Contacts of the helix formed by residues 295 - 315 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A THR 4.2 1.4 + - - -
294A LEU* 1.3 73.1 - - - +
296A PRO* 1.3 88.4 - - + +
297A HIS* 3.1 31.9 + - - +
298A LEU* 2.9 23.3 + - + +
299A ALA* 3.0 10.4 + - - +
413A ILE* 4.7 8.1 - - + +
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Residues in contact with PRO 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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294A LEU 3.7 0.6 - - - +
295A GLU* 1.3 98.7 - - + +
297A HIS* 1.3 62.3 + - - +
299A ALA* 3.2 4.3 + - + +
300A LEU* 3.0 23.8 + - - +
412A THR* 4.0 15.7 - - + -
413A ILE* 3.7 25.6 - - + +
414A VAL* 6.0 2.5 - - + -
460A VAL* 5.5 17.7 - - + +
461A LEU* 6.0 4.5 - - + -
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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
----------------------------------------------------------
295A GLU* 3.1 27.0 + - - +
296A PRO* 1.3 79.6 - - - +
298A LEU* 1.3 57.4 + - - +
300A LEU* 3.4 7.2 + - - +
301A ARG* 3.1 35.2 + - + +
493A SER* 6.2 4.3 - - - -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 4.3 9.9 - - + -
292A GLN* 5.3 2.0 - - + -
293A THR 4.8 3.6 - - - +
294A LEU* 3.8 28.7 - - + -
295A GLU* 2.9 19.2 + - + +
297A HIS* 1.3 76.0 - - - +
299A ALA* 1.3 66.6 + - - +
301A ARG* 3.1 14.3 + - - +
302A LEU* 3.0 36.4 + - + +
342A LEU* 4.0 39.5 - - + -
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Residues in contact with ALA 299 (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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294A LEU* 4.1 7.5 - - + +
295A GLU 3.0 10.3 + - - +
296A PRO* 3.2 10.1 + - + +
298A LEU* 1.3 77.6 - - - +
300A LEU* 1.3 57.3 + - - +
302A LEU* 3.6 0.7 + - - +
303A ALA* 3.0 28.3 + - - +
408A ILE* 3.7 23.3 - - + +
412A THR* 3.1 31.6 - - + +
464A LEU* 5.4 10.1 - - + -
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Residues in contact with LEU 300 (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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296A PRO 3.0 11.7 + - - +
297A HIS* 3.7 9.6 - - - +
299A ALA* 1.3 74.0 - - - +
301A ARG* 1.3 58.6 + - - +
303A ALA* 3.7 5.9 - - - +
304A VAL* 2.8 38.3 + - - +
460A VAL* 5.1 14.1 - - + -
464A LEU* 6.1 4.0 - - + -
489A LEU* 5.1 8.9 - - + +
492A ILE 6.0 1.1 - - - +
493A SER 5.7 9.9 - - - -
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Residues in contact with ARG 301 (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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297A HIS* 3.1 23.5 + - + +
298A LEU* 3.1 17.0 + - - +
300A LEU* 1.3 77.6 - - - +
302A LEU* 1.3 60.3 + - - +
304A VAL* 3.2 11.2 - - + +
305A SER* 2.9 27.9 + - - -
341A ASN* 2.6 42.6 + - - +
342A LEU* 3.4 23.5 + - - +
343A GLN* 4.2 22.2 - - + +
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Residues in contact with LEU 302 (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 LEU* 4.2 9.2 - - + -
288A PHE* 4.1 9.2 - - + -
289A LEU* 4.8 0.4 - - + -
294A LEU* 3.8 32.1 - - + -
298A LEU* 3.0 36.5 + - + +
299A ALA* 4.0 2.9 - - - +
301A ARG* 1.3 75.0 - - - +
303A ALA* 1.3 64.0 + - - +
305A SER* 3.1 6.1 + - - -
306A ALA* 3.0 27.2 + - - +
338A VAL* 3.9 28.9 - - + -
342A LEU* 3.9 14.8 - - - +
344A CYS* 3.4 23.2 - - - -
408A ILE* 4.4 12.1 - - + -
