Contacts of the helix formed by residues 239 - 257 (chain A) in PDB entry 4MWI
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 SER 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A LEU* 3.3 6.0 - - - -
236A GLN 2.9 33.8 + - - +
237A ALA 3.2 2.9 - - - -
238A GLY* 1.3 80.0 - - - +
240A ILE* 1.3 63.7 + - - +
241A ALA* 3.2 7.4 + - - +
242A ILE* 3.1 37.2 + - - +
243A VAL 4.0 4.0 + - - -
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Residues in contact with ILE 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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234A LYS 4.3 3.6 - - - +
235A LEU* 3.4 22.4 - - + +
238A GLY 4.2 0.4 + - - +
239A SER* 1.3 72.2 + - - +
241A ALA* 1.3 68.8 + - - +
243A VAL* 3.3 20.0 + - + +
244A ARG* 3.4 9.4 + - + +
275A THR* 5.1 8.7 - - + -
276A PRO* 3.9 31.9 - - + -
277A PRO* 4.4 12.8 - - + -
279A PHE* 5.7 0.2 - - - -
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Residues in contact with ALA 241 (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 SER* 3.2 5.9 + - - +
240A ILE* 1.3 80.8 - - - +
242A ILE* 1.3 64.7 + - + +
244A ARG* 3.3 6.8 + - - +
245A GLN* 3.0 23.4 + - - +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN* 3.6 40.8 - - + +
237A ALA* 4.4 12.3 - - + +
239A SER* 3.1 26.5 + - - +
240A ILE 3.3 0.2 - - - -
241A ALA* 1.3 76.5 - - + +
243A VAL* 1.3 57.7 + - - +
245A GLN* 3.3 17.7 + - - +
246A THR* 2.9 29.8 + - - +
354A LYS* 6.0 2.0 - - - -
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Residues in contact with VAL 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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214A VAL* 4.8 4.7 - - + +
232A PHE* 3.9 24.0 - - + -
233A LYS 3.4 22.0 - - - +
234A LYS 3.5 22.7 - - - +
235A LEU 4.6 1.1 - - - +
236A GLN* 3.8 30.7 - - + +
239A SER 4.0 2.5 + - - +
240A ILE* 3.3 14.9 + - + +
242A ILE* 1.3 80.7 - - - +
244A ARG* 1.3 60.6 + - - +
246A THR* 3.3 1.4 + - - -
247A PHE* 3.0 28.6 + - - +
277A PRO* 5.8 2.2 - - + +
279A PHE* 4.6 12.6 - - + -
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Residues in contact with ARG 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 ILE* 3.4 8.9 + - + +
241A ALA* 3.3 9.7 + - - +
243A VAL* 1.3 80.7 - - - +
245A GLN* 1.3 58.8 + - - +
247A PHE* 3.4 2.8 + - + +
248A ASN* 2.9 47.6 + - - +
270A ILE* 5.8 1.0 - - - +
272A GLU* 3.0 40.2 + - - -
277A PRO* 3.7 17.2 - - + +
279A PHE* 3.6 33.0 - - + -
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Residues in contact with GLN 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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241A ALA 3.0 13.7 + - - +
242A ILE* 3.3 23.7 + - - +
244A ARG* 1.3 77.8 - - - +
246A THR* 1.3 57.5 + - - +
248A ASN* 3.9 5.7 - - - +
249A LYS* 3.0 29.6 + - + +
352A LEU* 3.7 32.6 - - + +
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Residues in contact with THR 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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214A VAL* 4.7 7.2 - - + -
232A PHE* 3.9 20.0 - - + -
236A GLN* 2.8 34.8 + - - +
242A ILE* 2.9 15.9 + - - +
243A VAL* 3.6 4.0 - - - -
245A GLN* 1.3 75.8 + - - +
247A PHE* 1.3 66.6 + - - +
249A LYS* 3.8 5.8 - - - +
250A GLU* 3.0 29.8 + - + +
350A PHE 5.0 1.4 - - - +
351A GLU* 5.6 11.2 - - + +
354A LYS* 4.9 6.0 + - - +
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Residues in contact with PHE 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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232A PHE* 3.7 30.0 - + + -
243A VAL 3.0 17.5 + - - +
244A ARG* 3.6 7.0 - - + +
246A THR* 1.3 77.7 - - - +
248A ASN* 1.3 74.0 + - - +
250A GLU* 3.3 2.1 + - - +
251A ILE* 3.0 41.9 + - + +
268A ILE* 3.7 27.6 - - + -
270A ILE* 3.8 15.7 - - + -
279A PHE* 3.6 48.0 - + + -
280A SER 3.7 11.0 - - - -
281A ILE* 3.7 22.2 - - + -
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Residues in contact with ASN 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 ARG* 2.9 42.3 + - - +
245A GLN* 3.9 5.9 - - - +
247A PHE* 1.3 89.2 - - - +
249A LYS* 1.3 57.4 + - - +
251A ILE* 3.4 11.6 - - - +
252A LYS* 3.0 56.7 + - - +
