Contacts of the helix formed by residues 252 - 266 (chain A) in PDB entry 3SM9
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 3.0 23.2 + - - +
194A GLU 4.9 6.4 + - - -
197A TYR* 4.5 7.9 - - + -
224A ARG* 6.0 4.2 - - - +
251A MET* 1.3 71.0 - - - +
253A SER* 1.3 60.5 + - - +
254A ASP* 3.5 3.6 + - - +
255A ASP* 3.5 20.8 + - - +
256A SER* 3.0 30.8 + - - -
277A GLY 4.0 0.9 - - - -
482A SO4 2.8 44.3 + - - +
485A Z99 4.4 21.3 - - + -
487A CL 4.4 19.1 - - - -
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Residues in contact with SER 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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252A ARG* 1.3 72.1 - - - +
254A ASP* 1.3 64.6 + - - +
256A SER 3.2 1.9 + - - -
257A ARG* 3.0 20.9 + - - +
277A GLY* 2.7 26.7 + - - -
281A GLN* 3.1 23.9 + - - -
283A SER* 6.1 0.2 - - - -
284A ILE* 3.3 14.6 - - - +
482A SO4 3.3 21.1 + - - -
485A Z99 4.9 2.3 - - - -
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Residues in contact with ASP 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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252A ARG* 5.7 3.5 + - - +
253A SER* 1.3 76.1 - - - +
255A ASP* 1.4 67.1 + - - +
257A ARG* 3.3 7.3 + - - +
258A GLU* 3.1 32.4 + - + +
482A SO4 3.0 31.0 + - - +
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Residues in contact with ASP 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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193A SER* 2.5 39.4 + - - +
194A GLU 4.7 0.3 + - - -
222A VAL* 3.9 13.3 - - - +
223A GLY 4.6 5.4 - - - +
231A TYR* 3.0 30.4 + - - +
251A MET* 3.6 15.2 - - + +
252A ARG* 3.5 26.0 + - - +
253A SER 3.3 0.2 - - - -
254A ASP* 1.4 78.7 - - - +
256A SER* 1.4 56.9 + - - +
259A LEU* 3.0 27.4 + - - +
482A SO4 4.5 0.2 + - - -
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Residues in contact with SER 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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249A LEU* 5.0 4.3 - - - +
251A MET* 3.5 26.7 + - - +
252A ARG 3.0 23.1 + - - -
253A SER* 3.4 6.5 - - - -
255A ASP* 1.4 73.6 - - - +
257A ARG* 1.4 63.3 + - - +
259A LEU* 3.5 3.1 + - - +
260A ILE* 3.2 30.1 + - - +
278A TRP* 4.0 26.1 - - - +
284A ILE* 4.1 15.3 - - - -
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Residues in contact with ARG 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 SER 3.0 12.9 + - - +
254A ASP* 3.7 10.3 - - - +
256A SER* 1.4 74.4 - - - +
258A GLU* 1.3 68.3 + - + +
260A ILE* 3.4 4.0 + - - +
261A ALA* 3.0 27.3 + - - +
283A SER* 3.4 28.2 + - - +
284A ILE* 3.4 27.1 + - + +
286A LYS* 4.3 24.4 + - - +
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Residues in contact with GLU 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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227A ILE 5.7 0.2 - - - -
228A ARG* 4.9 12.5 + - - +
231A TYR* 3.5 41.3 - - + +
254A ASP* 3.1 21.4 + - + +
257A ARG* 1.3 85.8 + - + +
259A LEU* 1.3 59.5 + - - +
261A ALA* 3.4 11.9 + - - +
262A ALA* 3.1 26.7 + - - +
265A ARG* 4.9 6.8 + - - -
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Residues in contact with LEU 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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191A VAL* 3.8 15.3 - - + -
231A TYR* 3.5 28.0 - - + +
234A VAL* 3.8 25.8 - - + -
235A ILE* 3.6 20.7 - - + +
249A LEU* 3.8 21.8 - - + -
251A MET* 3.8 24.7 - - + -
