Contacts of the helix formed by residues 279 - 298 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ASP 3.0 7.8 + - - +
278A LYS* 1.3 80.4 - - - +
280A ASP* 1.3 61.7 + - - +
281A GLY 3.1 2.0 - - - -
282A GLU* 3.1 29.5 + - + +
283A GLN* 3.0 46.2 + - + +
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 4.0 8.1 + - - +
207A PRO* 3.3 29.3 - - + +
208A TRP* 3.2 32.2 + - - +
211A LYS* 5.4 2.1 + - - -
277A ASP* 3.9 26.0 - - - +
278A LYS 3.9 1.7 + - - -
279A LYS* 1.3 78.4 + - - +
281A GLY* 1.3 63.1 + - - -
283A GLN* 3.8 10.5 - - + +
284A ALA* 2.8 32.7 + - - +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TRP* 5.8 0.9 - - - -
278A LYS 4.9 1.0 - - - +
279A LYS* 3.1 2.8 - - - +
280A ASP* 1.3 83.9 + - - +
282A GLU* 1.3 59.6 + - - +
284A ALA* 3.7 2.4 - - - +
285A LYS* 2.9 27.3 + - - +
446A LEU* 4.3 24.9 - - - +
450A SER* 5.4 12.1 - - - -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS 3.3 21.0 - - - +
279A LYS* 3.1 42.8 + - + +
281A GLY* 1.3 71.5 + - - +
283A GLN* 1.3 70.1 + - - +
285A LYS* 3.6 8.5 - - + +
286A ALA* 3.0 29.1 + - - +
450A SER* 5.3 5.8 + - - +
277B ASP 6.0 4.9 - - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 5.8 2.2 - - - +
279A LYS* 3.0 40.7 + - + +
280A ASP* 3.8 9.6 - - + +
282A GLU* 1.3 85.3 - - - +
284A ALA* 1.3 57.4 + - - +
286A ALA* 3.4 6.6 + - - +
287A LEU* 2.9 31.8 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A SER* 4.0 11.4 + - - +
208A TRP* 4.8 2.7 - - + -
280A ASP 2.8 22.3 + - - +
281A GLY 3.8 0.2 - - - +
283A GLN* 1.3 69.8 - - - +
285A LYS* 1.3 60.4 + - - +
287A LEU* 3.6 2.7 - - - -
288A PHE* 2.8 34.8 + - - -
437A PHE* 3.4 29.7 - - + -
446A LEU* 3.7 20.6 - - + -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLY 2.9 17.4 + - - +
282A GLU* 3.6 10.5 - - + +
283A GLN 3.2 0.4 - - - -
284A ALA* 1.3 73.8 - - - +
286A ALA* 1.3 65.5 + - - +
288A PHE* 3.2 24.8 - - + +
289A GLU* 3.1 28.7 + - - +
292A ARG* 5.7 2.0 - - - +
443A GLU* 3.8 14.7 + - + +
446A LEU* 5.8 4.3 - - + -
447A ARG* 3.4 38.6 - - + +
478A MET* 6.6 0.2 - - - -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLU 3.0 16.7 + - - +
283A GLN* 3.8 7.6 - - - +
285A LYS* 1.3 76.7 - - - +
287A LEU* 1.3 58.6 + - - +
289A GLU* 3.2 11.4 + - - +
290A LYS* 3.0 33.3 + - + +
207B PRO* 4.5 22.0 - - + -
210B THR* 5.5 0.9 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 4.5 12.1 - - + +
202A LYS* 3.4 41.3 - - + +
203A CYS* 4.4 14.8 - - + -
206A SER* 5.6 5.2 - - - -
283A GLN* 2.9 19.7 + - + +
284A ALA* 3.8 1.8 - - - +
285A LYS 3.2 0.2 - - - -
286A ALA* 1.3 73.8 - - - +
288A PHE* 1.3 59.9 + - - +
290A LYS* 3.3 12.3 + - + +
291A VAL* 2.8 43.5 + - + +
437A PHE* 3.5 30.5 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TRP* 4.3 8.3 - + - -
284A ALA 2.8 16.1 + - - -
285A LYS* 3.2 19.7 - - + +
287A LEU* 1.3 75.7 - - - +
289A GLU* 1.3 53.7 + - - +
291A VAL* 3.1 7.0 + - + +
292A ARG* 2.6 54.0 + - - +
437A PHE* 3.1 57.0 - + - -
438A LEU 6.0 0.2 - - - -
439A SER 4.9 2.0 - - - -
442A SER* 4.7 0.7 - - - -
443A GLU* 3.6 48.0 - - + +
446A LEU* 3.5 34.8 - - + -
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LYS* 3.1 18.3 + - - +
286A ALA* 3.2 12.2 + - - +
288A PHE* 1.3 76.9 - - - +
290A LYS* 1.3 60.3 + - - +
292A ARG* 3.5 17.0 - - - +
293A LYS* 3.0 30.4 + - + +
207B PRO 5.0 0.7 - - - +
