Contacts of the helix formed by residues 253 - 274 (chain A) in PDB entry 3DAG
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 CYS 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLY 3.4 26.9 - - - -
248A PRO* 3.6 15.0 - - - -
251A ASP* 3.9 9.8 - - - +
252A MET* 1.3 72.5 - - - +
254A SER* 1.3 64.1 + - - +
255A ALA 3.0 3.8 - - - -
256A VAL* 2.9 25.0 + - + +
257A THR* 3.1 13.4 + - - +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PRO 3.3 13.7 + - - -
249A VAL* 3.3 22.7 - - - +
250A CYS 4.8 0.9 - - - -
251A ASP 2.9 17.4 + - - -
252A MET* 4.1 3.8 + - - -
253A CYS* 1.3 76.7 - - - +
255A ALA* 1.3 58.7 + - - +
257A THR* 3.7 1.2 - - - -
258A ALA* 2.9 32.9 + - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET 3.8 8.2 + - - +
253A CYS 3.0 1.2 + - - -
254A SER* 1.3 82.5 + - - +
256A VAL* 1.3 60.9 + - + +
258A ALA* 3.9 4.2 - - - +
259A THR* 2.9 33.3 + - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A CYS* 2.9 15.7 + - + +
255A ALA* 1.3 78.7 - - + +
257A THR* 1.3 66.3 + - - +
259A THR* 3.1 4.9 + - - -
260A VAL* 2.9 40.1 + - + +
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 6.0 2.5 - - + -
248A PRO* 2.8 50.1 + - + +
249A VAL* 4.4 14.1 - - + -
253A CYS* 3.1 8.7 + - - +
254A SER* 3.7 5.4 - - - -
256A VAL* 1.3 76.3 - - - +
258A ALA* 1.3 58.6 + - - +
260A VAL* 4.0 3.8 - - - +
261A TYR* 2.9 40.2 + - + +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 2.9 17.5 + - - +
255A ALA* 3.9 5.8 - - - +
257A THR* 1.3 79.9 - - - +
259A THR* 1.3 58.3 + - - +
261A TYR* 4.1 4.1 - - - +
262A ALA* 2.9 32.2 + - - +
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA 2.9 19.1 + - - -
256A VAL* 3.1 6.7 + - - -
258A ALA* 1.3 77.9 - - - +
260A VAL* 1.3 68.6 + - + +
262A ALA* 3.9 4.3 - - - +
263A GLY* 3.0 20.4 + - - -
329A ILE* 4.4 9.7 - - + +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 2.9 35.8 + - + +
257A THR* 4.1 3.8 - - - +
259A THR* 1.3 79.5 - - + +
261A TYR* 1.3 56.5 + - - +
263A GLY* 3.2 3.6 + - - -
264A LEU* 2.9 39.2 + - + +
290A LEU* 3.8 30.1 - - + -
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 2.9 27.6 + - + +
258A ALA* 4.1 4.3 - - - +
260A VAL* 1.3 76.3 - - - +
262A ALA* 1.3 57.4 + - - +
264A LEU* 3.3 16.7 + - + +
265A LEU* 3.0 64.5 + - + +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ALA 2.9 18.7 + - - +
259A THR* 3.9 1.8 - - - +
261A TYR* 1.3 74.9 - - - +
263A GLY* 1.3 57.9 + - - +
265A LEU* 3.9 8.5 - - - +
266A ALA* 2.9 33.1 + - - +
329A ILE* 3.6 20.9 - - + -
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A THR 3.0 14.7 + - - -
260A VAL* 3.2 4.2 + - - -
262A ALA* 1.3 75.5 - - - +
264A LEU* 1.3 57.1 + - - +
266A ALA* 4.1 2.3 - - - +
267A TYR* 2.9 34.1 + - - +
326A LEU* 4.5 3.5 - - - +
329A ILE* 3.9 13.3 - - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A VAL* 2.9 28.0 + - + +
261A TYR* 3.3 20.2 + - + +
263A GLY* 1.3 76.5 - - - +
265A LEU* 1.3 58.2 + - + +
267A TYR* 3.7 5.6 - - + +
268A ARG* 2.8 31.6 + - - +
286A ALA* 3.7 30.3 - - + -
