Contacts of the helix formed by residues 376 - 394 (chain A) in PDB entry 4MZ7
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 HIS 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 3.6 22.1 - - + +
157A PHE* 4.4 4.0 - + + -
370A HIS 4.3 0.4 + - - -
371A ARG 4.6 4.2 + - - -
372A ARG 3.8 11.9 - - - +
373A ALA* 3.1 19.7 + - - +
374A TYR 3.4 1.2 + - - -
375A GLN* 1.3 76.4 - - - +
377A LYS* 1.3 65.6 + - + +
378A VAL* 3.0 33.3 + - + -
379A GLY* 3.1 12.6 + - - +
380A ASN* 2.9 28.4 + - - +
551A ARG* 5.2 0.2 - - - +
703A DGT 2.7 70.1 + + - -
801B DGT 4.4 1.1 - - - -
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN 3.2 2.4 + - - -
376A HIS* 1.3 75.3 + - + +
378A VAL* 1.3 67.8 + - + +
381A ILE 3.3 13.2 + - - -
456A TYR* 3.5 56.1 - - + +
551A ARG* 4.0 16.2 - - - +
553A TYR* 2.6 35.3 + - - +
703A DGT 2.7 60.6 + - - -
801B DGT 5.0 1.8 - - - -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 3.9 8.7 - - + -
376A HIS* 3.0 11.1 + - + +
377A LYS* 1.3 82.7 - - + +
379A GLY* 1.3 66.7 + - - +
380A ASN 3.1 1.3 - - - -
381A ILE* 3.2 8.0 + - + +
382A ILE* 2.9 26.9 + - + +
453A LEU* 3.7 29.4 - - + -
456A TYR* 6.0 2.0 - - + -
553A TYR* 5.4 0.4 - - + -
703A DGT 3.6 22.0 - - - +
801B DGT 3.6 43.5 - - - +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLY 4.5 14.1 - - - -
153A GLY* 4.9 4.5 - - - -
156A VAL* 3.6 15.7 - - - +
373A ALA 5.7 1.3 - - - -
374A TYR 5.8 0.4 - - - -
376A HIS* 3.1 17.8 + - - -
378A VAL* 1.3 77.5 - - - +
380A ASN* 1.3 59.8 + - - +
382A ILE* 3.4 3.1 + - - +
383A ASP* 3.0 33.1 + - - +
702A DGT 6.2 1.6 - - - -
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Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.7 11.2 + - - +
374A TYR 3.2 22.2 - - - +
375A GLN* 3.1 22.9 + - - +
376A HIS 2.9 15.6 + - - +
377A LYS 3.9 5.2 - - - +
379A GLY* 1.3 76.7 - - - +
381A ILE* 1.3 59.6 + - - +
383A ASP* 3.3 10.9 + - - +
384A THR* 2.8 31.5 + - - -
501A ASP* 3.6 22.1 + - - +
503A ILE* 3.6 5.1 - - - +
551A ARG* 3.5 20.6 - - - +
553A TYR* 4.0 5.2 - - - +
702A DGT 4.7 4.2 + - - +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LYS 3.3 3.0 + - - +
378A VAL* 3.2 27.6 + - + +
380A ASN* 1.3 75.1 - - - +
382A ILE* 1.3 63.9 + - - +
384A THR* 3.3 17.7 + - + +
385A MET* 2.9 35.0 + - + +
453A LEU* 4.4 13.9 - - + -
454A PHE* 3.8 42.0 - - + +
499A ILE* 4.1 8.7 - - + -
553A TYR* 3.6 51.5 + - + -
801B DGT 5.8 0.7 - - - +
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Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLY* 4.2 6.3 - - - +
155A TYR* 3.5 40.8 - - + +
156A VAL* 4.4 3.8 - - + -
378A VAL* 2.9 31.1 + - + +
379A GLY 3.8 4.0 - - - +
381A ILE* 1.3 73.5 - - - +
383A ASP* 1.3 60.1 + - - +
385A MET* 3.3 6.6 + - - +
386A ILE* 2.9 48.1 + - + +
448A ILE* 4.5 14.4 - - + -
451A ARG* 4.0 17.5 - - - +
453A LEU* 4.2 25.6 - - + -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU 4.9 0.2 - - - +
151A GLY* 4.5 0.7 - - - -
152A GLY* 2.9 31.5 + - - -
153A GLY 5.1 0.2 + - - -
213A PHE* 4.8 0.5 - - - +
215A HIS* 5.1 1.9 + - - +
216A MET* 3.5 37.2 + - + +
220A ARG* 4.0 14.0 + - - +
379A GLY 3.0 17.3 + - - +
380A ASN* 3.5 12.7 - - - +
382A ILE* 1.3 75.3 - - - +
384A THR* 1.3 57.4 + - - +
