1.3 76.7 - - - +
257C LEU* 1.3 62.7 + - - +
259C ALA* 3.9 5.7 - - - +
260C ARG* 3.1 26.2 + - - +
267C ILE* 3.9 15.9 - - + +
287C LEU* 3.6 11.4 - - + -
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Residues in contact with LEU 257 (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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38C LEU* 5.0 2.9 - - + -
43C VAL* 3.6 33.0 - - + -
47C VAL* 3.9 12.3 - - + -
51C PHE* 4.6 22.2 - - + -
82C LEU* 4.0 23.1 - - + -
85C ALA* 3.8 31.2 - - + +
86C LEU* 3.7 17.5 - - + +
253C GLY 4.4 0.4 + - - -
254C GLY 2.9 11.3 + - - +
256C ALA* 1.3 75.8 - - - +
258C SER* 1.3 54.7 + - - +
260C ARG* 3.4 1.2 + - - +
261C HIS* 2.8 43.9 + - + +
291C ILE* 4.7 5.4 - - + +
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Residues in contact with SER 258 (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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42C ASP 4.4 0.3 + - - -
43C VAL* 4.1 0.2 - - - -
44C ASN* 3.1 34.8 + - - +
47C VAL* 3.9 13.0 - - - +
226C ALA* 3.9 4.5 - - - +
227C LEU* 3.8 29.5 - - - +
254C GLY 3.3 7.4 + - - -
255C ALA* 3.5 11.0 - - - -
257C LEU* 1.3 79.1 - - - +
259C ALA* 1.3 62.8 + - - +
261C HIS* 3.7 1.9 - - - +
262C VAL* 3.2 26.5 + - - +
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Residues in contact with ALA 259 (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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218C LEU* 3.7 12.3 - - + -
226C ALA 4.7 1.8 + - - +
230C ALA* 3.7 21.3 - - + -
242C LEU* 3.4 29.4 - - + -
255C ALA 2.9 20.4 + - - +
256C ALA* 3.9 3.6 - - - +
258C SER* 1.3 73.2 - - - +
260C ARG* 1.3 53.7 + - - +
262C VAL* 3.4 4.3 - - - +
263C THR* 2.7 37.3 + - - +
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Residues in contact with ARG 260 (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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84C GLU* 4.3 5.5 + - - -
85C ALA* 2.8 27.3 + - - +
86C LEU* 3.6 17.7 + - - +
87C GLY* 3.5 24.0 - - - +
91C ARG* 5.4 3.4 - - - +
242C LEU* 5.0 1.6 - - + -
256C ALA 3.1 15.1 + - - +
257C LEU* 4.1 1.6 - - - +
259C ALA* 1.3 77.1 - - - +
261C HIS* 1.3 62.1 + - - +
263C THR* 3.7 4.9 - - - -
264C GLY* 2.6 45.9 + - - -
265C LYS 3.1 46.3 + - - +
266C PRO* 3.6 9.1 - - - +
267C ILE* 4.2 13.2 - - + +
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Residues in contact with HIS 261 (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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46C GLU 5.8 0.2 - - - -
47C VAL* 3.7 34.2 - - + +
50C ASP* 3.9 37.3 + - + +
51C PHE* 5.7 3.8 - - + -
85C ALA* 5.2 5.7 + - + -
227C LEU* 5.0 1.9 - - + +
257C LEU* 2.8 25.4 + - + +
258C SER 3.7 3.4 - - - +
260C ARG* 1.3 79.2 - - - +
262C VAL* 1.3 63.1 + - - +
264C GLY* 4.5 2.1 + - - -
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Residues in contact with VAL 262 (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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227C LEU* 3.4 43.5 - - + +
230C ALA* 3.9 4.5 - - + -
231C ARG* 3.8 40.1 - - + +
234C ASP* 4.5 3.6 - - - +
258C SER 3.2 7.7 + - - +
259C ALA 3.4 11.4 - - - +
261C HIS* 1.3 81.7 - - - +
263C THR* 1.3 65.0 + - + +
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Residues in contact with THR 263 (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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216C LEU* 5.6 1.3 - - + -
230C ALA* 3.8 15.5 - - + +
231C ARG* 5.1 0.2 - - - -
234C ASP* 3.7 36.4 - - + +
239C VAL* 5.0 7.6 - - + -
242C LEU* 4.2 5.4 - - + +
259C ALA* 2.7 24.4 + - + +
260C ARG* 3.7 1.7 - - - -
262C VAL* 1.3 84.3 - - + +
264C GLY* 1.3 64.8 + - - +
265C LYS* 3.4 41.6 + - + +
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Residues in contact with GLY 264 (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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91C ARG* 5.8 0.2 + - - -
260C ARG* 2.6 41.1 + - - -
261C HIS 4.4 2.3 + - - -
262C VAL 3.7 0.6 - - - -
263C THR* 1.3 71.8 - - - +
265C LYS* 1.3 63.6 + - - +
266C PRO* 4.2 2.8 - - - +
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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