Contacts of the helix formed by residues 239 - 261 (chain A) in PDB entry 1SMK
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 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PHE* 1.3 78.3 - - - +
240A GLN* 1.3 66.0 + - - +
241A GLU* 3.4 11.3 + - - -
242A GLU* 2.9 41.7 + - - +
243A ILE* 3.1 18.9 + - - +
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Residues in contact with GLN 240 (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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239A THR* 1.3 72.6 - - - +
241A GLU* 1.3 64.5 + - - +
243A ILE* 3.3 13.6 + - + +
244A SER* 3.2 24.9 + - - -
331A TYR* 6.3 2.7 - - + -
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 3.4 8.4 + - - +
240A GLN* 1.3 81.0 - - - +
242A GLU* 1.3 85.8 + - - +
244A SER* 4.0 3.9 - - - -
245A TYR* 3.1 33.0 + - + +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.4 35.4 - - + +
205A LEU* 5.3 2.8 - - - +
237A SER 4.3 2.4 - - - +
238A PHE* 3.5 19.1 - - + +
239A THR* 2.9 44.5 + - - +
241A GLU* 1.3 93.9 - - - +
243A ILE* 1.3 61.0 + - - +
245A TYR* 4.4 3.8 - - - -
246A LEU* 2.8 38.1 + - + +
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.7 22.9 - - + +
238A PHE* 3.5 30.5 - - + +
239A THR 3.1 18.3 + - - +
240A GLN* 3.3 11.4 + - + +
242A GLU* 1.3 76.9 - - - +
244A SER* 1.3 54.9 + - - +
247A THR* 2.8 36.4 + - - -
329A ASN* 5.4 10.5 - - - +
331A TYR* 3.6 40.6 - - + -
332A GLU* 6.4 0.2 - - + -
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Residues in contact with SER 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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240A GLN* 3.2 15.3 + - - -
241A GLU* 4.0 3.6 - - - -
243A ILE* 1.3 78.2 - - - +
245A TYR* 1.3 66.1 + - - +
248A ASP* 3.0 42.7 + - - +
331A TYR* 3.7 23.7 + - - -
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Residues in contact with TYR 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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200A PHE* 5.6 0.4 - - + -
204A VAL* 3.8 30.1 - - + -
241A GLU* 3.1 31.2 + - - +
242A GLU* 3.8 2.7 - - - +
244A SER* 1.3 75.0 - - - +
246A LEU* 1.3 64.3 + - + +
248A ASP* 3.4 4.6 + - - +
249A ARG* 2.9 71.0 + - + +
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Residues in contact with LEU 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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200A PHE* 3.4 45.1 - - + +
201A VAL* 3.7 16.6 - - + +
204A VAL* 3.9 21.8 - - + -
229A LEU* 4.0 13.0 - - + -
238A PHE* 3.8 33.4 - - + -
242A GLU 2.8 23.7 + - - +
243A ILE 4.0 2.9 - - - +
245A TYR* 1.3 78.0 - - + +
247A THR* 1.3 57.8 + - - +
249A ARG* 3.1 3.6 + - - +
250A ILE* 2.8 40.5 + - + +
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Residues in contact with THR 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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226A LEU* 5.0 5.2 - - + -
227A PRO* 4.0 28.6 + - + +
229A LEU* 4.0 10.4 - - - +
243A ILE 2.8 21.4 + - - -
246A LEU* 1.3 76.6 - - - +
248A ASP* 1.3 64.2 + - - +
250A ILE* 3.3 1.0 + - - +
251A GLN* 2.9 56.8 + - - +
331A TYR* 3.4 34.5 - - + +
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Residues in contact with ASP 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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244A SER* 3.0 32.1 + - - +
245A TYR* 3.8 4.4 - - - +
247A THR* 1.3 77.8 - - - +
249A ARG* 1.3 62.7 + - - +
251A GLN* 3.5 11.6 + - - +
252A ASN* 2.7 39.0 + - - +
331A TYR* 4.1 9.4 + - - -
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 3.2 40.9 + - + +
203A GLU* 2.8 29.5 + - - +
245A TYR* 2.9 55.0 + - + +
246A LEU* 3.1 5.6 + - - +
248A ASP* 1.3 76.4 - - - +
250A ILE* 1.3 59.0 + - - +
252A ASN* 3.2 2.0 + - - -
253A GLY* 2.8 29.3 + - - -
256A GLU* 2.7 42.3 + - - +
89B SER* 5.4 2.0 + - - -
90B HIS* 4.3 3.0 + - - -
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Residues in contact with ILE 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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193A ASP* 4.1 20.0 - - + +
196A ARG* 4.6 9.8 + - + -
197A ALA* 3.5 37.0 - - + +
200A PHE* 3.8 18.6 - - + -
201A VAL* 4.7 7.4 - - + -
216A VAL* 5.2 0.9 - - + -
225A ILE* 4.1 26.3 - - + +
227A PRO* 3.7 27.8 - - + -
229A LEU* 4.9 1.6 - - + -
246A LEU* 2.8 31.6 + - + +
247A THR 3.8 3.6 - - - +
249A ARG* 1.3 76.6 - - - +
251A GLN* 1.3 63.4 + - - +
252A ASN 3.2 1.0 + - - -
253A GLY* 3.3 7.8 + - - -
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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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222A GLY* 3.5 31.7 + - - +
223A VAL* 3.7 34.2 + - - +
225A ILE* 2.8 42.9 + - + +
226A LEU* 4.8 6.1 - - - +
