Contacts of the helix formed by residues 363 - 376 (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 ASP 363 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315U HIS* 4.0 4.5 - - - -
361U GLN 3.4 2.1 + - - +
362U MET* 1.3 75.7 - - - +
364U LYS* 1.3 58.9 + - - +
365U THR* 3.0 5.9 + - - -
366U GLU* 2.8 48.1 + - - +
367U LEU* 2.8 28.9 + - - +
403U TYR* 2.7 26.5 + - - -
408U TYR* 2.8 31.9 + - - +
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Residues in contact with LYS 364 (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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635B ARG* 4.8 12.8 - - - +
236U LEU* 3.9 19.2 - - + -
239U GLU* 3.5 57.1 + - + +
240U LEU* 4.3 12.1 - - + -
244U PRO* 4.0 23.8 - - - +
315U HIS* 4.4 15.1 + - + -
363U ASP* 1.3 73.8 - - - +
365U THR* 1.3 60.8 + - - +
367U LEU* 4.1 16.8 - - + +
368U GLY* 3.0 20.1 + - - -
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Residues in contact with THR 365 (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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232U VAL* 3.9 36.3 - - + +
235U ILE* 4.6 0.7 - - - +
236U LEU* 3.5 32.2 - - - +
363U ASP* 3.0 9.4 + - - -
364U LYS* 1.3 76.5 - - - +
366U GLU* 1.3 62.5 + - - +
368U GLY* 3.3 1.9 + - - -
369U CYS* 2.9 30.1 + - - -
403U TYR* 3.7 36.3 + - + -
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Residues in contact with GLU 366 (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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362U MET* 3.2 5.7 - - + -
363U ASP* 2.8 50.9 + - - +
365U THR* 1.3 73.9 - - - +
367U LEU* 1.3 66.0 + - - +
369U CYS* 3.2 1.7 + - - +
370U LEU* 3.0 28.8 + - - +
400U LEU* 4.0 9.8 - - + +
403U TYR* 3.7 15.0 - - + -
404U CYS* 3.7 3.6 - - - -
408U TYR* 3.3 7.9 - - - -
414U ARG* 2.7 41.3 + - - -
418U LEU* 3.4 35.2 - - + +
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Residues in contact with LEU 367 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239U GLU* 3.4 25.1 - - - +
311U ALA* 3.7 18.6 - - + +
312U SER* 4.9 5.4 - - - +
315U HIS* 3.7 49.4 - - + +
357U MET* 4.6 5.4 - - + -
362U MET* 4.0 14.3 - - - -
363U ASP 2.8 17.7 + - - +
364U LYS* 3.9 17.9 - - + +
366U GLU* 1.3 77.8 - - - +
368U GLY* 1.3 60.9 + - - +
370U LEU* 3.3 5.7 + - + +
371U ARG* 3.1 36.4 + - + +
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Residues in contact with GLY 368 (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* 3.5 21.9 - - - +
239U GLU* 3.4 24.2 - - - -
282U TRP* 4.0 3.1 - - - -
364U LYS 3.0 15.6 + - - -
365U THR 3.6 4.0 - - - -
366U GLU 3.2 0.2 - - - -
367U LEU* 1.3 79.3 - - - +
369U CYS* 1.3 55.0 + - - +
371U ARG* 3.5 4.2 + - - +
372U ALA* 3.1 22.7 + - - +
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Residues in contact with CYS 369 (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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232U VAL* 3.7 30.5 - - - -
235U ILE* 4.1 17.7 - - - -
365U THR* 2.9 24.6 + - - +
366U GLU 3.2 1.1 + - - +
368U GLY* 1.3 73.6 - - - +
370U LEU* 1.3 65.7 + - - +
372U ALA* 3.3 1.6 + - - +
373U ILE* 3.0 28.4 + - - +
396U VAL* 3.3 12.8 - - + +
399U SER* 5.6 0.4 - - - -
400U LEU* 3.5 40.8 - - + -
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Residues in contact with LEU 370 (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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357U MET* 6.3 0.7 - - + -
362U MET* 3.5 34.8 - - + -
366U GLU 3.0 19.6 + - - +
367U LEU* 3.8 5.8 - - + +
369U CYS* 1.3 76.5 - - - +
