Contacts of the helix formed by residues 231 - 242 (chain U) in PDB entry 1FM6
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 PRO 231 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A PRO* 6.0 1.3 - - + -
227U ASN* 3.6 33.2 - - + +
228U GLU* 5.0 3.1 - - + +
230U MET* 1.3 86.8 - - - +
232U VAL* 1.3 64.3 + - - +
233U GLU* 3.0 31.4 + - - +
234U ARG* 3.1 37.9 + - + +
235U ILE* 3.2 10.9 + - - +
287U PRO* 3.7 14.6 - - + -
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Residues in contact with VAL 232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230U MET 3.4 2.4 + - - -
231U PRO* 1.3 72.1 - - + +
233U GLU* 1.3 68.9 + - + +
235U ILE* 3.6 9.3 - - + +
236U LEU* 2.8 30.5 + - - +
365U THR* 3.9 16.5 - - + +
369U CYS* 3.7 27.1 - - - -
399U SER* 3.8 31.0 - - - +
403U TYR* 4.2 21.3 - - + -
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Residues in contact with GLU 233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 5.3 0.4 - - - +
274A LYS* 3.7 39.7 - - + +
277A PHE* 3.5 38.8 - - + -
227U ASN* 4.7 0.3 - - - +
231U PRO* 3.0 25.0 + - - +
232U VAL* 1.3 95.4 + - + +
234U ARG* 1.3 58.2 + - + +
236U LEU* 3.1 10.1 + - - +
237U GLU* 2.8 36.7 + - - +
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Residues in contact with ARG 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO* 4.4 2.0 - - - +
259A SER* 3.5 34.1 - - - +
270A GLN* 4.6 23.1 + - - +
448A ASP* 5.0 10.5 + - - +
227U ASN 5.0 6.2 - - - +
231U PRO* 3.1 30.0 + - + +
233U GLU* 1.3 78.1 - - + +
235U ILE* 1.3 66.4 + - - +
237U GLU* 3.3 17.8 + - - +
238U ALA* 3.1 21.8 + - - +
284U LYS 5.5 1.6 + - - -
285U ARG* 4.2 15.1 + - - +
286U ILE 4.6 1.0 + - - -
287U PRO* 3.7 38.4 - - + +
288U HIS 4.7 1.4 - - - +
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Residues in contact with ILE 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230U MET* 4.1 22.9 - - + -
231U PRO 3.2 13.5 + - - +
232U VAL* 3.6 12.8 - - + +
233U GLU 3.2 0.6 - - - -
234U ARG* 1.3 76.6 - - - +
236U LEU* 1.3 65.9 + - - +
238U ALA* 3.0 6.6 + - - +
239U GLU* 3.0 18.9 + - - +
286U ILE* 4.2 18.2 - - + -
287U PRO* 3.9 17.9 - - + -
365U THR 4.6 1.3 - - - +
368U GLY* 3.5 35.4 - - - +
369U CYS* 3.9 22.4 - - - +
372U ALA* 4.7 11.7 - - + -
396U VAL* 4.8 6.3 - - + -
399U SER* 5.7 0.9 - - - -
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Residues in contact with LEU 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE* 3.9 27.1 - - + -
635B ARG* 3.8 20.6 - - - +
636B LEU* 5.5 2.7 - - + -
232U VAL 2.8 18.5 + - - +
233U GLU* 3.1 6.7 + - - +
235U ILE* 1.3 77.6 - - - +
237U GLU* 1.3 56.6 + - - +
239U GLU* 3.1 9.0 + - - +
240U LEU* 2.9 51.4 + - + +
364U LYS* 3.9 17.5 - - + +
365U THR* 3.5 30.5 - - - +
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Residues in contact with GLU 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.3 36.1 - - - +
277A PHE* 3.9 15.8 - - + -
448A ASP* 3.5 16.2 - - - +
449A THR* 3.1 38.0 + - - +
632B ILE* 5.7 0.7 - - + -
233U GLU* 2.8 20.2 + - - +
234U ARG* 3.7 21.9 + - - +
236U LEU* 1.3 71.3 - - + +
238U ALA* 1.3 56.6 + - - +
240U LEU* 3.5 10.7 - - + +
241U ALA* 2.6 38.3 + - - +
285U ARG* 5.9 0.4 - - - -
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Residues in contact with ALA 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234U ARG 3.1 12.6 + - - +
235U ILE 3.0 10.7 + - - +
237U GLU* 1.3 75.5 - - - +
239U GLU* 1.3 60.1 + - - +
241U ALA* 4.6 4.0 - - - -
242U VAL* 2.8 33.1 + - - +
282U TRP* 3.6 19.0 - - + +
285U ARG* 3.7 31.3 - - + +
286U ILE* 3.9 12.1 - - + -
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Residues in contact with GLU 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235U ILE 3.0 9.3 + - - +
236U LEU* 3.1 11.4 + - - +
238U ALA* 1.3 78.5 - - - +
240U LEU* 1.3 62.3 + - + +
242U VAL* 3.8 8.0 - - - +
243U GLU 3.0 17.3 - - - +
282U TRP* 2.8 28.6 + - - -
312U SER* 4.2 3.3 + - - -
364U LYS* 3.5 53.4 + - + +
367U LEU* 3.4 16.5 - - + +
368U GLY* 3.4 21.2 - - - +
371U ARG* 3.3 22.7 + - - -
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Residues in contact with LEU 240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE* 5.6 0.4 - - + -
449A THR* 5.4 4.0 - - + -
632B ILE* 3.7 35.7 - - + -
635B ARG* 3.5 29.6 - - - +
236U LEU* 2.9 46.3 + - + +
237U GLU* 3.5 12.3 - - + +
239U GLU* 1.3 75.8 - - - +
241U ALA* 1.3 62.3 + - - +
243U GLU 2.6 22.7 - - - +
244U PRO* 4.6 2.8 - - - +
364U LYS* 4.3 16.8 - - + +
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Residues in contact with ALA 241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A THR* 4.6 15.8 + - + +
237U GLU 2.6 20.8 + - - +
238U ALA* 4.0 3.4 - - - +
240U LEU* 1.3 73.4 - - - +
242U VAL* 1.3 52.0 + - + +
243U GLU* 2.4 22.0 + - - +
285U ARG* 3.7 34.1 - - - +
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Residues in contact with VAL 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238U ALA* 2.8 23.3 + - - +
239U GLU* 3.8 8.8 - - - +
241U ALA* 1.3 71.4 - - + +
243U GLU* 1.3 76.8 + - - +
275U GLN* 4.8 1.9 - - - +
278U THR* 3.3 27.3 - - + +
281U GLU* 4.0 8.5 - - + +
282U TRP* 3.4 53.4 - - + +
285U ARG* 4.7 7.9 - - - +
371U ARG* 5.0 4.5 - - - +
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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