210B THR* 2.8 56.4 + - + +
211B LYS* 4.4 5.4 + - - +
214B SER* 2.9 21.0 + - - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 5.3 4.6 + - + -
199A ILE* 4.3 21.1 - - + +
286A ALA* 3.0 22.2 + - - +
287A LEU* 3.3 15.7 + - + +
289A GLU* 1.3 76.6 - - - +
291A VAL* 1.3 56.1 + - - +
293A LYS* 3.4 20.0 + - + +
294A PHE* 2.9 31.1 + - - +
204B PHE* 3.5 38.0 + - + -
205B GLU* 4.6 13.5 - - - +
206B SER 4.8 2.8 + - - -
207B PRO* 5.6 4.0 - - - -
209B THR* 5.1 0.2 + - - -
210B THR* 4.9 16.3 - - + +
433B ARG* 4.3 9.5 - - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 4.5 15.0 - - + -
287A LEU* 2.8 37.8 + - + +
288A PHE* 3.1 9.1 + - - +
290A LYS* 1.3 76.2 - - + +
292A ARG* 1.3 61.4 + - + +
294A PHE* 3.3 9.8 + - + +
295A ARG* 2.8 26.5 + - + +
434A PHE* 4.6 16.2 - - + -
437A PHE* 4.0 16.2 - - + +
438A LEU* 3.8 35.7 - - + -
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LYS* 5.9 1.9 - - - +
288A PHE* 2.6 45.1 + - - +
289A GLU* 3.5 23.5 - - - +
291A VAL* 1.3 76.8 - - + +
293A LYS* 1.3 63.9 + - - +
295A ARG* 3.9 17.1 - - + +
296A ALA* 3.4 18.9 + - - +
438A LEU* 6.1 1.3 - - + -
443A GLU* 2.8 41.5 + - - -
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A GLU* 3.0 19.7 + - + +
290A LYS* 3.5 22.6 - - + +
291A VAL 3.2 0.2 - - - -
292A ARG* 1.3 79.0 - - - +
294A PHE* 1.3 57.7 + - - +
296A ALA* 3.1 8.3 + - - +
297A HIS* 3.0 25.7 + - + +
204B PHE* 5.0 5.9 - - + -
209B THR* 5.7 0.6 + - - -
210B THR* 4.8 19.3 - - - +
429B LEU* 4.3 21.2 - - - +
433B ARG* 3.7 33.5 - - - +
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 4.4 11.9 - - + -
195A HIS* 3.3 38.1 + + - +
196A PHE* 3.5 40.8 - + + -
199A ILE* 4.5 16.4 - - + -
290A LYS 2.9 17.7 + - - +
291A VAL* 3.6 7.0 - - + +
293A LYS* 1.3 73.5 - - - +
295A ARG* 1.3 67.5 + - - +
297A HIS* 3.1 17.5 + - + +
298A VAL* 3.3 46.4 + - + +
418A PHE* 4.0 20.2 - + - -
434A PHE* 5.4 5.6 - + - -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL* 2.8 19.6 + - + +
292A ARG* 3.9 14.8 - - - +
294A PHE* 1.3 81.2 - - - +
296A ALA* 1.3 60.5 + - - +
297A HIS 3.4 0.5 + - - -
298A VAL* 4.0 3.5 + - - +
299A GLU* 3.3 31.3 - - + +
412A VAL* 3.4 30.2 - - - +
414A ASN* 2.6 34.5 + - - +
415A ASP* 4.4 15.3 + - - +
418A PHE* 6.1 2.5 - - - -
438A LEU* 4.0 29.7 - - + +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ARG 3.4 10.6 + - - +
293A LYS* 3.1 10.7 + - - +
295A ARG* 1.3 78.4 - - - +
297A HIS* 1.3 64.5 + - - +
299A GLU* 4.6 9.5 + - - +
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER* 5.6 1.1 - - - -
192A LYS* 4.6 19.2 + - + +
195A HIS* 6.1 2.8 - + + -
293A LYS* 3.0 13.8 + - + +
294A PHE* 3.1 18.6 + + + +
296A ALA* 1.3 80.8 - - - +
298A VAL* 1.3 77.9 + - + +
299A GLU 3.0 9.5 + - - +
300A ASP* 5.1 4.2 - - - +
427B ASP* 5.5 7.0 + - - -
429B LEU* 4.0 45.2 + - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.7 42.0 - - + +
294A PHE* 3.3 43.0 + - + +
295A ARG* 4.0 2.4 + - - +
297A HIS* 1.3 90.6 - - - +
299A GLU* 1.3 76.2 + - - +
300A ASP 4.0 1.3 - - - -
302A ASP* 4.3 16.1 - - - +
416A PHE 4.3 3.1 - - - +
418A PHE* 4.3 16.0 - - + -
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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
------------------------------------------------------------
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