Contacts of the helix formed by residues 270 - 282 (chain D) in PDB entry 4IGM
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 ASP 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268D VAL* 2.8 13.3 + - - +
269D HIS* 1.3 85.4 - - - +
271D PRO* 1.3 62.0 - - + +
272D LEU* 3.3 3.8 - - + +
273D SER* 3.1 15.8 + - - +
274D LEU* 2.8 34.1 + - - +
304D LEU* 3.9 4.6 - - - +
233E VAL* 4.6 8.6 - - + +
234E GLY* 3.5 29.0 + - - +
256E LYS* 3.8 21.6 + - - -
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Residues in contact with PRO 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D HIS 4.2 0.7 - - - +
270D ASP* 1.3 88.5 - - + +
272D LEU* 1.3 61.0 + - + +
274D LEU* 3.0 2.6 + - + -
275D LYS* 2.7 33.5 + - - +
304D LEU* 3.6 17.7 - - + -
307D SER* 5.8 2.7 - - - +
308D MET* 3.4 33.1 - - + +
309D GLU* 6.0 2.0 - - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ASP* 3.3 3.7 - - + +
271D PRO* 1.3 85.0 - - + +
273D SER* 1.3 64.6 - - - +
275D LYS* 4.0 8.0 - - + +
276D LEU* 3.1 22.5 + - - +
276E LEU* 3.6 19.9 - - + +
279E ASP* 4.3 30.5 - - + +
280E VAL* 4.0 22.0 - - + -
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Residues in contact with SER 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D VAL* 3.8 25.8 - - - -
270D ASP* 3.1 17.7 + - - +
272D LEU* 1.3 76.7 - - - +
274D LEU* 1.3 66.6 + - - +
276D LEU 3.2 0.5 + - - -
277D LEU* 2.9 25.3 + - - +
230E PRO 4.3 3.1 + - - -
231E PHE* 2.6 51.7 + - - -
233E VAL* 5.8 0.3 - - - +
234E GLY 5.3 0.2 + - - -
276E LEU* 4.5 1.3 - - - +
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D ALA* 4.0 31.2 - - + +
268D VAL* 3.5 7.8 - - + +
270D ASP 2.8 17.2 + - - +
271D PRO 3.5 7.0 - - - +
273D SER* 1.3 73.9 - - - +
275D LYS* 1.3 63.1 + - - +
277D LEU* 3.1 10.2 + - + +
278D THR* 2.9 32.5 + - + -
286D VAL* 4.5 2.2 - - + -
304D LEU* 3.6 28.7 - - + -
305D ILE* 3.9 25.1 - - + -
308D MET* 4.1 23.1 - - + -
311D PHE* 4.4 7.9 - - + -
319D LEU* 5.1 2.9 - - + -
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Residues in contact with LYS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PRO 2.7 19.4 + - - +
272D LEU* 4.0 9.0 - - + +
274D LEU* 1.3 72.5 - - - +
276D LEU* 1.3 62.4 + - - +
278D THR* 2.9 26.2 + - - +
279D ASP* 3.0 46.1 + - - +
283D LYS* 6.2 2.5 - - - +
308D MET* 3.7 11.4 - - + +
310D GLU* 3.6 39.0 - - + +
311D PHE* 4.3 13.9 - - + -
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PRO* 3.7 19.1 - - + +
231D PHE* 4.1 9.4 - - + -
272D LEU 3.1 19.5 + - - +
273D SER* 3.2 3.8 + - - +
275D LYS* 1.3 75.8 - - - +
277D LEU* 1.3 57.4 + - - +
279D ASP* 3.2 5.5 + - + +
280D VAL* 2.9 43.2 + - + +
231E PHE* 3.8 17.0 - - + -
272E LEU* 3.6 47.6 - - + +
273E SER* 4.8 0.9 - - - +
276E LEU* 3.6 29.6 - - + -
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D GLY* 3.6 24.9 - - - +
230D PRO* 3.9 13.0 - - + -
264D THR* 3.3 19.7 - - - +
265D ASP 3.6 22.4 - - - +
266D ALA* 4.0 11.2 - - - -
268D VAL* 3.9 14.1 - - + -
273D SER 2.9 13.2 + - - +
274D LEU* 3.3 14.1 - - + +
276D LEU* 1.3 76.4 - - - +
278D THR* 1.3 56.0 + - - +
280D VAL 3.3 0.2 + - - -
281D ILE* 2.9 56.9 + - + +
286D VAL* 3.9 14.8 - - + -
231E PHE* 4.4 5.3 - - + -
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Residues in contact with THR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D LEU* 2.9 22.3 + - + +
275D LYS* 2.9 19.4 + - - +
277D LEU* 1.3 75.7 - - - +
279D ASP* 1.3 62.8 + - - +
282D GLY* 2.9 35.8 + - - +
283D LYS* 3.6 20.3 + - + +
286D VAL* 4.3 7.9 - - + -
311D PHE* 3.7 31.8 - - + -
319D LEU* 4.1 25.8 - - + -
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Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LYS* 3.0 56.2 + - - +
276D LEU* 3.5 7.8 - - - +
278D THR* 1.3 82.5 + - - +
280D VAL* 1.3 60.3 + - - +
282D GLY* 4.6 0.7 - - - -
283D LYS* 5.6 4.7 - - - -
272E LEU* 4.0 32.3 - - + +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D PHE* 5.8 0.2 - - + -
230D PRO* 3.8 31.2 - - + +
233D VAL* 4.1 19.5 - - + -
259D LEU* 3.7 45.1 - - + +
260D GLY 5.0 0.2 + - - -
276D LEU* 2.9 26.5 + - + +
277D LEU 4.2 0.9 - - - +
279D ASP* 1.3 80.3 - - - +
281D ILE* 1.3 66.6 + - + +
282D GLY* 3.4 1.2 + - - -
272E LEU* 3.8 21.3 - - + -
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Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D PHE* 4.8 6.1 - - + -
230D PRO* 4.7 12.6 - - + -
259D LEU* 4.7 9.6 - - + -
260D GLY* 4.0 18.4 + - - +
262D PHE* 3.8 31.9 - - + +
264D THR* 3.9 21.1 - - + -
277D LEU* 2.9 37.9 + - + +
280D VAL* 1.3 74.9 - - + +
282D GLY* 1.3 59.8 + - - +
285D LYS* 3.5 43.7 - - + +
286D VAL* 4.1 6.5 - - + -
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Residues in contact with GLY 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D THR* 2.9 19.8 + - - -
279D ASP 5.2 0.9 - - - -
280D VAL 3.4 1.6 - - - -
281D ILE* 1.3 80.5 - - - +
283D LYS* 1.3 64.3 + - - -
284D ASP 3.2 3.1 - - - -
285D LYS* 3.4 10.3 + - - -
286D VAL* 3.4 18.5 - - - +
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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