Contacts of the helix formed by residues 279 - 298 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ASP 3.1 7.4 - - - +
278B LYS* 1.3 79.9 - - - +
280B ASP* 1.3 66.2 + - - +
281B GLY 3.2 2.2 - - - -
282B GLU* 3.1 24.7 + - + +
283B GLN* 3.1 43.7 + - + +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 5.5 1.3 - - - +
207B PRO* 4.6 19.6 - - + +
208B TRP* 4.1 25.3 + - + +
211B LYS* 3.5 17.5 + - - -
277B ASP* 3.4 24.1 - - - +
278B LYS* 3.7 9.2 + - - -
279B LYS* 1.3 82.6 + - - +
281B GLY* 1.3 65.5 + - - +
283B GLN* 3.9 6.7 - - - +
284B ALA* 2.9 34.7 + - - +
446B LEU* 4.4 2.9 - - - +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LYS* 4.9 1.5 - - - -
279B LYS 3.2 1.6 - - - +
280B ASP* 1.3 85.4 + - - +
282B GLU* 1.3 59.0 + - - +
284B ALA 3.8 0.2 - - - -
285B LYS* 2.9 31.0 + - - +
446B LEU* 3.9 27.7 - - - +
449B ILE* 6.3 0.9 - - - -
450B SER* 5.7 9.2 - - - -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B LYS 3.1 27.3 - - - +
279B LYS* 3.1 36.4 + - + +
281B GLY* 1.3 71.3 + - - +
283B GLN* 1.3 72.8 + - - +
285B LYS* 3.7 7.0 - - - +
286B ALA* 3.0 29.6 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LYS* 3.1 40.7 + - + +
280B ASP* 3.9 6.5 - - - +
282B GLU* 1.3 87.6 - - - +
284B ALA* 1.3 58.4 + - - +
286B ALA* 3.3 6.5 + - - +
287B LEU* 3.0 26.5 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 4.5 12.8 - - - +
208B TRP* 4.4 10.8 - - + -
280B ASP 2.9 21.9 + - - +
283B GLN* 1.3 72.2 - - - +
285B LYS* 1.3 60.1 + - - +
287B LEU* 3.5 11.0 - - + +
288B PHE* 2.8 41.5 + - + -
437B PHE* 4.8 5.8 - - + -
446B LEU* 3.7 19.1 - - + -
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLY 2.9 21.2 + - - +
282B GLU* 3.7 8.3 - - - +
283B GLN 3.2 0.2 - - - -
284B ALA* 1.3 74.0 - - - +
286B ALA* 1.3 65.4 + - - +
288B PHE* 3.1 23.4 + - + +
289B GLU* 3.1 35.7 + - - +
292B ARG* 4.7 11.3 - - - +
443B GLU 5.5 1.8 - - - +
446B LEU* 5.6 2.9 - - + -
447B ARG* 3.7 46.5 - - + +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU 3.0 13.6 + - - +
283B GLN* 3.5 11.0 - - - +
285B LYS* 1.3 76.2 - - - +
287B LEU* 1.3 56.9 + - - +
289B GLU* 3.4 7.8 + - - +
290B LYS* 2.9 35.8 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 5.1 11.4 - - + +
202B LYS* 4.2 29.6 - - + +
203B CYS* 5.2 3.8 - - + -
206B SER* 5.4 5.6 - - - -
283B GLN 3.0 15.8 + - - +
284B ALA* 3.5 13.2 - - - +
285B LYS 3.2 0.2 - - - -
286B ALA* 1.3 75.5 - - - +
288B PHE* 1.3 59.2 + - - +
290B LYS* 3.3 10.6 + - + +
291B VAL* 2.9 43.8 + - + +
437B PHE* 3.6 39.3 - - + -
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TRP* 3.5 28.9 - + - -
284B ALA* 2.8 26.6 + - + -
285B LYS* 3.3 26.7 - - + +
287B LEU* 1.3 73.0 - - - +
289B GLU* 1.3 57.6 + - - +
291B VAL* 3.1 6.7 + - - +
292B ARG* 2.9 36.3 + - - +
437B PHE* 3.5 38.4 - + - -
442B SER* 6.2 0.2 - - - -
443B GLU* 3.3 57.4 - - + +
446B LEU* 3.6 29.2 - - + -
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LYS* 3.1 21.7 + - - +
286B ALA* 4.0 6.7 - - - +
288B PHE* 1.3 79.0 - - - +
290B LYS* 1.3 56.6 + - - +
292B ARG* 3.3 22.0 + - + +
293B LYS* 3.0 35.9 + - - +
207C PRO* 4.5 14.6 - - - +
210C THR* 4.4 17.3 - - + +
211C LYS* 6.1 0.5 - - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 5.1 6.3 - - + -
