Contacts of the helix formed by residues 270 - 285 (chain A) in PDB entry 4IM0
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 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 2.7 36.4 + - - -
268A SER 3.5 1.5 + - - -
269A LEU* 1.3 75.9 - - - +
271A ARG* 1.3 59.3 + - - +
272A GLY 3.6 3.4 + - - -
273A LEU* 3.1 13.0 + - - -
274A GLN* 2.8 26.9 + - - +
322A HIS* 5.9 0.9 - - - -
323A LYS* 3.7 27.7 - - - +
325A TYR* 3.7 6.6 - - - -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP* 4.3 22.4 + - - -
269A LEU 3.8 1.2 + - - -
270A SER* 1.3 72.2 - - - +
272A GLY* 1.3 62.9 + - - +
274A GLN* 3.6 28.6 + - - +
275A VAL* 2.9 55.9 + - + +
322A HIS* 5.8 1.3 - - - +
342A GLN* 4.2 19.9 + - + +
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER* 3.1 4.4 + - - -
271A ARG* 1.3 80.8 - - - +
273A LEU* 1.3 59.7 + - - +
275A VAL* 3.7 9.8 + - - +
276A LEU* 3.7 19.1 + - - +
323A LYS 3.5 12.3 + - - -
325A TYR* 3.8 10.2 - - - +
342A GLN* 3.4 28.6 + - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.3 41.1 - - + +
112A PHE* 4.2 11.0 - - + -
113A LEU* 3.9 21.8 - - + -
116A LEU* 5.7 0.9 - - + -
269A LEU* 4.1 23.1 - - + -
270A SER* 3.1 10.6 + - - +
272A GLY* 1.3 72.4 - - - +
274A GLN* 1.3 67.9 + - - +
276A LEU* 2.9 7.2 + - + -
277A LEU* 2.9 31.1 + - + +
305A ILE* 4.0 26.7 - - + -
325A TYR* 3.6 14.6 - - + +
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Residues in contact with GLN 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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262A ASP* 5.9 0.3 - - - +
263A MET* 3.4 38.9 + - + +
264A PRO 4.9 2.0 + - - +
265A VAL 5.8 0.2 + - - -
267A CYS* 4.0 20.4 + - - +
269A LEU* 2.8 33.5 + - + +
270A SER 2.8 21.9 + - - +
271A ARG* 3.6 33.3 + - - +
273A LEU* 1.3 72.2 - - - +
275A VAL* 1.3 57.1 + - - +
277A LEU* 4.5 6.3 - - - +
278A THR* 3.0 39.8 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 2.9 43.3 + - + +
272A GLY* 3.9 8.3 - - - +
273A LEU 3.1 0.4 - - - -
274A GLN* 1.3 76.7 - - - +
276A LEU* 1.3 66.8 + - + +
278A THR* 4.8 1.5 - - - -
279A PRO* 3.2 22.4 - - - +
341A LYS* 6.4 1.8 - - + -
342A GLN* 6.2 3.1 - - + -
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Residues in contact with LEU 276 (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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272A GLY 3.7 11.4 - - - +
273A LEU* 2.9 8.8 + - + +
275A VAL* 1.3 88.6 - - + +
277A LEU* 1.3 63.7 + - - +
279A PRO* 3.2 10.3 - - - +
280A VAL* 3.6 16.1 - - - +
304A ASP* 5.2 4.0 - - - +
305A ILE* 3.7 29.0 - - + +
308A ARG* 3.9 27.4 - - - +
325A TYR* 3.8 35.0 - - + +
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Residues in contact with LEU 277 (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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112A PHE* 3.4 38.8 - - + -
116A LEU* 5.5 6.3 - - + -
211A PHE* 5.0 6.3 - - + -
215A ALA* 4.2 5.2 - - + -
263A MET* 4.1 16.6 - - + -
269A LEU* 3.9 17.9 - - + -
273A LEU* 2.9 22.8 + - + +
274A GLN* 4.1 3.8 - - - +
276A LEU* 1.3 77.1 - - - +
278A THR* 1.3 66.9 - - - +
280A VAL* 2.9 24.5 + - + +
281A LEU* 3.1 36.1 + - + +
305A ILE* 4.3 9.1 - - + +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLY 5.7 0.2 - - - +
246A ILE* 3.9 5.4 - - + +
261A GLY 3.2 28.2 + - - +
262A ASP* 4.7 7.0 + - - +
263A MET* 3.9 28.8 + - - +
274A GLN* 3.0 20.2 + - - +
275A VAL* 4.8 1.6 - - - -
277A LEU* 1.3 79.0 - - - +
279A PRO* 1.3 70.5 - - + +
280A VAL 3.3 0.2 + - - -
281A LEU* 3.3 3.6 + - - +
282A ALA* 3.0 24.1 + - + +