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Residues in contact with LYS 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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245A GLN* 3.0 19.9 + - + +
246A THR* 3.8 5.6 - - - +
248A ASN* 1.3 76.6 - - - +
250A GLU* 1.3 64.7 + - - +
252A LYS* 3.9 4.7 - - - +
253A THR* 3.0 42.8 + - - +
327A GLU* 3.0 30.7 + - - +
328A LEU 4.6 8.3 + - - -
329A HIS 5.2 0.7 - - - -
350A PHE* 4.2 5.8 - - - +
351A GLU* 3.9 41.3 - - - +
352A LEU* 4.1 29.3 - - + +
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Residues in contact with GLU 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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230A LYS* 2.8 38.6 + - - +
232A PHE* 3.6 13.0 - - - -
246A THR* 3.0 21.7 + - + +
247A PHE* 3.7 3.8 - - - +
249A LYS* 1.3 78.8 - - - +
251A ILE* 1.3 59.0 + - - +
253A THR* 3.9 1.9 - - - -
254A MET* 3.0 45.9 + - + +
263A LEU* 6.1 0.3 - - - +
281A ILE* 3.8 18.3 - - + +
283A MET* 4.8 3.3 - - - +
348A ALA* 5.5 1.2 - - - +
349A GLY* 4.1 17.1 + - - +
350A PHE* 4.0 26.4 - - + +
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Residues in contact with ILE 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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193A ILE* 3.7 17.9 - - + +
247A PHE* 3.0 42.9 + - + +
248A ASN* 3.4 19.5 - - - +
250A GLU* 1.3 75.3 - - - +
252A LYS* 1.3 72.7 + - + +
254A MET* 3.7 3.8 - - - +
255A LYS* 3.0 24.6 + - - +
265A ILE* 3.8 23.1 - - + +
268A ILE* 3.9 15.7 - - + -
281A ILE* 3.6 32.5 - - + -
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Residues in contact with LYS 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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193A ILE* 4.8 4.8 - - + +
248A ASN* 3.0 44.3 + - - +
249A LYS* 4.0 4.9 - - - +
251A ILE* 1.3 83.1 - - + +
253A THR* 1.3 58.5 + - - +
255A LYS* 3.4 5.6 + - - +
256A LYS* 2.9 30.7 + - - +
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Residues in contact with THR 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 LYS* 3.0 39.1 + - - +
250A GLU 3.9 2.5 - - - -
252A LYS* 1.3 73.5 - - - +
254A MET* 1.3 66.0 + - - +
256A LYS* 4.3 5.2 - - - -
257A PHE* 3.1 37.5 + - + +
320A LEU* 4.7 2.7 - - + -
327A GLU* 3.3 21.0 + - - +
350A PHE* 3.5 38.3 - - + -
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Residues in contact with MET 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 GLU* 3.0 37.7 + - - +
251A ILE* 3.4 5.6 + - - +
253A THR* 1.3 78.9 - - - +
255A LYS* 1.3 59.6 + - - +
257A PHE 3.9 1.0 - - - -
258A GLU* 3.4 20.8 + - - +
262A ILE* 4.1 7.5 - - - +
263A LEU* 3.3 43.9 - - + +
264A ARG 3.9 4.9 - - - +
265A ILE* 3.9 23.8 + - + +
281A ILE* 4.4 12.3 - - - -
283A MET* 3.7 28.7 - - + +
348A ALA* 5.7 1.1 - - + -
349A GLY 6.1 0.9 - - - -
350A PHE* 3.7 24.7 - - + -
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Residues in contact with LYS 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 ILE* 4.1 36.3 - - + +
251A ILE 3.0 17.2 + - - +
252A LYS* 3.8 4.7 - - - +
254A MET* 1.3 76.5 - - - +
256A LYS* 1.3 65.2 + - - +
257A PHE 3.3 0.7 + - - -
258A GLU* 3.1 49.5 + - - +
265A ILE* 4.3 14.3 + - + +
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Residues in contact with LYS 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 LYS 2.9 18.4 + - - +
253A THR* 3.3 5.6 + - - +
255A LYS* 1.3 78.3 - - - +
257A PHE* 1.3 81.5 + - + +
258A GLU* 3.4 2.0 + - - +
319A ARG* 3.7 11.1 + - - -
324A GLU 4.5 2.0 - - - -
325A ALA* 2.8 46.4 + - - +
327A GLU* 2.9 23.9 + - - +
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Residues in contact with PHE 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 THR* 3.1 29.4 + - + +
254A MET 3.9 2.9 - - - -
256A LYS* 1.3 106.0 - - + +
258A GLU* 1.3 67.6 + - - +
259A SER* 2.8 15.4 + - - -
262A ILE* 3.2 13.6 - - + +
319A ARG* 3.4 51.2 + - + +
320A LEU* 3.9 20.9 - - + -
323A SER* 4.0 11.9 - - - -
324A GLU 4.4 1.6 - - - -
325A ALA 3.5 13.7 - - - -
327A GLU* 3.5 39.9 - - + -
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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