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Residues in contact with ALA 303 (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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299A ALA 3.0 19.3 + - - +
300A LEU* 3.7 7.2 - - - +
301A ARG 3.3 0.2 - - - -
302A LEU* 1.3 77.8 - - - +
304A VAL* 1.3 61.0 + - - +
306A ALA* 3.6 4.3 + - - +
307A ALA* 3.1 18.2 + - - +
401A PHE* 4.0 3.5 - - - -
405A LEU* 3.8 25.6 - - + -
408A ILE* 4.2 12.7 - - + +
464A LEU* 5.0 7.0 - - + -
489A LEU* 3.3 21.4 - - + +
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Residues in contact with VAL 304 (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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300A LEU* 2.8 20.7 + - + +
301A ARG* 3.2 19.1 - - + +
303A ALA* 1.3 72.5 - - - +
305A SER* 1.3 64.3 + - - +
307A ALA* 3.2 4.6 + - + +
308A CYS* 2.9 34.4 + - - -
343A GLN* 6.4 0.4 - - - +
486A LYS* 4.6 2.7 - - - +
489A LEU* 3.4 25.0 - - + +
490A GLN* 3.6 34.1 - - + +
493A SER 5.2 6.1 - - - +
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Residues in contact with SER 305 (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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255A ASN* 3.4 29.9 - - - +
301A ARG 2.9 18.8 + - - -
302A LEU* 3.1 5.9 + - - -
304A VAL* 1.3 81.2 - - - +
306A ALA* 1.3 67.0 + - - +
308A CYS* 3.1 9.1 + - - +
309A GLY 3.1 18.7 + - - -
343A GLN* 3.7 15.7 - - - -
344A CYS* 2.9 26.3 + - - -
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Residues in contact with ALA 306 (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 LEU* 5.9 2.0 - - + -
302A LEU 3.0 18.9 + - - +
303A ALA* 3.8 5.4 - - - +
305A SER* 1.3 77.5 + - - +
307A ALA* 1.3 62.3 + - - +
309A GLY* 3.1 4.6 + - - +
310A LEU* 3.1 21.7 + - - +
331A PHE* 4.8 9.8 - - + -
336A VAL* 4.9 5.6 - - + -
344A CYS* 3.9 19.0 - - + +
345A CYS* 6.3 0.2 - - - +
346A ILE* 4.2 8.3 - - - +
401A PHE* 4.0 15.3 - - + -
404A VAL* 5.9 3.4 - - + -
408A ILE* 5.8 3.6 - - + -
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Residues in contact with ALA 307 (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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303A ALA 3.1 16.2 + - - +
304A VAL 3.4 8.7 - - - +
306A ALA* 1.3 74.8 - - - +
308A CYS* 1.3 57.5 + - - +
310A LEU* 4.0 3.2 - - - +
311A ALA* 3.0 29.8 + - - +
401A PHE* 3.7 21.0 - - + -
482A ALA* 4.4 4.3 - - - +
485A ILE* 4.2 2.9 - - + -
486A LYS* 4.0 23.1 - - - +
489A LEU* 3.8 13.5 - - + -
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Residues in contact with CYS 308 (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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253A HIS* 4.2 8.2 + - + -
255A ASN* 3.5 17.0 - - - +
304A VAL* 2.9 27.7 + - - +
305A SER* 3.1 11.2 + - - +
307A ALA* 1.3 74.0 - - - +
309A GLY* 1.3 65.5 + - - +
311A ALA* 3.4 2.1 + - - +
312A HIS* 3.0 24.6 + - - +
486A LYS* 4.1 35.5 + - + +
490A GLN* 4.7 7.2 - - - -
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Residues in contact with GLY 309 (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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255A ASN* 3.5 31.2 - - - +
256A ILE* 4.2 3.3 - - - +
305A SER 3.1 10.9 + - - -
306A ALA 3.1 3.8 + - - -
308A CYS* 1.3 76.7 - - - +