371U ARG* 1.3 57.8 + - + +
373U ILE* 3.3 15.3 + - + +
374U VAL* 3.0 32.9 + - - +
400U LEU* 4.3 10.5 - - + -
418U LEU* 3.6 38.6 - - + +
419U LEU* 4.2 2.7 - - - +
421U ARG* 4.4 6.5 - - + -
422U LEU* 3.9 29.5 - - + +
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Residues in contact with ARG 371 (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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239U GLU* 3.3 28.1 + - - -
242U VAL* 5.0 3.8 - - - +
279U LEU* 3.8 19.4 - - - +
282U TRP* 3.5 49.2 - - + +
308U LEU* 2.9 47.7 + - + +
309U LEU* 4.2 6.9 - - - +
311U ALA* 4.2 16.4 - - + -
312U SER* 2.7 26.6 + - - -
367U LEU* 3.1 30.5 + - + +
368U GLY 3.7 0.9 - - - +
370U LEU* 1.3 75.9 - - + +
372U ALA* 1.3 59.1 + - - +
374U VAL* 3.3 2.4 + - - -
375U LEU* 2.9 24.4 + - - +
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Residues in contact with ALA 372 (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* 4.7 6.3 - - + -
282U TRP* 3.8 9.1 - - + -
286U ILE* 4.3 22.9 - - + -
368U GLY 3.1 14.9 + - - +
369U CYS* 3.6 9.4 - - - +
370U LEU 3.3 0.2 - - - -
371U ARG* 1.3 73.4 - - - +
373U ILE* 1.3 60.6 + - - +
375U LEU* 3.2 5.4 + - - +
376U PHE* 2.9 35.2 + - + -
396U VAL* 4.1 19.7 - - + -
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Residues in contact with ILE 373 (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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369U CYS 3.0 20.9 + - - +
370U LEU* 3.4 17.9 - - + +
371U ARG 3.2 0.2 - - - -
372U ALA* 1.3 78.9 - - - +
374U VAL* 1.3 55.0 + - - +
376U PHE* 3.5 4.4 + - - +
393U ARG* 2.8 48.1 + - - +
396U VAL* 3.5 21.5 - - + -
397U TYR* 3.7 28.5 - - + +
400U LEU* 4.5 6.3 - - + -
419U LEU* 3.8 17.9 - - + -
422U LEU* 4.2 10.5 - - + -
437X GLN* 3.6 27.4 - - - +
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Residues in contact with VAL 374 (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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304U GLY* 4.4 14.6 - - - +
307U GLU* 3.9 33.2 - - + +
308U LEU* 3.8 16.4 - - + +
370U LEU 3.0 17.4 + - - +
371U ARG* 3.5 8.5 - - - +
372U ALA 3.2 0.2 - - - -
373U ILE* 1.3 79.0 - - + +
375U LEU* 1.3 63.3 + - - +
377U ASN* 3.5 16.8 + - - +
393U ARG* 4.0 5.6 - - - +
422U LEU* 4.3 14.8 - - + -
425U LEU* 4.1 22.9 - - + -
426U ARG* 5.1 5.6 + - - +
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Residues in contact with LEU 375 (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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282U TRP* 3.8 23.1 - - + -
283U ALA* 4.5 3.4 - - + -
286U ILE* 4.3 13.0 - - + -
289U PHE* 3.6 42.2 - - + -
300U LEU* 3.6 31.5 - - + +
301U LEU* 4.0 20.4 - - + -
308U LEU* 4.3 10.8 - - + -
371U ARG 2.9 14.7 + - - +
372U ALA* 3.2 8.5 + - - +
374U VAL* 1.3 78.0 - - - +
376U PHE* 1.3 73.7 + - + +
377U ASN* 2.9 8.0 + - - +
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Residues in contact with PHE 376 (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* 3.7 22.4 - - + -
286U ILE* 3.8 20.9 - - + -
287U PRO 3.7 13.9 - - - -
289U PHE* 3.8 29.2 - + + -
292U LEU* 4.5 0.7 - - + -
300U LEU* 3.9 15.3 - - + -
372U ALA* 2.9 27.0 + - + +
373U ILE 3.6 4.7 - - - +
374U VAL 3.4 0.6 - - - -
375U LEU* 1.3 71.6 - - + +
377U ASN* 1.3 58.8 + - - +
378U PRO* 3.2 7.6 - - - +
389U VAL* 3.4 23.4 - - + +
392U LEU* 3.3 44.0 - - + -
393U ARG* 2.9 29.6 + - + +
396U VAL* 4.3 8.1 - - + -
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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