Contacts of the helix formed by residues 271 - 288 (chain E) in PDB entry 6IGM
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 ILE 271 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D GLN* 4.6 14.6 - - - +
125D ARG* 3.5 35.9 - - - +
245D HIS* 6.4 2.9 - - + -
258D LEU 5.5 2.7 - - - +
259D ALA 6.0 1.1 - - - -
260D LEU 3.4 15.7 - - - +
261D PHE* 3.6 23.6 - - - +
269E THR* 6.4 0.7 - - + -
270E GLU* 1.3 80.7 - - - +
272E THR* 1.3 62.0 + - - +
273E ASP* 3.1 33.2 + - + +
274E LYS* 3.6 5.0 + - - +
275E LEU* 3.7 9.1 + - - +
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Residues in contact with THR 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D THR* 5.8 1.7 - - - +
107D GLU* 4.1 20.0 - - - +
125D ARG* 3.7 21.9 + - - +
270E GLU* 5.1 4.0 - - + +
271E ILE* 1.3 73.2 - - - +
273E ASP* 1.3 59.5 + - - +
274E LYS 3.6 0.2 - - - -
275E LEU* 3.7 23.8 - - + -
276E ARG* 2.9 54.6 + - - +
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Residues in contact with ASP 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D HIS* 4.7 12.8 + - - -
259D ALA 3.5 18.4 - - - +
260D LEU* 3.1 22.3 - - - +
271E ILE* 3.3 18.9 - - + +
272E THR* 1.3 72.5 + - - +
274E LYS* 1.3 75.0 + - - +
276E ARG* 5.3 0.2 - - - -
277E GLY* 2.9 28.2 + - - +
278E GLU* 3.4 9.0 + - + +
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Residues in contact with LYS 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.7 59.7 - - + +
261D PHE* 4.2 13.6 - - - +
244E ASP* 3.5 22.8 + - - -
247E ASN* 3.4 48.6 - - + +
248E ALA* 5.3 1.2 - - - +
270E GLU* 4.9 4.5 + - - +
271E ILE 3.6 1.5 + - - +
273E ASP* 1.3 82.4 + - - +
275E LEU* 1.3 65.5 + - - +
278E GLU* 3.6 26.2 - - + +
279E ILE* 3.5 18.2 + - + +
1970H SER* 5.4 3.1 - - - +
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Residues in contact with LEU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E MET* 3.7 26.0 - - + -
117E ARG* 2.6 59.8 + - + +
244E ASP* 4.4 8.7 - - - +
270E GLU* 3.4 39.0 - - + +
271E ILE 3.7 6.2 + - - +
272E THR* 3.5 32.3 + - + +
273E ASP 3.2 0.6 - - - -
274E LYS* 1.3 82.2 - - - +
276E ARG* 1.3 62.7 - - + +
279E ILE* 3.3 15.6 - - + +
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Residues in contact with ARG 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PHE 5.4 5.1 + - - -
101D THR* 5.7 1.8 - - - +
102D ALA* 4.4 25.9 + - - +
117E ARG* 4.6 2.7 - - - +
272E THR* 2.9 39.3 + - - +
273E ASP* 5.3 0.2 - - - -
275E LEU* 1.3 85.3 - - + +
277E GLY* 1.3 60.6 + - - +
278E GLU 3.6 0.4 - - - -
279E ILE 3.6 0.2 + - - -
280E ASN* 2.8 46.6 + - - +
317E ARG* 4.7 11.5 - - - +
321E SER* 5.8 2.0 + - - -
323E ILE* 6.5 0.2 - - + -
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Residues in contact with GLY 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E ASP* 2.9 13.6 + - - +
276E ARG* 1.3 76.5 - - - +
278E GLU* 1.3 59.3 + - - +
280E ASN* 4.7 3.1 - - - -
281E LYS* 2.9 50.5 + - - +
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Residues in contact with GLU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 4.9 10.5 - - + -
273E ASP* 3.4 5.3 + - - +
274E LYS* 3.6 37.0 + - + +
276E ARG 3.6 0.2 - - - -
277E GLY* 1.3 75.9 - - - +
279E ILE* 1.3 60.0 + - - +
281E LYS* 4.6 11.6 + - - +
282E VAL* 3.5 24.1 - - - +
1968H GLN 5.1 4.0 - - - +
1970H SER* 5.3 9.4 + - - +
1976H PHE* 4.7 20.0 - - - -
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Residues in contact with ILE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG* 4.1 26.9 - - - +
240E LEU* 4.4 20.2 - - + +
243E LEU* 5.9 6.1 - - + -
244E ASP* 5.1 11.2 - - + +
247E ASN* 4.8 17.5 - - - +
274E LYS* 3.5 13.6 + - + +
