Contacts of the helix formed by residues 279 - 298 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277D ASP 3.0 7.6 + - - +
278D LYS* 1.3 80.6 - - - +
280D ASP* 1.3 61.9 + - - +
281D GLY 3.1 2.0 - - - -
282D GLU* 3.1 27.6 + - + +
283D GLN* 3.0 46.8 + - + +
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Residues in contact with ASP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D SER* 4.0 9.0 + - - +
207D PRO* 3.3 28.7 - - + +
208D TRP* 3.2 31.8 + - - +
211D LYS* 5.4 2.9 + - - -
277D ASP* 3.9 26.0 + - - +
278D LYS 3.9 1.9 + - - -
279D LYS* 1.3 78.8 + - - +
281D GLY* 1.3 63.9 + - - -
283D GLN* 3.8 11.2 - - + +
284D ALA* 2.8 32.6 + - - +
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Residues in contact with GLY 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D TRP* 5.8 0.2 - - - -
278D LYS* 4.9 1.1 - - - +
279D LYS* 3.1 3.2 - - - +
280D ASP* 1.3 85.6 + - - +
282D GLU* 1.3 59.8 + - - +
284D ALA* 3.3 2.4 + - - +
285D LYS* 2.9 26.4 + - - +
446D LEU* 4.3 25.4 - - - +
450D SER* 5.4 12.3 - - - -
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D LYS 3.3 19.6 - - - +
279D LYS* 3.1 42.6 + - + +
281D GLY* 1.3 71.5 + - - +
283D GLN* 1.3 69.5 + - - +
285D LYS* 3.6 8.7 - - + +
286D ALA* 3.0 29.3 + - - +
450D SER* 5.3 5.6 + - - +
277E ASP 6.0 4.3 - - - +
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Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D SER* 5.8 1.8 - - - +
279D LYS* 3.0 41.4 + - + +
280D ASP* 3.8 9.4 - - + +
282D GLU* 1.3 85.4 - - - +
284D ALA* 1.3 56.5 + - - +
286D ALA* 3.4 6.0 + - - +
287D LEU* 2.9 32.2 + - + +
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Residues in contact with ALA 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D SER* 4.0 12.3 + - - +
208D TRP* 4.8 2.9 - - + -
280D ASP 2.8 23.1 + - - +
283D GLN* 1.3 70.7 - - - +
285D LYS* 1.3 60.6 + - - +
287D LEU* 4.0 2.5 - - - -
288D PHE* 2.8 34.9 + - - -
437D PHE* 3.4 29.3 - - + -
446D LEU* 3.7 20.4 - - + -
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Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D GLY 2.9 17.0 + - - +
282D GLU* 3.6 10.5 - - + +
283D GLN 3.2 0.4 - - - -
284D ALA* 1.3 74.8 - - - +
286D ALA* 1.3 64.8 + - - +
288D PHE* 3.2 22.6 + - + +
289D GLU* 3.1 28.7 + - - +
292D ARG* 5.6 2.0 - - - +
443D GLU* 3.8 15.8 + - + +
446D LEU* 5.8 4.0 - - + -
447D ARG* 3.4 39.3 - - + +
478D MET* 6.6 0.2 - - - -
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D GLU 3.0 16.3 + - - +
283D GLN* 3.8 7.4 - - - +
285D LYS* 1.3 76.5 - - - +
287D LEU* 1.3 58.5 + - - +
289D GLU* 3.2 11.8 + - - +
290D LYS* 3.0 34.2 + - + +
207E PRO* 4.5 21.8 - - + -
210E THR* 5.5 1.3 - - - +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE* 4.5 10.3 - - + +
202D LYS* 3.4 40.2 - - + +
203D CYS* 4.4 15.3 - - + +
206D SER* 5.5 5.2 - - - -
283D GLN* 2.9 20.6 + - + +
284D ALA* 3.8 1.3 - - - +
285D LYS 3.2 0.2 - - - -
286D ALA* 1.3 76.2 - - - +
288D PHE* 1.3 59.5 + - - +
290D LYS* 3.3 12.4 + - + +
291D VAL* 2.8 43.2 + - + +
437D PHE* 3.5 31.2 - - + -
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D TRP* 4.2 8.7 - + - -
284D ALA 2.8 17.5 + - - -
285D LYS* 3.2 19.1 - - + +
287D LEU* 1.3 75.8 - - - +
289D GLU* 1.3 52.2 + - - +
291D VAL* 3.1 5.5 + - + +
292D ARG* 2.7 51.4 + - - +
437D PHE* 3.1 59.0 - + - -
439D SER 4.9 1.8 - - - -
442D SER* 4.7 0.9 - - - -
443D GLU* 3.6 49.8 - - + +
446D LEU* 3.5 35.0 - - + -
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Residues in contact with GLU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LYS* 3.1 18.4 + - - +
286D ALA* 3.2 12.6 + - - +
288D PHE* 1.3 80.2 - - - +
290D LYS* 1.3 57.4 + - - +
292D ARG* 3.4 17.8 - - - +
293D LYS* 3.0 30.5 + - + +
207E PRO 5.1 0.3 - - - +
