Contacts of the helix formed by residues 295 - 315 (chain B) in PDB entry 3MY0
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 GLU 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B THR 4.0 2.2 + - - -
294B LEU* 1.3 71.6 - - - +
296B PRO* 1.3 78.9 - - + +
297B HIS* 3.2 19.1 - - - +
298B LEU* 2.9 24.3 + - + +
299B ALA* 3.0 10.7 + - - +
413B ILE* 4.8 7.1 - - - +
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Residues in contact with PRO 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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294B LEU 3.7 0.9 - - - +
295B GLU* 1.3 92.7 - - + +
297B HIS* 1.3 61.6 + - - +
299B ALA* 3.3 4.5 + - + +
300B LEU* 3.1 22.7 + - - +
412B THR* 4.1 17.0 - - + -
413B ILE* 3.9 23.3 - - + +
414B VAL* 5.7 0.2 - - + -
458B ASP* 5.6 2.7 - - + -
460B VAL* 3.6 31.0 - - + +
461B LEU* 4.8 6.1 - - + -
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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
----------------------------------------------------------
295B GLU* 3.2 18.2 - - - +
296B PRO* 1.3 79.6 - - - +
298B LEU* 1.3 61.1 + - + +
300B LEU* 3.3 13.0 + - - +
301B ARG* 3.1 52.2 + - + -
460B VAL* 5.8 1.6 - - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PHE* 4.4 13.0 - - + -
292B GLN* 6.2 0.4 - - + -
293B THR 4.6 4.0 - - - +
294B LEU* 3.9 30.1 - - + -
295B GLU* 2.9 19.4 + - + +
297B HIS* 1.3 79.8 - - + +
299B ALA* 1.3 67.1 + - - +
301B ARG* 3.1 9.3 + - + +
302B LEU* 3.0 46.0 + - + +
342B LEU* 4.0 31.9 - - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 3.9 16.3 - - + +
295B GLU 3.0 11.4 + - - +
296B PRO* 3.5 13.2 - - + +
298B LEU* 1.3 78.0 - - - +
300B LEU* 1.3 56.1 - - - +
302B LEU* 4.0 0.6 - - - +
303B ALA* 3.0 28.6 + - - +
408B ILE* 3.7 17.5 - - + +
412B THR* 3.7 24.0 - - + +
461B LEU* 4.6 8.1 - - + -
464B LEU* 4.6 4.4 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO 3.1 13.2 + - - +
297B HIS* 3.6 14.1 - - - +
298B LEU 3.2 0.2 - - - -
299B ALA* 1.3 73.9 - - - +
301B ARG* 1.3 58.2 + - - +
303B ALA* 4.3 3.6 - - - -
304B VAL* 2.8 35.1 + - + +
460B VAL* 4.0 24.7 - - + +
464B LEU* 5.1 4.2 - - + +
489B LEU* 3.3 46.2 - - + +
492B ILE* 4.0 7.9 - - + +
493B SER* 3.2 42.0 - - - +
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Residues in contact with ARG 301 (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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297B HIS* 3.1 40.3 + - + +
298B LEU* 3.1 13.9 + - + +
300B LEU* 1.3 77.2 - - - +
302B LEU* 1.3 52.9 + - - +
304B VAL* 3.1 21.3 - - + +
305B SER* 2.8 22.9 + - - -
341B ASN* 2.8 29.1 + - - +
342B LEU* 3.3 23.6 + - - +
343B GLN* 3.2 30.7 - - + +
490C GLN* 2.8 28.3 + - - +
491C LYS* 3.7 16.7 + - - +
492C ILE 5.6 1.6 - - - -
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Residues in contact with LEU 302 (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 LEU* 4.2 12.1 - - + -
288B PHE* 3.8 30.7 - - + -
294B LEU* 4.1 17.5 - - + -
298B LEU* 3.0 26.2 + - + +
299B ALA* 4.0 3.6 - - - +
301B ARG* 1.3 74.2 - - - +
303B ALA* 1.3 61.2 + - - +
305B SER* 3.0 14.7 + - - -
306B ALA* 3.1 16.6 + - - +
338B VAL* 4.3 11.4 - - + -
342B LEU 3.0 32.3 - - - +
343B GLN* 4.4 0.4 - - - +
344B CYS* 3.4 22.6 - - - -
408B ILE* 4.4 11.7 - - + -
