Contacts of the helix formed by residues 259 - 273 (chain B) in PDB entry 2C47
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 THR 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.7 11.8 - - - +
111A CSD 4.3 4.7 - - - -
112A GLY* 3.8 27.8 - - - +
257B ALA* 3.2 3.3 - - - +
258B ASP* 1.3 85.0 - - + +
260B LEU* 1.3 60.2 + - - +
261B LYS* 3.4 6.5 + - - +
262B GLU* 3.0 35.7 + - - +
263B ARG* 3.0 26.2 + - - +
1301B MG 3.9 11.2 - - - -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.8 29.3 - - + +
49A GLY 4.1 2.7 - - - +
59A GLU* 4.0 3.6 - - - +
61A ARG* 3.6 42.6 - - - +
76A LEU* 3.8 18.2 - - + -
111A CSD 5.7 0.6 + - - -
114A TYR* 3.7 30.5 - - + +
259B THR* 1.3 72.0 - - - +
261B LYS* 1.3 65.3 + - - +
263B ARG* 3.1 11.5 + - - +
264B TYR* 3.0 39.6 + - + -
1301B MG 3.6 9.1 - - - -
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 5.7 11.0 - - + -
259B THR* 3.3 8.4 + - - +
260B LEU* 1.3 79.0 - - - +
262B GLU* 1.3 63.8 + - + +
264B TYR* 3.3 13.2 + - - +
265B GLN* 3.2 19.9 + - - +
1301B MG 3.4 11.2 - - - -
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ALA* 3.5 13.8 - - + +
258B ASP* 3.6 35.5 + - - +
259B THR* 3.0 24.3 + - - +
261B LYS* 1.3 79.4 - - + +
263B ARG* 1.3 57.2 + - - +
265B GLN* 3.2 17.3 + - - +
266B LYS* 2.9 30.3 + - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL 3.4 22.0 - - - +
49A GLY 3.4 19.8 - - - -
50A LYS* 3.8 22.2 - - - +
61A ARG* 3.5 16.3 - - - +
216B ALA* 3.9 22.6 - - - +
217B ARG* 5.8 5.3 - - - +
253B GLN* 6.2 0.2 - - - +
254B GLY* 5.4 5.1 - - - +
255B LEU* 3.1 30.2 + - + +
257B ALA* 3.2 10.5 - - + +
259B THR 3.0 14.7 + - - +
260B LEU* 3.1 18.5 + - - +
262B GLU* 1.3 73.6 - - - +
264B TYR* 1.3 68.8 + - - +
266B LYS* 3.4 3.9 + - - +
267B ILE* 3.0 41.6 + - + +
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 5.6 4.4 + - - -
212B LEU* 3.6 54.4 + - + -
213B THR* 3.9 1.2 - - - -
214B GLY 2.8 36.5 + - - -
216B ALA* 3.6 25.5 - - + +
219B MET* 3.8 19.5 - - + -
224B HIS* 3.0 15.0 + + - -
260B LEU* 3.0 38.6 + - + -
261B LYS* 3.4 11.7 - - - +
263B ARG* 1.3 76.7 - - - +
265B GLN* 1.3 59.0 + - - +
267B ILE* 3.3 2.7 + - - -
268B GLY 2.9 24.9 + - - -
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B HIS* 5.1 3.1 - - - -
261B LYS* 3.2 10.5 + - - +
262B GLU* 3.4 20.8 - - - +
263B ARG 3.2 0.2 - - - -
264B TYR* 1.3 79.5 - - - +
266B LYS* 1.3 58.3 + - - +
268B GLY* 3.1 3.4 + - - -
269B ASP* 2.8 54.4 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 4.1 19.2 - - - +
255B LEU* 3.9 34.5 - - + -
256B LYS 3.2 30.7 + - - +
257B ALA* 4.6 4.9 - - + -
262B GLU 2.9 16.8 + - - +
263B ARG* 3.8 6.1 - - - +
265B GLN* 1.3 78.3 - - - +
267B ILE* 1.3 61.3 + - - +
269B ASP* 3.5 11.5 + - - +
270B THR* 3.1 28.1 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA* 3.6 27.6 - - + +
217B ARG* 5.1 2.0 - - + +
224B HIS* 3.5 18.8 - - + +
252B TRP* 3.8 37.2 - - + +
255B LEU* 3.9 16.6 - - + -
263B ARG* 3.0 57.8 + - + +
264B TYR 3.7 2.7 - - - +
266B LYS* 1.3 76.1 - - - +
268B GLY* 1.3 56.9 + - - +
270B THR* 3.4 2.9 + - - -
271B LYS* 3.0 32.5 + - - +
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ILE* 5.1 1.0 - - - +
224B HIS* 3.4 33.8 - - - -
264B TYR 2.9 11.1 + - - -
265B GLN* 3.5 2.9 - - - -
267B ILE* 1.3 73.5 - - - +
269B ASP* 1.3 65.7 + - - +
271B LYS* 3.2 5.1 + - - +
272B ARG* 3.0 31.7 + - - +
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B GLN* 2.8 47.4 + - - +
266B LYS* 3.6 10.3 - - - +
268B GLY* 1.3 71.1 - - - +
270B THR* 1.3 57.6 + - - +
272B ARG* 3.2 29.0 + - - +
273B ALA* 2.9 29.8 + - - +
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Residues in contact with THR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PRO* 4.5 8.5 - - + +
252B TRP* 3.9 24.2 - - + -
255B LEU* 3.7 16.7 - - + +
266B LYS* 3.1 17.9 + - - +
267B ILE 3.7 4.5 - - - -
268B GLY 3.2 0.4 - - - -
269B ASP* 1.3 74.9 - - - +
271B LYS* 1.3 61.8 + - - +
273B ALA* 3.3 6.8 + - + +
274B THR* 2.6 41.4 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA 2.6 30.1 + - - -
217B ARG 3.5 8.6 + - - -
219B MET 2.7 27.3 + - - +
221B ILE* 3.9 22.6 - - + +
224B HIS* 2.8 27.0 + - + +
240B HIS* 4.0 10.5 - - - +
252B TRP* 3.7 48.4 - - + +
267B ILE* 3.0 17.0 + - - +
268B GLY 3.5 6.1 - - - +
270B THR* 1.3 75.5 - - - +
272B ARG* 1.3 62.7 + - - +
274B THR* 3.1 21.7 + - - +
295B ARG* 4.8 5.1 + - - +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.8 36.9 - - + +
224B HIS* 6.2 0.9 - - - -
225B LEU* 4.0 26.6 - - - +
268B GLY* 3.0 17.6 + - - -
269B ASP* 3.4 34.6 + - - +
271B LYS* 1.3 76.5 - - - +
273B ALA* 1.3 58.3 + - - +
274B THR 3.3 3.3 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ASP 2.9 16.7 + - - +
270B THR* 3.5 9.2 - - - +
271B LYS 3.2 0.6 - - - -
272B ARG* 1.3 76.3 - - - +
274B THR* 1.3 56.3 + - - +
275B PRO* 3.6 9.9 - - - +
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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