Contacts of the helix formed by residues 375 - 394 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ARG* 5.2 1.2 + - - -
371A GLY 3.0 7.1 + - - -
372A CYS 3.6 2.4 + - - -
373A LYS 3.5 2.8 + - - -
374A LEU* 1.3 81.6 - - - +
376A GLY* 1.3 67.9 + - - -
378A ALA* 3.5 8.1 + - - +
379A ALA* 3.2 18.0 + - - -
520A EDO 3.5 19.3 + - - -
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLY* 1.3 72.3 - - - -
377A ASP* 1.3 63.3 + - - -
379A ALA* 3.1 12.8 + - - +
380A VAL* 3.2 16.4 + - - +
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Residues in contact with ASP 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLY 3.6 0.2 + - - -
376A GLY* 1.3 69.9 - - - -
378A ALA* 1.3 65.7 + - - +
380A VAL* 3.2 11.2 + - - +
381A GLN* 3.0 43.4 + - - +
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Residues in contact with ALA 378 (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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233A ARG* 3.8 25.5 - - - +
236A PHE* 3.4 30.5 - - + -
371A GLY* 3.5 9.6 - - - -
374A LEU* 3.8 22.0 - - + -
375A GLY 3.5 9.1 + - - +
376A GLY 3.3 0.4 - - - -
377A ASP* 1.3 78.9 - - - +
379A ALA* 1.3 55.6 + - - +
381A GLN* 4.9 0.4 - - - -
382A GLY 2.8 23.9 + - - -
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Residues in contact with ALA 379 (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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371A GLY 3.4 21.7 + - - +
375A GLY* 3.2 19.6 + - - -
376A GLY 3.1 12.4 + - - +
378A ALA* 1.3 73.7 - - - +
380A VAL* 1.3 66.3 + - - +
383A LEU* 2.9 21.8 + - - +
401A MSE 4.4 5.8 - - + -
404A TYR* 3.1 20.5 - - + -
520A EDO 4.0 14.6 - - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLY 3.2 11.2 + - - +
377A ASP* 3.2 16.4 + - - +
379A ALA* 1.3 76.8 - - - +
381A GLN* 1.3 66.2 + - + +
383A LEU* 3.4 4.6 + - - +
384A GLY* 3.2 16.5 + - - -
401A MSE 4.0 21.5 - - + +
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Residues in contact with GLN 381 (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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236A PHE* 3.4 32.2 - - + -
240A ASP* 4.3 10.3 - - - +
244A LYS* 5.2 2.8 + - - -
377A ASP* 3.0 35.2 + - - +
378A ALA* 4.9 0.2 - - - -
380A VAL* 1.3 80.4 - - + +
382A GLY* 1.3 58.4 + - - +
384A GLY* 3.0 16.6 + - - -
385A TYR* 3.1 24.8 + - + -
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Residues in contact with GLY 382 (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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236A PHE* 4.1 1.3 - - - -
367A ALA 3.9 18.8 - - - -
368A ALA* 3.6 7.7 - - - +
378A ALA 2.8 19.9 + - - -
379A ALA 3.3 0.2 + - - -
381A GLN* 1.3 70.0 - - - +
383A LEU* 1.3 59.9 + - - +
385A TYR* 3.3 6.1 + - - +
386A LEU* 2.8 29.1 + - - +
404A TYR* 3.2 18.2 - - - -
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Residues in contact with LEU 383 (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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379A ALA 2.9 17.0 + - - +
380A VAL 3.5 6.3 - - - +
382A GLY* 1.3 75.2 - - - +
384A GLY* 1.3 59.4 + - - +
386A LEU* 3.3 3.6 + - + -
387A ASN* 2.9 47.8 + - - +
399A VAL* 3.5 29.2 - - + +
400A THR 4.1 0.4 - - - -
401A MSE 3.6 49.6 - - + +
404A TYR* 3.4 33.7 + - + -
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Residues in contact with GLY 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL 3.2 7.4 + - - -
381A GLN* 3.0 9.5 + - - -
383A LEU* 1.3 78.7 - - - +
385A TYR* 1.3 62.7 + - - +
387A ASN* 3.3 7.9 + - - +
388A GLU* 3.0 22.9 + - - +
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Residues in contact with TYR 385 (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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236A PHE* 4.8 3.6 - + - -
240A ASP* 2.6 40.7 + - + -
243A ILE* 3.8 32.5 - - + +
244A LYS* 4.3 8.5 - - - +
364A TYR* 3.6 43.2 - + + +
367A ALA* 3.6 21.5 - - + -
381A GLN* 3.1 25.0 + - + -
382A GLY* 3.7 7.0 - - - +
383A LEU 3.3 0.2 - - - -
384A GLY* 1.3 75.0 - - - +
386A LEU* 1.3 66.9 + - - +
388A GLU* 3.2 13.5 + - + +
389A ILE* 3.4 16.1 + - - +
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Residues in contact with LEU 386 (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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364A TYR 5.4 0.2 - - - -
