Contacts of the helix formed by residues 242 - 259 (chain A) in PDB entry 3SAJ
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 ASP 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ASN* 3.2 35.0 + - + +
241A THR* 1.3 83.4 - - - +
243A THR* 1.3 82.0 + - - +
244A ILE* 3.5 2.4 + - - +
245A PRO* 3.5 12.7 - - + +
246A ALA* 3.0 20.3 + - - +
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Residues in contact with THR 243 (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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242A ASP* 1.3 84.5 + - - +
244A ILE* 1.3 67.8 + - + +
246A ALA* 3.8 3.0 - - - +
247A ARG* 3.3 52.1 + - - +
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Residues in contact with ILE 244 (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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242A ASP* 4.8 1.9 + - - +
243A THR* 1.3 79.8 - - + +
245A PRO* 1.3 70.2 - - + +
247A ARG* 3.4 33.8 - - - +
248A ILE* 3.1 37.8 + - + +
329A GLU* 3.5 53.4 - - + +
330A GLY 4.5 4.3 - - - +
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Residues in contact with PRO 245 (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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238A VAL* 4.5 1.6 - - + -
239A ASN* 3.1 30.1 - - + +
240A TYR* 4.3 6.3 - - + -
242A ASP* 3.5 21.8 - - + +
244A ILE* 1.3 95.4 - - + +
246A ALA* 1.3 55.9 + - - +
248A ILE* 3.8 1.0 - - - +
249A MET* 3.0 33.7 + - - +
330A GLY 4.6 3.8 - - - +
331A LEU* 3.5 42.8 - - + +
333A GLY* 5.7 0.9 - - - +
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Residues in contact with ALA 246 (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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240A TYR 4.0 15.6 + - - +
241A THR* 4.4 7.0 - - - +
242A ASP 3.0 21.6 + - - +
243A THR* 3.8 4.7 - - - +
245A PRO* 1.3 72.7 - - - +
247A ARG* 1.3 65.9 + - - +
249A MET* 3.4 5.5 + - - +
250A GLN* 3.0 23.3 + - - +
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Residues in contact with ARG 247 (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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243A THR* 3.3 36.7 + - - +
244A ILE* 3.4 38.1 - - - +
246A ALA* 1.3 75.5 - - - +
248A ILE* 1.3 60.6 + - + +
250A GLN* 2.9 27.7 + - + +
251A GLN* 3.3 26.3 + - - +
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Residues in contact with ILE 248 (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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26A PHE* 4.4 5.4 - - + -
30A GLN* 4.7 0.4 - - - +
244A ILE* 3.1 35.8 + - + +
245A PRO 3.8 3.8 - - - +
246A ALA 3.4 0.2 - - - -
247A ARG* 1.3 76.4 - - + +
249A MET* 1.3 70.4 + - - +
250A GLN 3.1 0.3 + - - -
251A GLN* 3.3 13.7 + - - +
252A TRP* 3.1 21.3 + - + +
276A TYR* 3.5 48.2 - - + +
330A GLY* 4.8 1.8 - - - -
331A LEU* 4.0 37.5 - - + +
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Residues in contact with MET 249 (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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240A TYR* 3.5 36.8 - - + +
245A PRO 3.0 21.4 + - - +
246A ALA* 3.8 6.3 - - - +
248A ILE* 1.3 81.2 - - - +
250A GLN* 1.3 52.6 + - - +
252A TRP* 3.8 29.3 - - + +
253A ARG* 2.4 72.8 + - + +
268A PRO* 3.5 31.4 - - + -
331A LEU* 4.7 3.8 - - - -
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Residues in contact with GLN 250 (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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246A ALA 3.0 12.4 + - - +
247A ARG* 2.9 20.2 - - - +
248A ILE 3.0 0.2 - - - -
249A MET* 1.3 77.0 - - - +
251A GLN* 1.3 63.7 + - + +
253A ARG* 3.1 11.5 + - - +
254A THR* 3.1 30.8 + - + +
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Residues in contact with GLN 251 (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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26A PHE* 3.9 4.0 - - + -
30A GLN* 2.8 36.2 + - - +
247A ARG* 3.3 32.6 + - - +
248A ILE* 3.3 16.0 + - - +
250A GLN* 1.3 75.3 - - + +
252A TRP* 1.3 62.4 + - - +
254A THR* 2.6 24.6 + - - +
255A SER* 2.8 22.6 + - - +
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Residues in contact with TRP 252 (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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19A GLN* 4.9 7.4 - - + -
22A ALA* 4.3 8.0 + - + +
23A ALA* 3.4 45.8 - - + -
26A PHE* 3.4 46.7 - + + +
248A ILE* 3.1 21.2 + - + +
249A MET* 3.8 27.1 - - + +
251A GLN* 1.3 75.7 - - - +
253A ARG* 1.3 63.3 + - - +
255A SER* 3.2 1.1 + - - -
256A ASP* 3.2 41.9 + - - +
268A PRO* 4.3 24.5 - - + -
272A SER* 4.8 5.4 - - - -
276A TYR* 4.5 7.0 - + + -
331A LEU* 4.5 15.7 - - + -
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Residues in contact with ARG 253 (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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249A MET* 2.4 63.6 + - + +
250A GLN* 3.1 11.6 + - - +
252A TRP* 1.3 79.2 - - - +
254A THR* 1.3 61.5 + - + +
256A ASP* 3.5 5.0 + - - +
257A SER* 3.1 25.9 + - - -
266A LYS* 3.1 44.3 + - - +
267A ARG* 4.6 2.0 - - - +
268A PRO* 4.4 3.4 - - - +
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Residues in contact with THR 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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250A GLN* 3.1 20.0 + - + +
251A GLN* 2.6 28.6 + - - +
253A ARG* 1.3 76.9 - - + +
255A SER* 1.3 62.4 + - - +
256A ASP 3.4 0.3 + - - -
257A SER* 3.5 16.0 + - - -
258A ARG* 4.3 9.2 + - - +
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Residues in contact with SER 255 (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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26A PHE* 3.3 28.5 - - - -
251A GLN* 2.8 22.1 + - - +
252A TRP 3.2 6.3 + - - -
254A THR* 1.3 80.6 + - - +
256A ASP* 1.3 63.8 + - - +
258A ARG* 4.3 4.2 + - - +
259A ASP* 4.3 12.8 + - - +
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Residues in contact with ASP 256 (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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252A TRP* 3.2 35.8 + - - +
253A ARG* 4.0 5.4 - - - +
254A THR 3.3 0.2 - - - -
255A SER* 1.3 80.2 - - - +
257A SER* 1.3 64.0 + - - +
258A ARG 3.1 3.1 + - - -
259A ASP 3.8 18.8 - - - +
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Residues in contact with SER 257 (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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253A ARG 3.1 17.2 + - - -
254A THR* 3.9 9.5 - - - -
255A SER 3.4 1.4 - - - -
256A ASP* 1.3 79.3 - - - +
258A ARG* 1.3 73.2 + - - +
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Residues in contact with ARG 258 (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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254A THR 4.3 10.3 + - - +
255A SER 4.3 2.2 + - - +
256A ASP 3.2 0.4 - - - -
257A SER* 1.3 90.2 + - - +
259A ASP* 1.3 67.1 + - - +
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Residues in contact with ASP 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 SER 4.3 12.2 + - - +
256A ASP* 3.8 14.5 + - - +
258A ARG* 1.3 83.6 - - - +
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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