Contacts of the helix formed by residues 279 - 296 (chain F) in PDB entry 6M04
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 LYS 279 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ASP 3.0 8.2 + - - +
278F LYS* 1.3 77.3 - - - +
280F ASP* 1.3 67.5 + - - +
281F GLY 3.2 2.6 + - - -
282F GLU* 3.2 27.7 + - + +
283F GLN* 3.0 44.9 + - + +
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Residues in contact with ASP 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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206F SER* 5.7 1.1 - - - -
207F PRO* 4.6 14.6 - - + +
208F TRP* 3.9 24.0 - - + +
211F LYS* 3.2 30.0 + - - -
277F ASP* 3.3 27.6 - - - +
278F LYS* 3.7 4.5 + - - -
279F LYS* 1.3 73.5 - - - +
281F GLY* 1.3 64.9 + - - +
283F GLN* 4.5 4.9 - - - -
284F ALA* 2.9 35.3 + - - +
446F LEU* 3.3 13.5 - - - +
449F ILE* 5.8 2.0 - - - +
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Residues in contact with GLY 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F LYS 4.9 0.6 - - - -
279F LYS* 3.2 1.4 - - - +
280F ASP* 1.3 85.4 + - - +
282F GLU* 1.3 60.4 + - - +
284F ALA 3.9 0.2 - - - -
285F LYS* 2.9 31.2 + - - +
446F LEU* 3.7 24.8 - - - +
450F SER* 4.8 16.6 - - - -
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Residues in contact with GLU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F LYS 3.0 27.4 - - - +
279F LYS* 3.2 42.2 + - + +
281F GLY* 1.3 72.2 + - - +
283F GLN* 1.3 67.5 + - - +
285F LYS* 3.7 6.4 - - - +
286F ALA* 2.9 29.6 + - - +
450F SER* 5.4 3.9 + - - -
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Residues in contact with GLN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F LYS* 5.8 5.7 - - - +
206F SER* 6.0 1.3 - - - +
279F LYS* 3.0 45.1 + - + +
280F ASP* 4.1 4.3 - - - +
282F GLU* 1.3 83.5 - - - +
284F ALA* 1.3 58.2 + - - +
286F ALA* 3.3 7.8 + - - +
287F LEU* 2.9 28.3 + - - +
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Residues in contact with ALA 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F SER* 4.6 11.6 + - - +
208F TRP* 4.0 19.5 - - + -
280F ASP 2.9 22.4 + - - +
283F GLN* 1.3 74.4 - - - +
285F LYS* 1.3 56.2 + - - +
287F LEU* 3.5 9.8 - - + +
288F PHE* 2.8 36.5 + - + -
437F PHE* 4.5 7.9 - - + -
446F LEU* 3.7 16.8 - - + -
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Residues in contact with LYS 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F GLY 2.9 20.1 + - - +
282F GLU* 3.7 8.1 - - - +
283F GLN 3.2 0.2 - - - -
284F ALA* 1.3 74.6 - - - +
286F ALA* 1.3 60.3 + - - +
288F PHE* 3.2 22.0 + - + +
289F GLU* 2.9 38.2 + - - +
292F ARG* 4.3 17.6 - - - +
446F LEU* 6.1 1.8 - - + -
447F ARG* 3.5 39.4 - - + +
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Residues in contact with ALA 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F GLU 2.9 18.2 + - - +
283F GLN* 3.7 9.0 - - - +
285F LYS* 1.3 76.8 - - - +
287F LEU* 1.3 57.2 + - - +
289F GLU* 3.3 12.6 + - - +
290F LYS* 2.9 27.4 + - - +
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Residues in contact with LEU 287 (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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199F ILE* 4.4 12.8 - - + +
202F LYS* 3.3 39.9 - - + +
203F CYS* 4.0 17.5 - - + -
206F SER* 4.8 9.0 - - - -
283F GLN 2.9 19.8 + - - +
284F ALA* 3.5 9.2 - - - +
285F LYS 3.2 0.2 - - - -
286F ALA* 1.3 75.2 - - - +
288F PHE* 1.3 58.6 + - - +
290F LYS* 3.2 9.9 + - + +
291F VAL* 2.9 37.6 + - + +
437F PHE* 3.5 30.5 - - + -
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Residues in contact with PHE 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F TRP* 3.4 33.2 - + - -
284F ALA* 2.8 26.1 + - + -