210E THR* 2.8 56.6 + - + +
211E LYS* 4.5 4.5 + - - +
214E SER* 3.0 20.2 + - - -
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D HIS* 5.2 4.3 + - + +
199D ILE* 4.3 20.1 - - + +
286D ALA* 3.0 22.5 + - + +
287D LEU* 3.5 14.1 - - + +
289D GLU* 1.3 75.6 - - - +
291D VAL* 1.3 57.7 + - - +
293D LYS* 3.4 22.3 + - + +
294D PHE* 2.9 31.2 + - - +
204E PHE* 3.5 36.8 + - + -
205E GLU* 4.7 10.6 - - - +
206E SER 4.8 4.5 + - - -
207E PRO* 5.5 4.0 - - - -
209E THR* 5.0 0.2 + - - -
210E THR* 4.9 17.4 - - + +
433E ARG* 4.2 9.9 - - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ILE* 4.4 16.8 - - + -
287D LEU* 2.8 37.2 + - + +
288D PHE* 3.1 8.3 + - + +
290D LYS* 1.3 75.7 - - - +
292D ARG* 1.3 60.4 + - + +
294D PHE* 3.3 11.1 + - + +
295D ARG* 2.8 25.3 + - + +
434D PHE* 4.5 16.2 - - + -
437D PHE* 4.0 17.3 - - + +
438D LEU* 3.8 34.8 - - + -
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LYS* 5.6 1.3 - - - +
288D PHE* 2.7 39.6 + - - +
289D GLU* 3.4 30.1 - - - +
291D VAL* 1.3 77.9 - - + +
293D LYS* 1.3 61.1 + - - +
295D ARG* 3.5 16.4 - - + +
296D ALA* 2.9 27.7 + - - +
438D LEU* 5.8 2.5 - - + -
443D GLU* 3.0 40.8 + - - -
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Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D GLU* 3.0 20.3 + - + +
290D LYS* 3.6 22.6 - - + +
292D ARG* 1.3 78.7 - - - +
294D PHE* 1.3 56.4 + - - +
296D ALA* 3.2 9.1 + - + +
297D HIS* 2.9 26.6 + - + +
204E PHE* 5.2 4.5 - - - -
209E THR* 5.6 0.8 + - - -
210E THR* 4.6 21.7 - - - +
213E LEU* 6.3 0.4 - - - +
429E LEU* 4.4 20.5 - - - +
433E ARG* 3.8 32.5 - - - +
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Residues in contact with PHE 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LYS* 4.3 11.4 - - + -
195D HIS* 3.3 38.1 + + - +
196D PHE* 3.5 40.8 - + + -
199D ILE* 4.5 16.4 - - + -
290D LYS 2.9 17.7 + - - +
291D VAL* 3.5 7.9 - - + +
293D LYS* 1.3 72.9 - - - +
295D ARG* 1.3 68.9 + - + +
297D HIS* 3.1 16.5 + - + -
298D VAL* 3.3 48.1 + - + +
418D PHE* 4.0 20.9 - + - -
434D PHE* 5.4 5.6 - + - -
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Residues in contact with ARG 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D VAL 2.8 14.7 + - - +
292D ARG* 3.5 18.2 - - - +
293D LYS 3.2 0.2 - - - -
294D PHE* 1.3 80.9 - - - +
296D ALA* 1.3 61.6 + - - +
297D HIS 3.3 0.5 + - - -
298D VAL* 4.0 3.3 + - - +
299D GLU* 3.3 30.7 - - + +
412D VAL* 3.4 29.9 - - - +
414D ASN* 2.6 35.7 + - - +
415D ASP* 4.4 15.0 + - - +
418D PHE* 6.1 2.9 - - - -
438D LEU* 4.0 32.0 - - + +
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Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ARG 2.9 14.0 + - - +
293D LYS* 3.2 10.7 + - - +
295D ARG* 1.3 76.5 - - - +
297D HIS* 1.3 63.1 + - - +
299D GLU* 4.7 7.9 + - - +
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Residues in contact with HIS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D SER* 5.7 1.3 - - - -
192D LYS* 4.5 19.7 - - + +
195D HIS* 6.2 2.4 - + + -
293D LYS* 2.9 13.8 + - + +
294D PHE* 3.1 17.9 + + + +
296D ALA* 1.3 80.5 - - - +
298D VAL* 1.3 79.1 + - + +
299D GLU* 2.9 9.7 + - - +
300D ASP* 5.1 4.0 - - - +
427E ASP* 5.5 6.6 + - - -
429E LEU* 4.0 44.6 + - + +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LYS* 3.7 42.2 - - + +
294D PHE* 3.3 43.9 + - + +
295D ARG* 4.0 2.0 + - - +
296D ALA 3.8 0.2 - - - -
297D HIS* 1.3 89.5 - - - +
299D GLU* 1.3 75.6 + - - +
300D ASP 4.0 2.0 - - - -
302D ASP* 4.3 15.7 - - - +
416D PHE 4.3 3.6 - - - +
418D PHE* 4.3 15.1 - - + -
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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
------------------------------------------------------------
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