Contacts of the helix formed by residues 270 - 282 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D VAL* 4.2 7.3 - - + +
234D GLY* 3.4 25.4 + - - -
256D LYS* 2.8 37.9 + - - -
268E VAL* 3.0 11.1 + - - +
269E HIS* 1.3 82.3 - - - +
271E PRO* 1.4 73.2 - - + +
272E LEU* 4.3 7.4 - - + +
273E SER* 3.0 25.1 + - - +
274E LEU* 3.0 10.6 + - - +
304E LEU* 4.0 3.8 - - - +
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Residues in contact with PRO 271 (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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269E HIS 4.3 1.3 - - - +
270E ASP* 1.4 88.4 - - + +
272E LEU* 1.3 62.4 + - + +
274E LEU* 3.8 1.6 - - + -
275E LYS* 3.0 30.1 + - - +
304E LEU* 3.8 15.9 - - + -
307E SER* 5.4 2.2 - - - +
308E MET* 3.6 30.0 - - + +
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Residues in contact with LEU 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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230D PRO 6.0 0.2 - - - +
276D LEU* 3.6 25.9 - - + +
279D ASP* 4.0 36.1 - - + +
280D VAL* 3.8 25.6 - - + -
270E ASP* 3.1 5.5 + - + -
271E PRO* 1.3 82.0 - - + +
273E SER* 1.3 65.3 + - - +
275E LYS* 3.6 5.7 + - + +
276E LEU* 3.2 17.5 + - - +
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Residues in contact with SER 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D PRO 4.1 4.5 + - - -
231D PHE* 2.8 52.7 + - - -
233D VAL* 5.7 0.9 - - - +
234D GLY 5.6 0.3 + - - -
276D LEU* 4.8 1.6 - - - +
268E VAL* 3.6 22.6 + - - -
270E ASP* 3.0 16.1 + - - +
272E LEU* 1.3 77.9 - - - +
274E LEU* 1.3 58.5 + - - +
276E LEU* 3.4 1.5 + - - -
277E LEU* 2.8 30.3 + - - +
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Residues in contact with LEU 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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266E ALA* 3.8 35.2 - - + +
268E VAL* 3.5 4.5 - - + +
270E ASP 3.0 11.6 + - - +
271E PRO* 3.8 7.9 - - + +
273E SER* 1.3 75.6 - - - +
275E LYS* 1.3 65.6 + - - +
277E LEU* 2.9 23.5 + - + +
278E THR* 3.0 17.3 + - + -
286E VAL* 4.5 6.7 - - + -
304E LEU* 4.0 19.7 - - + -
305E ILE* 3.9 26.5 - - + -
308E MET* 4.0 23.1 - - + -
311E PHE* 4.3 13.2 - - + -
319E LEU* 5.3 1.8 - - + -
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Residues in contact with LYS 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E PRO 3.0 18.4 + - - +
272E LEU* 3.9 7.9 - - + +
274E LEU* 1.3 74.9 - - - +
276E LEU* 1.3 64.0 + - - +
278E THR* 3.0 8.8 + - - -
279E ASP* 2.9 59.1 + - - +
283E LYS* 5.5 2.6 - - - +
308E MET* 4.0 12.9 - - + +
310E GLU* 3.3 44.8 + - + +
311E PHE* 4.0 24.8 - - + -
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Residues in contact with LEU 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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231D PHE* 3.7 19.1 - - + -
272D LEU* 3.6 35.7 - - + +
273D SER* 4.5 1.6 - - - +
276D LEU* 3.6 32.3 - - + -
230E PRO* 4.2 5.2 - - + +
231E PHE* 4.0 23.1 - - + +
272E LEU 3.2 16.0 + - - +
273E SER 3.8 2.2 - - - +
275E LYS* 1.3 77.0 - - - +
277E LEU* 1.3 53.8 + - - +
279E ASP* 3.1 6.8 + - - -
280E VAL* 2.7 61.1 + - + +
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Residues in contact with LEU 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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231D PHE* 4.5 6.7 - - + -
225E GLY* 3.6 25.1 - - - +
230E PRO* 3.9 11.0 - - + -
264E THR* 3.5 26.0 - - - +
265E ASP 3.7 12.8 - - - +
266E ALA* 4.0 13.7 - - - -
268E VAL* 4.2 8.7 - - + -
273E SER 2.8 17.6 + - - +
274E LEU* 2.9 11.0 + - + +
276E LEU* 1.3 77.7 - - - +
278E THR* 1.3 53.5 + - - +
280E VAL* 3.7 0.2 - - - -
281E ILE* 2.7 53.1 + - + +
286E VAL* 3.8 14.6 - - + -
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Residues in contact with THR 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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274E LEU* 3.0 14.1 + - + +
275E LYS 3.0 14.0 + - - -
277E LEU* 1.3 75.1 - - - +
279E ASP* 1.3 61.4 + - - +
282E GLY* 2.8 41.8 + - - +
283E LYS* 3.7 12.8 + - - +
286E VAL* 4.0 15.7 - - + -
311E PHE* 3.2 33.0 - - + -
315E THR* 6.0 0.4 - - + -
319E LEU* 4.0 27.6 - - + -
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Residues in contact with ASP 279 (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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272D LEU* 4.3 29.2 - - + +
275E LYS* 2.9 52.0 + - - +
276E LEU* 3.6 7.6 - - + +
278E THR* 1.3 81.0 + - - +
280E VAL* 1.3 62.7 + - - +
282E GLY* 4.8 0.9 + - - -
283E LYS* 4.5 11.6 + - - -
311E PHE* 5.6 0.2 - - - -
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Residues in contact with VAL 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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272D LEU* 4.0 13.0 - - + -
230E PRO* 3.6 36.8 - - + +
233E VAL* 4.0 9.9 - - + -
259E LEU* 3.7 44.5 - - + +
276E LEU* 2.7 45.8 + - + +
279E ASP* 1.3 77.7 - - - +
281E ILE* 1.3 66.1 + - + +
282E GLY 3.5 0.3 + - - -
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Residues in contact with ILE 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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229E PHE* 4.4 11.2 - - + -
230E PRO* 4.7 4.9 - - + -
259E LEU* 4.4 6.7 - - + -
260E GLY* 3.7 26.5 + - - +
262E PHE* 3.6 42.8 - - + +
264E THR* 4.2 11.7 - - + -
277E LEU* 2.7 40.2 + - + +
280E VAL* 1.3 84.7 - - + +
282E GLY* 1.3 55.3 + - - +
285E LYS* 3.5 37.2 - - + +
286E VAL* 4.2 7.2 - - + -
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Residues in contact with GLY 282 (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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278E THR* 2.8 24.6 + - - -
279E ASP 5.2 0.7 - - - -
280E VAL 3.4 1.2 - - - -
281E ILE* 1.3 76.1 - - - +
283E LYS* 1.3 66.1 + - - -
284E ASP* 3.1 5.6 + - - -
285E LYS* 3.3 10.2 + - - -
286E VAL* 3.7 14.6 - - - +
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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