Contacts of the helix formed by residues 375 - 394 (chain B) in PDB entry 3MYV
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 GLY 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B ARG* 5.1 1.7 + - - -
371B GLY 2.9 8.1 + - - -
372B CYS 4.1 5.1 + - - -
373B LYS 3.7 0.8 - - - -
374B LEU* 1.3 82.5 - - - +
376B GLY* 1.3 67.2 + - - -
378B ALA* 3.5 8.1 + - - +
379B ALA* 3.1 25.1 + - - -
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Residues in contact with GLY 376 (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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375B GLY* 1.3 70.1 - - - -
377B ASP* 1.3 64.2 + - - -
379B ALA* 3.2 11.9 + - - +
380B VAL* 3.3 16.3 + - - +
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Residues in contact with ASP 377 (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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376B GLY* 1.3 72.6 - - - -
378B ALA* 1.3 57.8 + - - +
380B VAL* 3.2 10.9 + - - +
381B GLN* 2.9 43.8 + - + +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.9 16.0 - - - +
236B PHE* 3.5 21.2 - - + -
371B GLY* 3.5 7.7 - - - -
374B LEU* 3.9 29.4 - - + -
375B GLY 3.5 8.5 + - - +
376B GLY 3.3 0.6 - - - -
377B ASP* 1.3 79.0 - - - +
379B ALA* 1.3 53.0 + - - +
381B GLN* 3.8 10.7 + - - -
382B GLY* 2.7 32.6 + - - -
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Residues in contact with ALA 379 (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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371B GLY 3.4 20.1 + - - +
372B CYS* 4.9 0.9 - - - -
375B GLY* 3.1 27.6 + - - -
376B GLY 3.2 3.8 + - - +
378B ALA* 1.3 73.6 - - - +
380B VAL* 1.3 60.3 + - - +
383B LEU* 2.8 28.8 + - - +
401B MSE 4.2 9.9 - - + -
404B TYR* 3.3 25.2 - - + -
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLY 3.3 12.1 + - - +
377B ASP* 3.2 11.1 + - - +
379B ALA* 1.3 78.7 - - - +
381B GLN* 1.3 65.3 + - + +
383B LEU* 3.4 2.8 + - - +
384B GLY* 3.2 17.5 + - - -
401B MSE 4.0 21.5 - - + -
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Residues in contact with GLN 381 (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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236B PHE* 3.5 34.9 - - + -
240B ASP* 3.8 21.2 + - - -
244B LYS* 4.2 7.7 - - - +
377B ASP* 2.9 33.3 + - + +
378B ALA 3.8 0.9 + - - -
380B VAL* 1.3 78.1 - - + +
382B GLY* 1.3 64.5 + - - +
384B GLY* 3.1 4.4 + - - -
385B TYR* 3.1 33.0 + - + -
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Residues in contact with GLY 382 (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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236B PHE* 4.0 2.4 - - - -
367B ALA 3.8 18.4 - - - -
368B ALA* 3.6 5.8 - - - -
378B ALA 2.7 23.3 + - - -
381B GLN* 1.3 72.1 - - - +
383B LEU* 1.3 56.9 + - - +
385B TYR* 3.2 6.4 + - - +
386B LEU* 2.9 28.1 + - - +
404B TYR* 3.3 15.9 - - - -
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Residues in contact with LEU 383 (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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379B ALA 2.8 21.2 + - - +
380B VAL 3.7 5.2 - - - +
381B GLN 3.2 0.2 - - - -
382B GLY* 1.3 72.3 - - - +
384B GLY* 1.3 57.9 + - - +
386B LEU* 3.3 2.8 + - + +
387B ASN* 2.9 57.1 + - - +
399B VAL* 3.4 30.5 - - + +
400B THR* 3.9 1.1 - - - -
401B MSE 3.5 50.7 - - + +
404B TYR* 3.5 23.5 + - + -
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Residues in contact with GLY 384 (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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380B VAL 3.2 10.1 + - - -
381B GLN* 3.1 8.9 + - - -
383B LEU* 1.3 77.0 - - - +
385B TYR* 1.3 62.1 + - - +
387B ASN* 3.3 8.1 + - - +
388B GLU* 3.1 23.0 + - - +
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Residues in contact with TYR 385 (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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236B PHE* 4.7 3.1 - + - -
240B ASP* 2.6 42.3 + - + -
243B ILE* 3.7 30.3 - - + +
244B LYS* 4.1 9.4 - - - +
364B TYR* 3.7 46.5 - + + +
367B ALA* 3.6 23.8 - - + -
381B GLN* 3.1 29.4 + - + -
382B GLY* 3.6 6.1 - - - +
384B GLY* 1.3 73.0 - - - +
386B LEU* 1.3 67.7 + - - +
388B GLU* 3.1 19.4 + - + +
389B ILE* 3.4 7.3 + - - +
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Residues in contact with LEU 386 (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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365B LEU* 4.1 12.3 - - + -