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Residues in contact with PRO 279 (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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275A VAL 3.2 25.6 - - - +
276A LEU* 3.2 13.7 - - - +
278A THR* 1.3 96.0 - - + +
280A VAL* 1.3 61.1 + - + +
282A ALA* 3.7 5.7 - - + +
283A ASN* 2.7 39.4 + - - +
293A TRP* 4.5 5.4 - - + -
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Residues in contact with VAL 280 (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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211A PHE* 5.8 2.7 - - + -
276A LEU 3.6 17.5 - - - +
277A LEU* 2.9 16.4 + - + +
279A PRO* 1.3 75.0 - - + +
281A LEU* 1.3 68.5 + - + +
283A ASN* 3.1 2.8 + - - -
284A ILE* 3.0 28.7 + - + +
293A TRP* 3.7 27.6 - - + -
298A PHE* 3.9 29.2 - - + -
301A GLU* 4.4 10.5 - - + +
302A THR* 4.1 9.2 - - + -
305A ILE* 4.3 15.7 - - + -
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Residues in contact with LEU 281 (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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208A GLY* 3.5 31.0 - - - +
211A PHE* 3.9 18.6 - - + -
212A TYR* 4.2 24.2 - - + -
246A ILE* 4.1 11.0 - - + -
263A MET* 3.5 32.1 - - + -
277A LEU* 3.1 25.9 + - + +
278A THR 3.7 5.6 - - - +
280A VAL* 1.3 78.8 - - + +
282A ALA* 1.3 54.0 + - - +
284A ILE* 3.1 8.9 + - + -
285A LEU* 2.7 45.8 + - + +
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Residues in contact with ALA 282 (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 LYS* 4.5 2.8 + - - -
244A GLY* 3.6 32.9 + - - +
245A ALA 4.4 5.5 - - - +
246A ILE* 3.6 10.2 - - + +
278A THR* 3.0 19.3 + - + +
279A PRO* 3.7 9.0 - - + +
281A LEU* 1.3 76.2 - - - +
283A ASN* 1.3 65.1 + - - +
285A LEU* 3.9 6.5 + - - -
286A GLU* 3.9 19.2 + - - +
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Residues in contact with ASN 283 (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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279A PRO* 2.7 32.4 + - - +
280A VAL 3.1 0.9 + - - +
281A LEU 3.1 0.4 - - - -
282A ALA* 1.3 80.2 - - - +
284A ILE* 1.3 60.4 + - - +
285A LEU 3.6 0.2 - - - -
286A GLU* 4.4 6.9 - - - +
291A LYS 4.5 5.8 - - - +
292A CYS* 4.0 6.4 - - - -
293A TRP* 3.3 69.9 + - + +
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Residues in contact with ILE 284 (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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204A LEU* 3.7 32.4 - - + +
205A TRP* 3.7 24.1 + - - +
207A ILE* 4.3 4.0 - - + -
208A GLY* 3.6 26.9 - - - +
211A PHE* 5.0 1.1 - - + -
280A VAL* 3.0 25.7 + - + +
281A LEU* 3.6 10.5 - - + +
283A ASN* 1.3 80.2 - - - +
285A LEU* 1.3 58.6 + - - +
286A GLU 3.2 7.2 + - - -
292A CYS* 4.2 13.1 - - - -
293A TRP* 4.0 9.9 - - + -
298A PHE* 3.7 40.8 - - + -
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Residues in contact with LEU 285 (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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205A TRP* 3.1 37.8 - - + +
208A GLY* 3.7 15.0 - - - +
209A VAL* 3.7 33.9 - - + +
212A TYR* 5.2 2.9 - - + -
220A PRO* 4.9 4.9 - - + -
221A PHE* 4.4 8.1 - - + -
241A LYS* 2.4 39.8 + - - +
246A ILE* 3.6 31.6 - - + +
281A LEU* 2.7 30.5 + - + +
282A ALA* 4.1 3.8 - - - +
284A ILE* 1.3 79.9 - - - +
286A GLU* 1.3 51.8 + - - +
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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
------------------------------------------------------------
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