365A LEU* 4.1 11.9 - - + -
368A ALA* 3.8 15.6 - - + +
382A GLY 2.8 21.2 + - - +
383A LEU* 3.3 5.8 + - + +
385A TYR* 1.3 70.8 - - - +
387A ASN* 1.3 58.8 + - - +
389A ILE* 3.1 9.2 + - - +
390A VAL* 3.0 34.2 + - + +
399A VAL* 3.9 27.8 - - + -
404A TYR* 3.8 28.0 - - + -
408A ARG* 4.6 7.4 - - + +
409A VAL* 4.2 13.9 - - + -
412A GLU* 3.8 33.7 - - + -
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 2.9 39.0 + - - +
384A GLY* 3.7 6.5 - - - +
386A LEU* 1.3 73.2 - - - +
388A GLU* 1.3 60.2 + - - +
390A VAL* 4.1 5.3 - - - +
391A LYS* 2.8 57.3 + - + +
398A GLU* 3.4 11.4 - - - +
399A VAL* 2.8 49.1 + - - +
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Residues in contact with GLU 388 (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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254A LEU* 3.7 24.9 - - + -
364A TYR* 3.9 18.4 - - + -
384A GLY 3.0 13.5 + - - +
385A TYR* 3.2 11.2 + - - +
387A ASN* 1.3 76.5 - - - +
389A ILE* 1.3 57.0 + - - +
391A LYS* 4.2 2.7 - - - +
392A ARG* 3.1 28.4 + - - +
519A EDO 4.0 17.2 + - - -
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Residues in contact with ILE 389 (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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254A LEU* 4.0 17.9 - - + -
321A ARG* 3.9 2.6 + - - +
361A SER* 3.9 25.8 - - - +
364A TYR* 3.6 38.1 - - + -
365A LEU* 4.4 14.8 - - + -
385A TYR 3.7 4.9 - - - +
386A LEU 3.1 7.6 + - - +
388A GLU* 1.3 74.1 - - - +
390A VAL* 1.3 66.7 + - - +
392A ARG* 3.4 9.5 + - - +
393A GLY* 3.1 18.9 + - - -
412A GLU* 3.8 22.1 - - + +
416A GLU* 3.6 25.8 - - + +
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Residues in contact with VAL 390 (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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319A ASP* 4.9 0.5 - - - +
321A ARG* 4.5 3.3 + - - +
386A LEU* 3.0 19.8 + - + +
387A ASN* 3.8 7.0 - - - +
389A ILE* 1.3 76.1 - - - +
391A LYS* 1.3 56.9 + - + +
393A GLY* 3.3 3.5 + - - -
394A ASN* 3.0 25.5 + - - +
397A ASN* 3.6 36.4 + - + +
398A GLU* 3.9 9.2 - - - +
399A VAL* 3.9 13.2 - - + -
408A ARG* 3.8 19.1 - - - +
412A GLU* 3.4 33.9 - - + +
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Residues in contact with LYS 391 (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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257A HIS* 5.1 1.0 - - - +
387A ASN* 2.8 48.4 + - + +
388A GLU* 4.4 2.9 - - - +
390A VAL* 1.3 75.3 - - + +
392A ARG* 1.3 65.6 + - - +
393A GLY 3.2 0.2 - - - -
394A ASN 3.4 7.0 - - - +
395A PRO* 3.1 37.1 - - + +
397A ASN 3.3 23.3 - - - +
398A GLU* 4.0 12.3 + - - +
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Residues in contact with ARG 392 (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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254A LEU* 4.1 6.7 - - + +
255A TYR 2.8 47.3 + - - +
257A HIS* 2.9 40.0 + - - +
260A TYR* 3.6 28.3 - - - -
273A GLU* 2.9 22.4 + - - -
320A VAL* 4.3 1.4 - - - +
321A ARG* 5.6 0.2 - - - +
361A SER* 2.9 24.0 + - - -
388A GLU 3.1 20.0 + - - +
389A ILE* 3.8 14.2 + - - +
391A LYS* 1.3 77.1 - - - +
393A GLY* 1.3 61.6 + - - +
416A GLU* 3.1 30.3 + - - -
519A EDO 3.5 25.7 + - - +
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Residues in contact with GLY 393 (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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257A HIS* 3.0 10.4 + - - -
319A ASP* 3.2 19.9 - - - -
320A VAL* 2.9 32.8 + - - -
321A ARG* 4.0 10.3 - - - -
389A ILE 3.1 13.9 + - - -
390A VAL 3.6 4.0 - - - -
391A LYS 3.2 0.2 - - - -
392A ARG* 1.3 79.0 - - - +
394A ASN* 1.3 58.7 + - - +
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Residues in contact with ASN 394 (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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316A ASP* 2.9 31.3 + - - -
318A GLY* 3.5 25.0 - - - +
319A ASP* 3.8 6.7 - - + +
390A VAL 3.0 13.9 + - - +
391A LYS* 3.2 5.8 - - - -
392A ARG 3.4 0.2 - - - -
393A GLY* 1.3 77.7 - - - +
395A PRO* 1.3 72.1 - - - +
396A ASP* 3.0 29.3 + - - +
397A ASN* 3.0 35.1 + - - +
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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
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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