368B ALA* 3.9 14.2 - - + +
382B GLY 2.9 15.0 + - - +
383B LEU* 3.5 8.7 - - + +
385B TYR* 1.3 75.4 - - - +
387B ASN* 1.3 63.8 + - - +
389B ILE* 3.1 7.3 + - - -
390B VAL* 2.9 27.0 + - + +
399B VAL* 3.9 27.6 - - + -
404B TYR* 3.8 27.6 - - + -
408B ARG* 4.4 8.5 - - + +
409B VAL* 4.2 12.6 - - + -
412B GLU* 3.8 33.2 - - + -
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Residues in contact with ASN 387 (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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383B LEU* 2.9 38.4 + - - +
384B GLY* 3.7 7.4 - - - +
385B TYR 3.3 0.2 - - - -
386B LEU* 1.3 76.4 - - - +
388B GLU* 1.3 56.5 + - - +
390B VAL* 4.1 4.4 - - - +
391B LYS* 2.8 51.5 + - + +
398B GLU* 3.4 13.3 - - - +
399B VAL* 2.8 48.9 + - - +
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Residues in contact with GLU 388 (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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254B LEU* 3.7 24.7 - - + -
364B TYR* 3.7 18.9 + - + -
384B GLY 3.1 12.8 + - - +
385B TYR* 3.1 12.0 + - - +
387B ASN* 1.3 76.5 - - - +
389B ILE* 1.3 58.0 + - - +
391B LYS* 4.0 3.2 - - - +
392B ARG* 3.0 28.8 + - - +
517B EDO 4.1 16.1 + - - -
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Residues in contact with ILE 389 (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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254B LEU* 3.8 25.1 - - + -
321B ARG* 4.0 2.1 + - - +
361B SER* 3.9 24.0 - - - +
364B TYR* 3.6 33.7 - - + -
365B LEU* 4.5 13.2 - - + -
385B TYR 3.9 3.6 - - - +
386B LEU 3.1 7.6 + - - +
388B GLU* 1.3 73.7 - - - +
390B VAL* 1.3 66.0 + - - +
392B ARG* 3.4 10.8 + - - +
393B GLY* 3.1 19.2 + - - -
412B GLU* 3.7 22.0 - - + +
416B GLU* 3.6 28.5 - - + +
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Residues in contact with VAL 390 (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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319B ASP* 4.8 0.3 - - - +
321B ARG* 4.4 3.7 + - - +
386B LEU* 2.9 22.7 + - + +
387B ASN* 3.7 6.7 - - - +
389B ILE* 1.3 77.9 - - - +
391B LYS* 1.3 57.0 + - + +
393B GLY* 3.3 3.5 + - - -
394B ASN* 3.0 24.4 + - - +
397B ASN* 3.7 36.1 + - + +
398B GLU* 4.0 10.3 - - - +
399B VAL* 3.8 11.7 - - + -
408B ARG* 3.6 18.4 - - - +
412B GLU* 3.4 34.8 - - + +
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Residues in contact with LYS 391 (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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257B HIS* 4.7 1.0 + - - +
387B ASN* 2.8 45.6 + - + +
388B GLU* 4.3 3.6 - - - +
390B VAL* 1.3 70.9 - - + +
392B ARG* 1.3 65.8 + - - +
393B GLY 3.2 1.6 - - - -
394B ASN 3.6 6.1 - - - -
395B PRO* 3.1 41.6 + - + +
397B ASN 2.9 27.3 + - - +
398B GLU* 3.8 13.0 + - - +
517B EDO 5.2 0.4 - - - -
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Residues in contact with ARG 392 (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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254B LEU* 4.1 5.9 - - + +
255B TYR 2.9 38.2 + - - +
257B HIS* 2.8 43.0 + - - +
260B TYR* 3.5 30.1 - - - -
273B GLU* 2.8 23.4 + - - -
320B VAL* 3.9 1.1 - - - +
321B ARG* 5.6 0.4 - - - +
361B SER* 2.9 24.4 + - - -
388B GLU 3.0 18.9 + - - +
389B ILE* 3.7 14.7 + - - +
391B LYS* 1.3 75.4 - - - +
393B GLY* 1.3 62.4 + - - +
416B GLU* 3.1 29.5 + - - -
517B EDO 3.6 26.1 + - - +
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Residues in contact with GLY 393 (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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257B HIS* 3.0 20.6 + - - -
319B ASP* 3.2 20.0 - - - -
320B VAL* 3.0 22.7 + - - -
321B ARG* 4.0 9.9 - - - -
389B ILE 3.1 13.8 + - - -
390B VAL 3.3 3.8 + - - -
391B LYS 3.2 0.2 - - - -
392B ARG* 1.3 80.8 - - - +
394B ASN* 1.3 58.8 + - - +
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Residues in contact with ASN 394 (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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257B HIS* 4.1 0.6 - - - -
316B ASP* 3.0 29.4 + - - +
318B GLY* 3.7 20.6 - - - +
319B ASP* 3.9 10.2 + - + +
390B VAL 3.0 14.8 + - - +
391B LYS* 3.3 5.3 - - - -
393B GLY* 1.3 78.3 - - - +
395B PRO* 1.3 72.6 - - - +
396B ASP* 3.0 32.5 + - - +
397B ASN* 3.0 33.0 + - - +
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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