275E LEU* 3.3 30.1 - - + +
276E ARG 3.6 1.0 + - - +
277E GLY 3.1 0.4 - - - -
278E GLU* 1.3 80.3 - - + +
280E ASN* 1.3 64.3 + - - +
281E LYS 3.3 0.4 - - - -
282E VAL* 3.3 8.2 - - + +
283E VAL* 3.0 43.9 + - + +
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Residues in contact with ASN 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU* 4.4 10.5 - - - +
117E ARG* 5.3 6.8 + - - +
275E LEU 4.9 0.8 + - - -
276E ARG* 2.8 38.9 + - - +
277E GLY* 4.3 2.7 - - - +
279E ILE* 1.3 82.0 - - - +
281E LYS* 1.3 58.2 + - + +
283E VAL* 3.8 8.5 - - - +
284E ASN* 2.9 30.3 + - - +
323E ILE* 3.6 32.5 - - - +
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Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E GLY* 2.9 30.4 + - - +
278E GLU* 5.2 10.7 + - - +
280E ASN* 1.3 77.9 - - + +
282E VAL* 1.3 62.2 + - + +
284E ASN* 3.3 6.5 + - - +
285E LYS* 2.9 44.8 + - - +
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Residues in contact with VAL 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E GLU* 3.5 19.9 + - - +
279E ILE* 3.3 17.0 - - + +
281E LYS* 1.3 77.2 - - + +
283E VAL* 1.3 62.5 + - + +
285E LYS* 3.4 12.9 + - + +
286E TYR* 2.9 54.1 + - + +
1967H ASP 5.0 10.5 - - - +
1968H GLN* 4.6 21.3 - - + +
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Residues in contact with VAL 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG 5.5 0.2 - - - +
20D GLU* 4.6 13.5 - - - +
122E LEU* 4.4 32.5 - - + -
240E LEU* 5.6 1.8 - - + -
279E ILE* 3.0 35.2 + - + +
280E ASN* 3.8 9.0 - - - +
281E LYS 3.3 0.2 - - - -
282E VAL* 1.3 80.4 - - + +
284E ASN* 1.3 57.4 + - - +
286E TYR* 3.2 4.8 + - + -
287E ILE* 2.9 52.2 + - + +
292E ALA* 6.0 0.2 - - + -
294E LEU* 4.9 6.7 - - + -
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Residues in contact with ASN 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 3.3 37.3 + - - +
280E ASN 2.9 19.0 + - - +
281E LYS* 3.3 6.0 + - - +
283E VAL* 1.3 77.3 - - - +
285E LYS* 1.3 59.4 + - + +
286E TYR 3.5 0.3 + - - -
288E ASP* 3.0 29.4 + - - +
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Residues in contact with LYS 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E LYS* 2.9 30.5 + - - +
282E VAL* 3.9 11.6 - - + +
283E VAL 3.3 0.2 - - - -
284E ASN* 1.3 76.9 - - + +
286E TYR* 1.3 71.5 + - + +
288E ASP* 2.9 17.0 - - - +
289E GLN* 4.0 10.9 - - - +
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Residues in contact with TYR 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E VAL* 2.9 35.7 + - + +
283E VAL* 3.2 3.3 + - + +
285E LYS* 1.3 91.8 - - + +
287E ILE* 1.3 64.0 + - - +
288E ASP 3.5 0.2 - - - -
289E GLN* 3.9 16.3 + - - +
290E GLY 3.9 2.1 + - - -
291E ILE* 3.5 20.5 + - + +
292E ALA* 3.2 33.8 + - + +
1964H GLN 5.1 4.0 - - - -
1967H ASP* 3.3 32.7 + - + +
1968H GLN* 3.6 38.4 - - + -
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Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 3.4 30.3 - - + +
19D ILE* 3.8 39.0 - - + +
20D GLU* 5.4 0.9 - - - +
122E LEU* 5.8 0.4 - - + -
283E VAL* 2.9 37.8 + - + +
284E ASN 3.8 0.2 + - - -
286E TYR* 1.3 77.4 - - - +
288E ASP* 1.3 63.2 + - - +
290E GLY* 3.1 15.9 + - - -
292E ALA* 3.4 28.7 - - + +
293E GLU* 4.8 1.6 - - - +
294E LEU* 4.2 16.8 - - + +
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Residues in contact with ASP 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 4.4 20.4 - - - +
284E ASN* 3.0 19.9 + - - +
285E LYS* 2.9 26.2 - - - +
287E ILE* 1.3 77.0 - - - +
289E GLN* 1.3 62.2 + - - +
290E GLY* 4.8 0.2 - - - -
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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