227A PRO* 4.8 1.8 - - + -
247A THR* 2.9 39.9 + - + +
248A ASP* 3.8 16.9 - - - +
249A ARG 3.3 0.2 - - - -
250A ILE* 1.3 76.4 - - - +
252A ASN* 1.3 65.4 + - - +
253A GLY 4.0 0.2 + - - -
254A GLY 5.2 0.7 + - - -
335A GLY* 5.9 1.6 + - - -
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Residues in contact with ASN 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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222A GLY* 5.0 6.1 - - - -
248A ASP* 2.7 35.5 + - - +
249A ARG* 3.5 2.9 - - - +
250A ILE 3.1 0.2 - - - -
251A GLN* 1.3 87.7 + - - +
253A GLY* 1.3 66.1 + - - +
254A GLY 2.8 5.1 + - - -
255A THR* 3.0 30.4 + - + +
256A GLU* 3.5 5.0 + - - +
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Residues in contact with GLY 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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196A ARG* 3.8 18.9 + - - -
200A PHE* 4.6 1.8 - - - -
249A ARG 2.8 15.3 + - - -
250A ILE 3.3 5.3 + - - -
251A GLN 3.6 0.4 - - - -
252A ASN* 1.3 78.4 - - - +
254A GLY* 1.3 62.2 + - - +
256A GLU* 3.1 27.1 + - - +
257A VAL* 3.7 0.7 + - - +
90B HIS* 3.2 21.1 + - - -
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Residues in contact with GLY 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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196A ARG* 3.6 26.9 + - - +
251A GLN 5.2 0.8 + - - -
252A ASN 2.8 3.4 + - - -
253A GLY* 1.3 75.6 - - - +
255A THR* 1.3 61.1 + - - +
257A VAL* 3.1 16.3 + - - +
258A VAL* 3.3 15.7 + - - +
266A SER* 5.5 0.5 - - - -
267A ALA* 5.4 1.8 + - - -
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Residues in contact with THR 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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252A ASN* 3.0 25.7 + - + +
254A GLY* 1.3 71.3 - - - +
256A GLU* 1.3 58.6 + - - +
257A VAL 3.1 0.2 - - - -
258A VAL* 3.6 14.4 - - + -
259A GLU* 2.8 32.1 + - - +
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Residues in contact with GLU 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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200A PHE* 4.2 1.2 - - - -
249A ARG* 2.7 51.1 + - - +
252A ASN 3.5 3.4 + - - +
253A GLY* 3.1 17.7 + - - +
255A THR* 1.3 79.6 + - - +
257A VAL* 1.3 58.6 + - - +
259A GLU* 3.6 5.9 - - - +
260A ALA* 3.1 25.5 + - - +
86B ALA* 4.3 5.9 - - + +
89B SER* 5.3 0.3 + - - -
90B HIS* 2.7 32.1 + - + +
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Residues in contact with VAL 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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196A ARG* 4.8 0.7 - - - +
253A GLY 4.1 2.5 - - - +
254A GLY 3.1 7.0 + - - +
256A GLU* 1.3 74.6 - - - +
258A VAL* 1.3 65.2 - - - +
259A GLU 3.1 1.6 - - - -
260A ALA* 3.2 1.7 + - - +
261A LYS* 3.1 38.8 + - - +
266A SER 3.9 4.3 - - - -
267A ALA* 3.5 39.0 - - + +
83B GLY 4.1 2.7 - - - +
86B ALA* 3.8 10.3 - - - +
87B ASP* 3.8 26.2 - - + +
90B HIS* 3.8 27.6 - - + +
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Residues in contact with VAL 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 GLY 3.3 15.1 + - - +
255A THR* 3.3 17.2 + - + +
257A VAL* 1.3 76.3 - - - +
259A GLU* 1.3 59.2 + - - +
261A LYS* 3.1 6.1 + - - +
263A GLY* 2.8 51.0 + - - +
265A GLY 3.5 20.6 - - - +
266A SER* 4.0 15.5 - - - -
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Residues in contact with GLU 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 THR 2.8 18.6 + - - +
256A GLU* 3.6 6.9 - - - +
258A VAL* 1.3 74.2 - - - +
260A ALA* 1.3 67.0 + - - +
261A LYS 3.0 5.5 + - - -
262A ALA* 3.0 14.6 + - - +
263A GLY 4.8 1.3 - - - +
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Residues in contact with ALA 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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256A GLU 3.1 8.2 + - - +
257A VAL 3.2 4.4 + - - +
259A GLU* 1.3 85.2 + - - +
261A LYS* 1.3 58.7 + - - +
262A ALA 3.4 1.6 + - - -
80B ASN* 6.0 0.7 - - - -
82B PRO* 3.7 14.5 - - + +
83B GLY* 3.5 22.1 + - - +
86B ALA* 3.5 32.1 - - + -
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Residues in contact with LYS 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 VAL* 3.1 23.6 + - + +
258A VAL 3.8 2.2 - - - +
259A GLU 3.0 1.4 - - - -
260A ALA* 1.3 77.6 - - - +
262A ALA* 1.3 56.8 + - - +
263A GLY 3.0 2.0 - - - -
264A ALA* 2.8 34.7 + - + +
265A GLY* 3.9 30.6 - - - +
266A SER 3.2 20.1 + - - +
268A THR* 4.3 8.7 + - - +
58B GLN* 4.9 9.3 + - - +
80B ASN* 6.2 1.6 - - + -
83B GLY* 3.5 36.1 - - - -
84B VAL* 4.2 6.0 - - - +
87B ASP* 4.0 12.4 + - - +
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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