286B ALA* 2.9 24.3 + - - +
287B LEU* 3.3 14.4 - - + +
288B PHE 3.1 0.2 - - - -
289B GLU* 1.3 77.2 - - - +
291B VAL* 1.3 56.1 + - - +
293B LYS* 3.0 28.1 + - + +
294B PHE* 2.9 60.2 + - + -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 4.8 7.0 - - + -
287B LEU* 2.9 34.9 + - + +
288B PHE* 3.1 8.0 + - - +
290B LYS* 1.3 70.8 - - - +
292B ARG* 1.3 61.6 + - - +
294B PHE* 3.1 16.9 + - + +
295B ARG* 2.9 29.4 + - + +
434B PHE* 5.0 13.0 - - + -
437B PHE* 3.7 38.6 - - + +
438B LEU* 4.5 15.9 - - + -
443B GLU* 5.3 0.2 - - - +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 4.7 12.3 - - - +
288B PHE* 2.9 24.2 + - - +
289B GLU* 3.3 29.0 - - + +
290B LYS 3.3 0.2 - - - -
291B VAL* 1.3 78.0 - - - +
293B LYS* 1.3 56.0 + - - +
295B ARG* 3.4 5.8 + - - +
296B ALA* 3.0 28.5 + - - +
438B LEU* 6.5 0.2 - - - -
440B GLU* 5.4 7.7 - - - +
443B GLU* 3.1 30.5 + - - +
447B ARG* 4.2 16.5 - - - +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLU* 3.0 22.0 + - - +
290B LYS* 3.0 33.3 + - + +
292B ARG* 1.3 76.0 - - - +
294B PHE* 1.3 64.6 + - + +
296B ALA* 3.3 7.4 + - + +
297B HIS* 2.9 34.3 + - + +
204C PHE* 4.7 37.0 - - + -
205C GLU* 5.9 4.0 - - - +
206C SER 5.5 3.5 + - - -
207C PRO* 5.5 3.4 - - - +
210C THR* 4.1 30.8 - - - +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B HIS* 3.3 41.3 - + - -
199B ILE* 3.4 46.7 - - + -
287B LEU* 6.0 0.4 - - + -
290B LYS* 2.9 51.4 + - + -
291B VAL* 3.1 14.6 + - + +
293B LYS* 1.3 83.3 - - + +
295B ARG* 1.3 62.2 + - - +
297B HIS* 4.2 7.0 - + + +
298B VAL* 2.9 49.8 + - + +
299B GLU 3.9 0.2 + - - -
418B PHE* 5.9 2.7 - - + -
434B PHE* 5.9 1.6 - + + -
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B VAL* 2.9 15.6 + - + +
292B ARG* 4.0 5.8 - - - +
294B PHE* 1.3 75.6 - - - +
296B ALA* 1.3 61.4 + - - +
298B VAL* 5.4 0.2 - - - -
299B GLU* 3.2 36.9 + - + +
413B LYS* 2.8 25.0 + - - +
414B ASN 2.7 27.3 + - - -
418B PHE* 5.7 6.0 - - + -
438B LEU* 3.5 39.3 - - + +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ARG 3.0 15.1 + - - +
293B LYS* 3.4 12.8 - - + +
294B PHE 3.1 0.2 - - - -
295B ARG* 1.3 79.3 - - - +
297B HIS* 1.3 62.5 + - + +
299B GLU* 4.6 0.7 + - - +
300B ASP* 4.2 12.1 - - - +
429C LEU* 5.6 3.7 - - + +
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Residues in contact with HIS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 4.4 22.6 - - + +
293B LYS* 2.9 22.9 + - + +
294B PHE* 3.0 8.4 + + + +
296B ALA* 1.3 74.4 - - + +
298B VAL* 1.3 84.1 + - + +
299B GLU 3.2 1.8 - - - -
300B ASP* 2.9 21.3 - - - +
301B SER* 5.0 2.1 - - - -
204C PHE* 5.0 11.8 - + + -
427C ASP* 5.4 10.9 + - + -
429C LEU* 3.4 41.4 - - + +
430C TYR* 5.4 8.6 + + - -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 4.4 28.5 - - + +
196B PHE* 5.8 7.4 - - + -
199B ILE* 6.1 3.6 - - + -
294B PHE* 2.9 36.0 + - + +
297B HIS* 1.3 93.9 - - + +
299B GLU* 1.3 64.0 + - - +
300B ASP 3.3 2.1 + - - -
301B SER* 3.4 20.2 + - - -
417B ALA 3.8 9.4 - - - +
418B PHE* 3.6 28.3 - - + -
419B LEU* 6.5 0.2 - - + -
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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
------------------------------------------------------------
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