Contacts of the helix formed by residues 354 - 365 (chain M) in PDB entry 2DFS
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 HIS 354 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337M ASN 4.4 2.0 - - - -
338M VAL* 4.1 6.3 - - + -
339M GLU* 3.0 36.5 + - + -
350M ILE* 3.5 35.0 - - + -
351M PRO* 3.6 24.8 - - + +
352M PRO 4.5 0.2 - - - -
353M LYS* 1.3 73.6 - - - +
355M ASP* 1.3 56.1 + - - +
356M PRO* 3.4 29.1 - - + +
357M LEU* 3.1 10.5 + - + +
358M THR* 2.7 37.5 + - - -
368M TYR* 3.1 10.5 + - - +
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Residues in contact with ASP 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284M TYR* 5.9 2.7 - - - +
353M LYS* 2.6 33.4 + - - +
354M HIS* 1.3 71.1 + - - +
356M PRO* 1.3 71.5 - - + +
358M THR* 3.9 2.4 - - - -
359M ILE* 3.3 32.1 + - + +
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Residues in contact with PRO 356 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284M TYR* 5.9 2.9 - - - +
334M HIS* 3.6 39.9 - - - +
337M ASN* 3.3 35.0 - - + +
338M VAL* 4.1 1.1 - - - +
354M HIS* 3.4 26.7 - - + +
355M ASP* 1.3 95.5 - - + +
357M LEU* 1.3 56.8 + - - +
359M ILE* 3.5 0.9 + - - +
360M PHE* 3.0 25.8 + - - +
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Residues in contact with LEU 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335M LEU* 5.3 0.2 - - + -
338M VAL* 4.1 18.5 - - + +
350M ILE* 4.0 27.4 - - + -
354M HIS* 3.1 16.2 + - + +
356M PRO* 1.3 76.7 - - - +
358M THR* 1.3 58.8 + - - +
360M PHE* 3.2 22.9 + - + +
361M CYS* 3.0 37.9 + - - -
368M TYR* 3.6 22.9 - - + +
371M MET* 4.4 3.6 - - + -
372M ALA* 4.0 25.1 - - + +
375M LEU* 3.9 20.4 - - + -
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Residues in contact with THR 358 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353M LYS* 3.5 24.1 + - + +
354M HIS 2.7 32.6 + - - -
355M ASP* 3.9 6.1 - - - -
357M LEU* 1.3 71.3 - - - +
359M ILE* 1.4 64.0 + - + +
361M CYS* 4.0 1.7 - - - +
362M ASP* 3.1 25.7 + - + +
368M TYR* 3.7 19.4 - - + -
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Residues in contact with ILE 359 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277M LEU 4.5 0.2 - - - +
278M ARG* 4.0 38.1 - - + +
334M HIS* 3.5 48.2 - - + +
355M ASP* 3.3 20.0 + - + +
356M PRO 3.8 0.2 - - - +
358M THR* 1.4 75.1 - - + +
360M PHE* 1.4 64.2 + - - +
362M ASP* 3.3 6.5 + - - +
363M LEU* 3.0 39.9 + - + +
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Residues in contact with PHE 360 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331M GLY* 3.2 34.1 - - - -
332M ILE 4.7 0.2 - - - -
334M HIS* 4.3 9.4 - - + +
335M LEU* 3.8 39.5 - - + +
356M PRO 3.0 15.1 + - - +
357M LEU* 3.2 27.8 + - + +
359M ILE* 1.4 75.7 - - - +
361M CYS* 1.3 67.6 + - - +
363M LEU* 3.4 4.5 + - - +
364M MET* 3.2 60.3 + - + +
366M VAL* 5.6 1.1 - - + -
371M MET* 4.0 24.2 - - + -
403M LEU* 5.0 2.0 - - + -
407M ILE* 5.0 5.4 - - + -
580M LEU* 4.3 12.1 - - + -
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Residues in contact with CYS 361 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357M LEU* 3.0 32.4 + - - +
358M THR 4.1 3.1 - - - +
360M PHE* 1.3 74.5 - - - +
362M ASP* 1.4 55.2 + - - +
364M MET 3.5 0.3 + - - -
365M GLY* 2.8 31.5 + - - -
366M VAL* 3.4 30.5 + - + +
367M ASP 3.7 16.8 - - - -
368M TYR* 3.8 24.7 - - + +
371M MET* 4.0 18.8 - - - -
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Residues in contact with ASP 362 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278M ARG* 2.6 48.9 + - - +
327M ARG* 3.9 7.6 + - - -
358M THR* 3.1 21.1 + - + +
359M ILE* 3.5 4.3 - - - +
361M CYS* 1.4 74.8 - - - +
363M LEU* 1.3 65.8 + - - +
365M GLY* 3.5 8.4 + - - -
585M LYS* 5.7 3.3 - - - +
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Residues in contact with LEU 363 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276M THR 3.1 28.9 - - - +
277M LEU* 4.2 4.7 - - - +
278M ARG* 3.4 16.6 - - - +
327M ARG* 2.9 43.6 + - + +
330M ALA* 3.6 20.4 - - + +
331M GLY* 3.6 29.8 - - - +
334M HIS* 4.8 0.4 - - + -
359M ILE* 3.0 32.4 + - + +
360M PHE 3.4 4.2 + - - +
362M ASP* 1.3 77.4 - - - +
364M MET* 1.3 64.2 + - + +
585M LYS* 6.0 1.6 - - - +
586M PHE* 3.6 16.0 - - - -
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Residues in contact with MET 364 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327M ARG 4.9 2.7 - - - +
328M ILE* 4.5 22.2 - - + +
331M GLY* 5.0 3.8 - - - -
332M ILE* 5.9 0.2 - - + -
360M PHE* 3.2 48.4 + - + +
361M CYS 4.2 1.3 - - - +
363M LEU* 1.3 77.8 - - + +
365M GLY* 1.4 58.6 + - - +
366M VAL* 3.5 14.8 - - + -
407M ILE* 4.3 14.8 - - + -
580M LEU* 4.3 10.8 - - + -
583M SER* 2.8 22.7 + - - -
585M LYS* 5.4 0.9 - - - -
586M PHE* 3.8 27.8 - - - +
589M LEU* 3.6 41.8 - - + +
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Residues in contact with GLY 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361M CYS 2.8 13.5 + - - -
362M ASP* 3.5 9.3 + - - -
364M MET* 1.4 73.7 - - - +
366M VAL* 1.3 62.5 + - - +
583M SER* 3.9 10.0 + - - -
584M LYS* 3.7 24.9 + - - +
585M LYS* 4.3 18.1 - - - +
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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