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Residues in contact with ALA 303 (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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299B ALA 3.0 18.6 + - - +
300B LEU* 3.8 5.4 - - - +
302B LEU* 1.3 78.6 - - - +
304B VAL* 1.3 61.6 + - - +
306B ALA* 3.9 3.6 - - - +
307B ALA* 3.1 22.7 + - - +
401B PHE* 4.0 3.1 - - - -
405B LEU* 3.8 25.6 - - + -
408B ILE* 4.1 12.3 - - + +
464B LEU* 3.9 12.3 - - + -
489B LEU* 3.5 14.8 - - + +
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Residues in contact with VAL 304 (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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300B LEU* 2.8 24.1 + - + +
301B ARG* 3.1 21.8 - - + +
303B ALA* 1.3 73.1 - - - +
305B SER* 1.3 65.0 + - - +
307B ALA* 3.2 4.4 + - - +
308B CYS* 2.8 39.2 + - - -
343B GLN* 5.9 2.5 - - + +
486B LYS 4.3 4.5 - - - +
489B LEU* 3.9 26.4 - - + +
490B GLN* 3.9 30.1 - - + +
493B SER* 5.4 5.6 - - - +
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Residues in contact with SER 305 (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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255B ASN* 3.4 18.1 - - - +
301B ARG 2.8 16.9 + - - -
302B LEU* 3.0 11.4 + - - -
304B VAL* 1.3 80.4 - - - +
306B ALA* 1.3 64.5 + - - +
308B CYS* 3.1 14.3 + - - +
309B GLY 3.0 17.8 + - - -
343B GLN* 3.1 32.5 - - - +
344B CYS* 2.9 20.5 + - - -
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Residues in contact with ALA 306 (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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255B ASN* 5.7 0.2 - - - -
285B LEU* 5.9 0.7 - - + -
302B LEU 3.1 18.6 + - - +
303B ALA* 3.9 5.2 - - - +
305B SER* 1.3 75.7 + - - +
307B ALA* 1.3 63.0 + - - +
309B GLY* 3.2 3.1 + - - -
310B LEU* 3.1 22.2 + - - +
331B PHE* 4.8 11.3 - - + -
336B VAL* 4.9 5.8 - - + -
344B CYS* 3.9 18.9 - - + +
346B ILE* 4.1 9.2 - - - +
401B PHE* 4.0 15.3 - - + -
404B VAL* 5.6 6.3 - - + -
408B ILE* 5.8 2.9 - - + -
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Residues in contact with ALA 307 (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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303B ALA 3.1 15.6 + - - +
304B VAL* 3.3 11.4 - - - +
306B ALA* 1.3 74.9 - - - +
308B CYS* 1.3 58.8 + - - +
310B LEU* 3.9 2.9 - - - +
311B ALA* 2.9 30.7 + - - +
401B PHE* 3.8 20.3 - - + -
482B ALA* 4.1 4.3 - - - +
485B ILE* 3.9 7.4 - - + -
486B LYS* 3.8 28.3 - - - +
489B LEU* 4.3 1.3 - - + -
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Residues in contact with CYS 308 (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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253B HIS* 3.9 6.6 + - + -
255B ASN* 3.3 20.4 - - - +
304B VAL* 2.8 43.3 + - - -
305B SER* 3.1 12.1 + - - +
307B ALA* 1.3 71.7 - - - +
309B GLY* 1.3 66.9 + - - +
311B ALA* 3.4 2.3 + - - +
312B HIS* 3.0 26.2 + - - +
486B LYS* 4.1 36.4 + - - +
490B GLN* 4.5 2.5 - - - -
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Residues in contact with GLY 309 (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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253B HIS* 4.5 3.4 - - - -
255B ASN* 3.5 31.0 - - - +