255A ASP 3.0 18.3 + - - +
256A SER 4.0 4.3 - - - +
258A GLU* 1.3 73.8 - - - +
260A ILE* 1.3 62.6 + - + +
262A ALA* 3.4 0.7 + - - +
263A ALA* 3.0 26.9 + - - +
272A TRP* 4.3 10.8 - - + -
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Residues in contact with ILE 260 (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 LEU* 4.6 3.1 - - + -
256A SER 3.2 18.8 + - - +
257A ARG 3.9 4.3 - - - +
258A GLU 3.4 0.2 - - - -
259A LEU* 1.3 76.2 - - + +
261A ALA* 1.4 56.4 + - - +
263A ALA* 3.4 4.4 + - - +
264A SER* 2.9 27.5 + - - -
272A TRP* 3.5 39.0 - - + +
278A TRP* 3.5 37.7 - - + -
284A ILE* 4.4 14.1 - - + +
285A ILE* 4.9 2.2 - - + -
288A SER* 3.7 22.2 - - - +
291A VAL* 3.6 4.5 - - + +
292A ALA* 3.8 20.2 - - + -
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Residues in contact with ALA 261 (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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257A ARG* 3.0 17.3 + - + +
258A GLU* 3.4 19.5 - - - +
259A LEU 3.3 0.2 - - - -
260A ILE* 1.4 73.5 - - - +
262A ALA* 1.4 57.5 + - - +
264A SER* 3.3 9.6 + - - -
265A ARG* 3.0 44.6 + - - +
288A SER* 4.2 7.8 + - - +
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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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231A TYR* 3.6 31.6 - - + -
232A ASP* 3.5 19.4 - - - +
235A ILE* 3.8 16.7 - - + +
258A GLU 3.1 8.6 + - - +
259A LEU 3.8 1.8 - - - +
261A ALA* 1.4 73.1 - - - +
263A ALA* 1.4 60.2 + - - +
265A ARG* 3.5 17.9 + - - +
266A ALA* 3.1 28.4 + - - +
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Residues in contact with ALA 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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235A ILE* 3.8 17.7 - - + +
259A LEU 3.0 14.4 + - - +
260A ILE* 3.4 11.0 - - - +
262A ALA* 1.4 75.6 - - - +
264A SER* 1.4 57.7 + - - +
266A ALA 3.6 0.3 + - - -
267A ASN 3.1 5.7 + - - -
268A ALA* 2.8 43.8 + - + +
272A TRP* 3.8 22.2 - - + -
291A VAL* 3.4 9.0 - - + +
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Residues in contact with SER 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 ILE 2.9 13.3 + - - -
261A ALA* 3.3 10.5 - - - -
263A ALA* 1.4 75.9 - - - +
265A ARG* 1.4 61.2 + - - +
267A ASN* 3.2 14.2 + - - +
287A GLY 4.1 4.9 + - - -
288A SER* 3.8 28.3 + - - -
291A VAL* 3.8 14.3 - - - +
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Residues in contact with ARG 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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228A ARG* 3.3 27.4 + - - +
231A TYR* 5.1 0.6 - - - +
232A ASP* 3.3 31.9 + - - +
258A GLU* 4.9 6.9 + - - -
261A ALA* 3.0 29.6 + - - +
262A ALA* 3.7 25.4 - - - +
263A ALA 3.4 0.2 - - - -
264A SER* 1.4 76.6 - - - +
266A ALA* 1.3 56.2 + - - +
267A ASN* 3.2 4.2 + - - +
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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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232A ASP* 5.3 3.8 - - - +
235A ILE* 3.8 22.4 - - + -
239A LEU* 4.7 10.4 - - + +
262A ALA 3.1 16.7 + - - +
263A ALA 3.6 1.3 + - - +
264A SER 3.4 0.4 - - - -
265A ARG* 1.3 74.5 - - - +
267A ASN* 1.4 68.4 + - - +
268A ALA* 3.0 6.2 + - + +
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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
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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