Contacts of the helix formed by residues 270 - 282 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A VAL* 4.0 7.8 - - - +
234A GLY* 3.7 19.7 + - - -
256A LYS* 2.9 39.7 + - - -
268F VAL* 2.9 11.3 + - - +
269F HIS* 1.3 78.0 - - - +
271F PRO* 1.3 61.5 - - + +
272F LEU* 4.3 5.7 - - + +
273F SER* 2.9 23.4 + - - +
274F LEU* 2.8 31.5 + - - +
304F LEU* 4.0 3.8 - - - -
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Residues in contact with PRO 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F HIS 4.0 2.2 - - - +
270F ASP* 1.3 90.0 - - + +
272F LEU* 1.3 55.6 + - + +
274F LEU* 3.0 2.0 + - + -
275F LYS* 2.8 33.5 + - - +
304F LEU* 3.5 24.8 - - + -
307F SER* 5.3 2.2 - - - +
308F MET* 3.3 27.7 - - + +
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Residues in contact with LEU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 3.6 24.7 - - + +
279A ASP* 3.4 46.2 - - + +
280A VAL* 4.3 14.8 - - + -
270F ASP* 3.3 5.5 - - + +
271F PRO* 1.3 83.2 - - + +
273F SER* 1.3 62.5 + - - +
275F LYS* 3.6 8.1 + - + +
276F LEU* 3.2 17.7 + - - +
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Residues in contact with SER 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO 4.3 4.2 + - - -
231A PHE* 2.8 52.2 + - - -
233A VAL* 5.6 0.9 - - - +
234A GLY 5.4 0.9 + - - -
276A LEU* 4.5 2.9 - - - +
268F VAL* 3.8 17.8 + - - -
270F ASP* 2.9 22.0 + - - +
272F LEU* 1.3 77.4 - - - +
274F LEU* 1.3 59.0 + - - +
276F LEU* 3.5 1.9 + - - -
277F LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ALA* 3.9 35.9 - - + +
268F VAL* 3.8 10.3 - - + +
270F ASP 2.8 11.5 + - - +
271F PRO* 3.0 9.4 + - + +
273F SER* 1.3 72.7 - - - +
275F LYS* 1.3 67.6 + - - +
277F LEU* 3.2 7.3 + - + +
278F THR* 3.0 33.2 + - + +
286F VAL* 4.7 1.3 - - + -
304F LEU* 4.1 15.3 - - + -
305F ILE* 3.9 22.7 - - + -
308F MET* 3.7 33.9 - - + -
311F PHE* 4.1 9.4 - - + -
319F LEU* 5.4 1.6 - - + -
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Residues in contact with LYS 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F PRO 2.8 15.2 + - - +
272F LEU* 3.8 10.5 - - + +
274F LEU* 1.3 76.9 - - - +
276F LEU* 1.3 61.6 + - - +
278F THR* 2.9 18.5 + - - -
279F ASP* 2.7 53.0 + - - +
283F LYS* 6.4 0.2 - - - +
308F MET* 3.7 8.2 - - + +
310F GLU* 3.9 39.0 - - + +
311F PHE* 4.1 23.1 - - + -
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Residues in contact with LEU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 4.3 10.3 - - + -
272A LEU* 3.6 31.6 - - + +
273A SER* 4.7 2.5 - - - +
276A LEU* 3.4 37.2 - - + -
230F PRO* 4.0 15.5 - - + +
231F PHE* 4.0 15.9 - - + -
272F LEU 3.2 15.2 + - - +
273F SER* 3.8 4.5 - - - +
275F LYS* 1.3 75.4 - - - +
277F LEU* 1.3 67.4 + - - +
279F ASP* 3.2 7.4 + - + +
280F VAL* 2.9 41.2 + - + +
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Residues in contact with LEU 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 4.5 4.5 - - + -
225F GLY* 3.7 23.6 - - - +
230F PRO* 3.9 13.0 - - + -
264F THR* 3.4 18.4 - - - +
265F ASP 3.7 23.6 - - - +
266F ALA* 4.1 10.1 - - - -
268F VAL* 3.9 13.2 - - + -
273F SER 2.9 20.2 + - - +
274F LEU* 3.5 10.8 - - + +
275F LYS 3.2 0.4 - - - -
276F LEU* 1.3 76.3 - - - +
278F THR* 1.3 56.9 + - - +
281F ILE* 3.0 52.0 + - + +
286F VAL* 4.0 14.6 - - + -
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Residues in contact with THR 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F LEU* 3.0 18.5 + - + +
275F LYS 2.9 15.9 + - - -
277F LEU* 1.3 76.0 - - - +
279F ASP* 1.3 64.2 + - - +
282F GLY* 2.9 32.7 + - - +
283F LYS* 3.6 17.7 + - + +
286F VAL* 4.0 26.9 - - + -
311F PHE* 3.2 37.5 - - + -
319F LEU* 4.4 12.8 - - + -
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Residues in contact with ASP 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 4.1 31.7 - - + +
275F LYS* 2.7 57.9 + - - +
276F LEU* 3.8 8.5 - - + +
278F THR* 1.3 79.6 + - - +
280F VAL* 1.3 61.7 + - - +
282F GLY* 4.8 0.9 + - - -
283F LYS* 6.0 2.6 - - - -
311F PHE* 5.8 0.2 - - - -
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 4.2 12.8 - - + -
230F PRO* 3.8 29.4 - - + +
233F VAL* 4.5 9.9 - - + -
259F LEU* 3.7 48.8 - - + +
260F GLY 4.9 0.2 + - - -
276F LEU* 2.9 37.1 + - + +
277F LEU 4.3 1.3 - - - +
279F ASP* 1.3 81.7 - - - +
281F ILE* 1.3 74.0 + - + +
282F GLY 3.5 0.2 - - - -
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Residues in contact with ILE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F PHE* 4.9 7.2 - - + -
230F PRO* 4.7 4.9 - - + -
259F LEU* 4.3 11.9 - - + -
260F GLY* 3.8 23.2 + - - +
262F PHE* 3.9 34.5 - - + +
264F THR* 3.9 13.9 - - + +
277F LEU* 3.0 35.0 + - + +
280F VAL* 1.3 90.8 - - + +
282F GLY* 1.3 54.5 + - - +
285F LYS* 3.8 33.2 - - + +
286F VAL* 3.8 15.0 - - + -
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Residues in contact with GLY 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F THR* 2.9 21.0 + - - -
279F ASP 5.2 0.9 - - - -
280F VAL 3.5 1.4 - - - -
281F ILE* 1.3 76.9 - - - +
283F LYS* 1.3 65.6 + - - -
284F ASP* 3.2 4.0 - - - -
285F LYS* 3.1 14.4 + - - -
286F VAL* 3.4 15.9 - - - +
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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