290A LEU* 4.2 31.9 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A TYR* 3.0 62.4 + - + +
262A ALA* 4.0 6.7 - - - +
264A LEU* 1.3 75.9 - - + +
266A ALA* 1.3 58.5 + - - +
268A ARG* 3.4 38.4 + - - +
269A ASP* 3.0 37.1 + - - +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ALA 2.9 17.0 + - - +
263A GLY 4.1 0.7 - - - +
265A LEU* 1.3 76.1 - - - +
267A TYR* 1.3 59.2 + - - +
269A ASP* 3.4 1.2 + - - -
270A ALA* 2.9 27.0 + - - +
325A PRO* 3.4 37.2 - - - +
326A LEU* 3.9 15.3 - - + -
329A ILE* 3.9 12.3 - - + -
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLY 2.9 20.1 + - - +
264A LEU* 3.7 5.4 - - + +
266A ALA* 1.3 73.7 - - - +
268A ARG* 1.3 70.7 + - + +
270A ALA* 3.1 1.2 + - - +
271A VAL* 2.9 53.7 + - + +
281A PHE* 5.2 1.4 - - - -
282A ALA* 3.5 28.9 - - + -
285A MET* 3.1 31.1 - - + +
286A ALA* 4.2 16.4 - - + -
321A MET* 3.9 16.1 - - + +
326A LEU* 3.7 25.0 - - + +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU 2.8 22.1 + - - +
265A LEU* 3.6 33.9 - - - +
267A TYR* 1.3 75.5 - - - +
269A ASP* 1.3 81.6 + - - +
271A VAL* 3.9 0.2 - - - -
272A THR* 2.7 47.5 + - + +
279A ALA* 5.6 8.3 - - + -
282A ALA* 4.3 17.9 - - + -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 3.0 20.4 + - - +
266A ALA 3.8 0.9 - - - +
268A ARG* 1.3 107.4 + - - +
270A ALA* 1.3 56.5 + - - +
272A THR* 3.8 5.1 + - - -
273A LYS* 2.9 64.8 + - + +
274A ILE 3.8 0.2 + - - -
325A PRO* 3.8 21.6 - - + +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA 2.9 17.6 + - - +
267A TYR 3.1 2.0 + - - +
269A ASP* 1.3 74.1 - - - +
271A VAL* 1.3 60.7 + - + +
274A ILE* 3.1 27.1 + - - +
275A LEU* 3.1 11.5 + - - +
323A PHE* 4.0 19.5 - - + +
325A PRO* 3.5 17.8 - - + +
326A LEU* 3.6 28.9 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 2.9 53.0 + - + +
268A ARG 4.0 1.8 - - - +
270A ALA* 1.3 77.7 - - + +
272A THR* 1.3 58.9 + - - +
275A LEU* 3.3 18.7 - - + +
276A GLY 3.2 7.4 + - - -
277A ALA* 2.9 38.1 + - + -
278A PRO 4.8 0.7 - - - +
281A PHE* 4.0 12.3 - - + -
282A ALA* 3.8 27.8 - - + +
321A MET* 4.5 11.4 - - + -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 2.7 36.5 + - + +
269A ASP* 3.7 6.6 + - - -
271A VAL* 1.3 78.8 - - - +
273A LYS* 1.3 69.0 + - - +
276A GLY* 3.1 22.9 - - - -
277A ALA 3.2 19.6 - - - +
278A PRO 4.0 2.5 - - - +
279A ALA* 3.9 27.8 - - + +
282A ALA* 4.5 4.7 - - + -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 2.9 53.1 + - + +
272A THR* 1.3 82.1 + - - +
274A ILE* 1.3 66.2 + - + +
276A GLY* 4.1 2.6 + - - -
325A PRO* 5.6 2.9 - - + -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ALA 3.1 12.0 + - - +
273A LYS* 1.3 83.5 - - + +
275A LEU* 1.3 71.7 + - + +
276A GLY 3.2 1.7 + - - -
323A PHE* 3.7 23.1 - - + -
324A GLY* 3.5 31.4 - - - -
325A PRO* 3.6 13.2 - - + -
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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
------------------------------------------------------------
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