285F LYS* 3.3 29.2 - - + +
287F LEU* 1.3 76.3 - - - +
289F GLU* 1.3 57.1 + - - +
291F VAL* 3.0 8.5 + - + +
292F ARG* 2.9 38.3 + - - +
437F PHE* 3.5 38.8 - + - -
443F GLU* 3.4 57.4 - - + +
446F LEU* 4.9 11.4 - - + -
447F ARG* 4.2 2.7 - - - +
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Residues in contact with GLU 289 (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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285F LYS* 2.9 25.8 + - - +
286F ALA* 3.7 12.7 - - - +
287F LEU 3.3 0.2 - - - -
288F PHE* 1.3 75.2 - - - +
290F LYS* 1.3 57.8 + - - +
292F ARG* 3.3 16.1 + - + +
293F LYS* 2.9 40.5 + - - +
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Residues in contact with LYS 290 (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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195F HIS* 3.4 27.4 + - + +
199F ILE* 3.9 23.6 - - + -
286F ALA 2.9 13.8 + - - +
287F LEU* 3.2 15.2 + - + +
289F GLU* 1.3 76.4 - - - +
291F VAL* 1.3 59.7 + - - +
293F LYS* 3.2 26.7 + - + +
294F PHE* 2.9 27.2 + - - +
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Residues in contact with VAL 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F ILE* 4.9 12.6 - - + -
287F LEU* 2.9 24.8 + - + +
288F PHE* 3.4 11.0 - - + +
290F LYS* 1.3 73.3 - - + +
292F ARG* 1.3 62.1 + - - +
294F PHE* 3.3 8.4 + - + +
295F ARG* 2.9 36.2 + - + +
434F PHE* 5.6 9.2 - - + -
437F PHE* 3.7 31.0 - - + +
438F LEU* 4.8 20.6 - - + +
443F GLU* 5.6 3.8 - - - +
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Residues in contact with ARG 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LYS* 4.3 18.8 - - - +
288F PHE* 2.9 26.6 + - - +
289F GLU* 3.5 19.9 - - + +
290F LYS 3.3 0.2 - - - -
291F VAL* 1.3 78.3 - - - +
293F LYS* 1.3 60.4 + - - +
295F ARG* 3.4 13.7 + - - +
296F ALA* 4.0 10.6 + - - +
443F GLU* 3.2 23.6 + - - -
447F ARG* 3.7 21.8 - - - +
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Residues in contact with LYS 293 (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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195F HIS* 4.8 7.7 - - - +
289F GLU* 2.9 31.1 + - - +
290F LYS* 3.2 32.8 + - + +
292F ARG* 1.3 76.6 - - - +
294F PHE* 1.3 59.3 + - - +
297F HIS* 3.3 22.0 + - + +
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Residues in contact with PHE 294 (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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192F LYS* 4.6 16.2 - - + -
195F HIS* 3.3 33.0 - + + -
196F PHE* 4.1 28.0 - + + -
199F ILE* 3.6 15.5 - - + -
290F LYS 2.9 16.6 + - - +
291F VAL* 3.8 7.6 - - + +
293F LYS* 1.3 79.1 - - - +
295F ARG* 1.3 73.2 + - + +
296F ALA 3.6 0.2 - - - -
297F HIS* 3.3 16.8 + - + +
298F VAL* 3.5 34.4 + - + +
299F GLU* 5.5 4.5 - - - -
415F ASP* 5.6 7.6 - - - -
419F LEU* 6.0 1.3 - - + -
434F PHE* 6.0 6.7 - + - -
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Residues in contact with ARG 295 (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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291F VAL* 2.9 23.0 + - + +
292F ARG* 3.4 8.3 + - - +
294F PHE* 1.3 88.2 - - + +
296F ALA* 1.3 62.8 + - + +
297F HIS 3.3 0.2 + - - -
298F VAL 3.6 4.2 - - - +
299F GLU* 3.3 47.4 + - + +
412F VAL* 3.4 34.0 - - - +
414F ASN* 3.4 34.6 + - - +
415F ASP* 3.9 3.8 - - - +
438F LEU* 3.4 32.3 - - - +
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Residues in contact with ALA 296 (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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292F ARG 4.0 8.1 + - - +
295F ARG* 1.3 77.8 - - + +
297F HIS* 1.3 63.5 + - - +
298F VAL 3.5 1.3 - - - -
299F GLU* 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