310A LEU* 1.3 60.8 + - - +
312A HIS* 3.3 8.5 + - - +
313A LEU* 3.1 24.3 + - - +
346A ILE* 3.3 10.1 - - - -
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Residues in contact with LEU 310 (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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306A ALA 3.1 14.5 + - - +
307A ALA* 4.1 6.1 - - - +
309A GLY* 1.3 71.8 - - - +
311A ALA* 1.3 65.0 + - - +
313A LEU* 3.3 12.3 + - + +
314A HIS* 3.0 48.5 + - + +
328A HIS* 4.8 0.9 - - + -
331A PHE* 4.2 21.3 - - + -
346A ILE* 3.2 11.2 - - + +
397A ASP* 3.8 18.8 - - + +
398A ILE* 4.3 12.1 - - + -
401A PHE* 3.8 36.1 - - + -
482A ALA* 4.1 14.1 - - + -
485A ILE* 6.2 0.4 - - + -
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Residues in contact with ALA 311 (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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307A ALA 3.0 20.1 + - - +
308A CYS 3.8 3.6 - - - +
310A LEU* 1.3 76.3 - - - +
312A HIS* 1.3 58.0 + - - +
314A HIS* 3.3 2.6 + - - +
315A VAL* 3.0 35.2 + - - +
482A ALA* 3.7 24.5 - - + +
483A LEU* 4.3 9.2 - - + +
486A LYS* 4.1 21.8 - - + +
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Residues in contact with HIS 312 (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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250A LEU 5.1 1.0 + - - -
251A LEU* 3.3 30.5 - - + -
252A ARG 4.2 2.6 + - - -
253A HIS* 3.6 35.5 - + + +
256A ILE* 3.1 20.5 - - + +
308A CYS 3.0 18.4 + - - +
309A GLY 3.4 4.5 - - - +
311A ALA* 1.3 76.6 - - - +
313A LEU* 1.3 54.7 + - - +
315A VAL* 3.5 12.3 - - + +
317A ILE* 4.6 16.8 - - + +
323A LYS* 2.7 56.0 + - - +
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Residues in contact with LEU 313 (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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251A LEU* 4.2 9.6 - - + -
256A ILE* 3.8 22.0 - - + -
309A GLY 3.1 13.6 + - - +
310A LEU* 3.5 13.9 - - + +
312A HIS* 1.3 76.3 - - - +
314A HIS* 1.3 56.9 + - + +
323A LYS* 3.0 13.2 + - - +
326A ILE* 2.7 64.9 + - + +
328A HIS* 4.1 37.2 - - + +
346A ILE* 4.1 21.3 - - + -
349A LEU* 4.9 11.2 - - + -
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Residues in contact with HIS 314 (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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310A LEU* 3.0 35.5 + - + +
311A ALA* 3.9 5.6 - - - +
313A LEU* 1.3 78.8 - - + +
315A VAL* 1.3 57.0 + - - +
316A GLU 3.5 0.3 + - - -
325A ALA* 3.1 23.9 - - - +
326A ILE 3.3 17.0 - - - +
327A ALA* 4.3 0.4 - - - -
394A LYS* 3.5 63.1 + - + +
397A ASP* 2.8 30.8 + - + +
398A ILE* 4.2 9.9 - - + +
482A ALA* 4.1 14.1 + - + +
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Residues in contact with VAL 315 (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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311A ALA 3.0 21.0 + - - +
312A HIS* 3.8 11.2 - - + +
313A LEU 3.4 0.2 - - - -
314A HIS* 1.3 76.2 - - - +
316A GLU* 1.3 71.4 + - - +
317A ILE* 4.5 16.4 - - + -
323A LYS* 3.3 21.5 + - - +
325A ALA* 4.4 0.2 - - - -
483A LEU* 5.4 13.0 - - + -
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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
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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