Contacts of the helix formed by residues 270 - 282 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B VAL* 2.6 13.8 + - - +
269B HIS* 1.3 96.7 - - - +
271B PRO* 1.3 62.8 - - + +
272B LEU* 4.3 7.2 - - + +
273B SER* 3.1 14.0 + - - +
274B LEU* 2.8 33.4 + - - +
304B LEU* 3.9 4.2 - - - +
233C VAL* 4.3 5.2 - - + +
234C GLY* 3.3 19.7 + - - +
256C LYS* 2.2 37.1 + - - -
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Residues in contact with PRO 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B HIS 4.0 2.0 - - - +
270B ASP* 1.3 90.3 - - + +
272B LEU* 1.3 66.4 + - + +
274B LEU* 3.1 1.8 + - + -
275B LYS* 3.0 25.7 + - - +
304B LEU* 3.6 17.4 - - + -
307B SER* 5.8 1.8 - - - +
308B MET* 3.6 29.8 - - + +
310B GLU* 4.9 5.8 - - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ASP* 3.2 5.7 - - + +
271B PRO* 1.3 84.3 - - + +
273B SER* 1.3 63.3 + - - +
275B LYS* 3.5 6.8 + - + +
276B LEU* 3.2 21.0 + - - +
276C LEU* 3.5 19.0 - - + +
279C ASP* 4.0 39.5 - - + +
280C VAL* 3.8 26.2 - - + -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.9 19.3 - - - -
270B ASP* 3.1 16.6 + - - +
272B LEU* 1.3 75.3 - - - +
274B LEU* 1.3 66.6 + - - +
276B LEU* 3.3 1.5 + - - +
277B LEU* 3.0 23.9 + - - +
230C PRO 4.2 4.3 + - - -
231C PHE* 2.8 54.6 + - - -
233C VAL* 5.7 0.7 - - - +
234C GLY 5.5 0.2 + - - -
276C LEU* 4.6 2.3 - - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 4.2 23.6 - - + +
268B VAL* 3.6 10.7 - - + +
270B ASP 2.8 13.5 + - - +
271B PRO* 3.1 7.2 + - + +
273B SER* 1.3 76.1 - - - +
275B LYS* 1.3 57.5 + - - +
277B LEU* 3.3 12.7 + - + +
278B THR* 3.1 28.7 + - + -
286B VAL* 4.4 0.4 - - + -
304B LEU* 3.7 29.8 - - + -
305B ILE* 3.9 29.4 - - + -
308B MET* 4.3 6.5 - - + -
311B PHE* 4.1 15.5 - - + -
319B LEU* 4.3 16.2 - - + -
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO 3.0 15.7 + - - +
272B LEU* 3.6 8.1 - - + +
274B LEU* 1.3 75.3 - - - +
276B LEU* 1.3 66.3 + - - +
278B THR* 3.0 12.1 + - - +
279B ASP* 2.9 57.2 + - - +
283B LYS* 5.7 4.0 - - - +
308B MET* 4.2 6.7 - - + -
310B GLU* 3.6 43.0 + - + +
311B PHE* 4.2 11.1 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PRO* 4.2 4.5 - - + +
231B PHE* 4.0 23.3 - - + +
272B LEU 3.2 10.8 + - - +
273B SER* 3.3 6.5 + - - +
275B LYS* 1.3 78.2 - - - +
277B LEU* 1.3 53.8 + - - +
279B ASP* 3.2 7.1 + - - +
280B VAL* 2.8 50.1 + - + +
231C PHE* 3.5 28.7 - - + -
272C LEU* 3.6 44.4 - - + +
273C SER* 4.3 2.0 - - - +
276C LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLY* 3.3 28.5 - - - +
230B PRO* 3.7 13.0 - - + -
264B THR* 3.3 20.6 - - - +
265B ASP 3.6 21.3 - - - +
266B ALA* 3.9 9.0 - - - -
268B VAL* 4.1 8.7 - - + -
273B SER 3.0 12.7 + - - +
274B LEU* 3.4 14.4 - - + +
276B LEU* 1.3 76.2 - - - +
278B THR* 1.3 57.7 + - - +
281B ILE* 2.7 54.7 + - + +
286B VAL* 3.8 20.2 - - + -
231C PHE* 4.5 4.7 - - + -
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.1 18.0 + - + +
275B LYS* 3.0 13.7 + - - +
277B LEU* 1.3 71.8 - - - +
279B ASP* 1.3 67.1 + - - +
282B GLY* 2.8 35.7 + - - +
283B LYS* 3.7 26.2 + - + -
286B VAL* 4.1 11.9 - - + -
311B PHE* 3.7 31.0 - - + -
315B THR* 5.8 0.2 - - + -
319B LEU* 3.9 22.7 - - + -
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B LYS* 2.9 55.8 + - - +
276B LEU* 3.6 6.4 - - - +
278B THR* 1.3 83.2 + - - +
280B VAL* 1.3 61.4 + - - +
282B GLY* 4.5 1.6 + - - -
283B LYS* 4.4 10.4 + - - +
272C LEU* 4.1 35.4 - - + +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PRO* 3.8 32.5 - - + +
233B VAL* 4.3 7.9 - - + -
259B LEU* 3.8 49.2 - - + +
276B LEU* 2.8 38.0 + - + +
277B LEU 4.2 0.9 - - - +
279B ASP* 1.3 77.3 - - - +
281B ILE* 1.3 71.2 + - + +
272C LEU* 4.1 15.7 - - + -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B PHE* 4.7 8.1 - - + -
230B PRO* 4.8 4.9 - - + -
259B LEU* 4.3 7.9 - - + -
260B GLY* 3.8 17.6 - - - +
262B PHE* 3.9 37.7 - - + +
264B THR* 4.1 12.8 - - + +
277B LEU* 2.7 43.4 + - + +
280B VAL* 1.3 88.7 - - + +
282B GLY* 1.3 54.1 + - - +
285B LYS* 3.5 44.4 - - + +
286B VAL* 4.0 9.6 - - + -
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B THR* 2.8 20.9 + - - -
279B ASP 5.0 1.3 - - - -
280B VAL 3.4 1.4 - - - -
281B ILE* 1.3 79.4 - - - +
283B LYS* 1.3 66.4 + - - -
284B ASP 3.3 3.1 - - - -
285B LYS* 3.1 13.7 + - - -
286B VAL* 3.4 16.5 - - - +
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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