256B ILE* 4.2 3.1 - - - +
305B SER 3.0 10.9 + - - -
306B ALA 3.2 4.0 + - - -
308B CYS* 1.3 77.5 - - - +
310B LEU* 1.3 60.5 + - - +
312B HIS* 3.3 3.8 + - - +
313B LEU* 3.1 24.4 + - - +
346B ILE* 3.4 9.9 - - - -
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Residues in contact with LEU 310 (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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306B ALA 3.1 14.5 + - - +
307B ALA* 4.1 4.5 - - - +
309B GLY* 1.3 72.3 - - - +
311B ALA* 1.3 66.5 + - - +
313B LEU* 3.4 14.7 + - + +
314B HIS* 3.1 46.6 + - + +
328B HIS* 4.8 0.9 - - + -
331B PHE* 4.2 20.9 - - + -
346B ILE* 3.2 7.1 - - + +
397B ASP* 3.8 21.1 - - + +
398B ILE* 4.3 13.0 - - + -
401B PHE* 3.8 36.1 - - + -
482B ALA* 3.7 16.6 - - + -
485B ILE* 5.9 0.2 - - + -
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Residues in contact with ALA 311 (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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307B ALA 2.9 19.4 + - - +
308B CYS 3.7 3.6 - - - +
310B LEU* 1.3 76.0 - - - +
312B HIS* 1.3 58.3 + - - +
314B HIS* 3.3 1.9 + - - +
315B VAL* 3.0 34.8 + - - +
482B ALA* 3.5 28.8 - - - +
483B LEU* 3.9 15.6 - - + +
486B LYS* 4.3 14.8 - - + +
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Residues in contact with HIS 312 (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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250B LEU 5.1 0.9 + - - -
251B LEU* 3.3 32.5 - - + -
252B ARG 4.4 2.6 + - - -
253B HIS* 3.4 36.5 - + + +
256B ILE* 3.1 21.3 - - + +
308B CYS 3.0 17.3 + - - +
309B GLY 3.5 4.5 - - - +
311B ALA* 1.3 73.7 - - - +
313B LEU* 1.3 54.9 + - - +
315B VAL* 3.5 11.1 - - + +
317B ILE* 4.0 25.5 - - + +
323B LYS* 2.7 48.0 + - + -
252C ARG* 4.9 5.1 + - - -
254C ASP* 6.0 1.8 - - - -
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Residues in contact with LEU 313 (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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251B LEU* 4.5 8.7 - - + -
256B ILE* 3.8 22.2 - - + -
309B GLY 3.1 12.8 + - - +
310B LEU* 3.6 15.7 - - + +
311B ALA 3.3 0.2 - - - -
312B HIS* 1.3 77.2 - - - +
314B HIS* 1.3 55.3 - - + +
323B LYS* 3.1 14.1 + - - +
326B ILE* 2.7 68.0 + - + +
328B HIS* 4.1 33.2 - - + +
346B ILE* 4.2 20.9 - - + -
349B LEU* 5.0 10.1 - - + -
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Residues in contact with HIS 314 (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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310B LEU* 3.1 31.6 + - + +
311B ALA* 3.9 3.4 - - - +
313B LEU* 1.3 80.1 - - + +
315B VAL* 1.3 58.2 + - - +
316B GLU 3.6 0.2 + - - -
325B ALA* 3.2 23.3 - - - +
326B ILE 3.3 17.7 - - - +
327B ALA* 4.3 0.2 - - - -
394B LYS* 3.5 66.4 + - + +
397B ASP* 2.8 30.8 + - + +
398B ILE* 4.2 11.2 - - + +
481B THR* 5.9 0.6 - - - -
482B ALA* 4.0 15.6 + - + +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA 3.0 20.8 + - - +
312B HIS* 3.8 12.3 - - + +
314B HIS* 1.3 75.1 - - - +
316B GLU* 1.3 71.1 + - - +
317B ILE* 3.4 12.4 + - + -
323B LYS* 2.5 30.4 + - - +
325B ALA* 4.4 0.2 - - - -
483B LEU* 5.3 19.7 - - + -
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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