386A ILE* 3.5 2.6 + - - +
387A THR* 2.9 34.2 + - - -
702A DGT 4.3 20.4 + - - -
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Residues in contact with THR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.5 21.8 + - - +
380A ASN 2.8 18.4 + - - -
381A ILE* 3.3 19.5 - - + +
382A ILE 3.2 0.2 - - - -
383A ASP* 1.3 73.6 - - - +
385A MET* 1.3 60.5 + - - +
387A THR* 3.4 7.3 + - - +
388A ASP* 2.9 41.9 + - - +
454A PHE* 4.9 1.3 - - + -
499A ILE* 4.0 34.4 - - + +
501A ASP* 4.8 3.5 + - - -
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Residues in contact with MET 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ILE 2.9 23.4 + - - +
382A ILE* 3.3 4.5 + - - +
384A THR* 1.3 71.3 - - - +
386A ILE* 1.3 67.2 + - - +
388A ASP* 3.2 9.9 + - - +
389A ALA 2.9 19.4 + - - -
444A ILE* 3.4 20.9 - - + +
447A GLN* 4.3 13.0 - - + -
448A ILE* 4.0 23.6 - - + -
452A ASN 3.8 21.3 - - - +
453A LEU* 3.8 32.1 - - + -
454A PHE* 3.7 44.6 - - + -
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLY* 4.8 0.9 - - - -
155A TYR* 4.7 4.5 - - + -
213A PHE* 4.0 26.5 - - + -
216A MET* 3.6 16.2 - - + -
382A ILE* 2.9 37.0 + - + +
383A ASP* 3.8 9.9 - - - +
385A MET* 1.3 75.4 - - - +
387A THR* 1.3 58.4 + - - +
389A ALA* 3.2 2.6 + - - +
390A PHE* 2.9 56.8 + - + -
427A PHE* 3.9 24.5 - - + -
445A LEU* 4.3 6.7 - - + -
448A ILE* 3.7 15.7 - - + -
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Residues in contact with THR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A MET* 3.2 26.2 + - - +
220A ARG* 3.7 11.8 - - + +
221A PHE* 3.8 26.6 + - + +
224A LEU* 4.1 22.0 - - + -
383A ASP 2.9 20.1 + - - -
384A THR* 3.5 8.5 - - - +
386A ILE* 1.3 76.5 - - - +
388A ASP* 1.3 57.4 + - - +
390A PHE* 3.3 8.2 + - - +
391A LEU* 2.9 33.8 + - + +
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Residues in contact with ASP 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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224A LEU* 5.4 2.9 - - - +
384A THR* 2.9 26.2 + - - +
385A MET* 3.2 9.9 + - - +
387A THR* 1.3 77.3 - - - +
389A ALA* 1.3 56.2 + - - +
391A LEU* 3.2 17.0 + - - +
392A LYS* 3.0 35.1 + - - +
444A ILE* 4.0 16.7 - - + +
454A PHE* 3.9 25.6 - - - -
499A ILE* 5.1 0.5 - - - +
555A LYS* 4.6 9.5 + - - -
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Residues in contact with ALA 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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385A MET 2.9 9.5 + - - +
386A ILE 3.5 4.9 - - - +
388A ASP* 1.3 72.3 - - - +
390A PHE* 1.3 63.3 + - + +
392A LYS 3.2 1.0 + - - -
393A ALA* 2.9 25.5 + - - +
430A ILE* 4.8 1.6 - - + -
441A ALA* 3.3 31.2 - - + +
444A ILE* 3.9 13.3 - - + +
445A LEU* 3.5 34.8 - - + -
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Residues in contact with PHE 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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212A PRO* 3.8 13.5 - - + -
213A PHE* 3.9 12.3 - + - -
216A MET* 3.8 26.5 - - + -
217A PHE* 4.9 1.3 - + - -
221A PHE* 3.5 23.6 - + + -
386A ILE* 2.9 35.2 + - + -
387A THR 3.3 6.3 + - - +
389A ALA* 1.3 76.4 - - + +
391A LEU* 1.3 57.3 + - - +
393A ALA* 3.2 5.4 + - - +
394A ASP* 2.9 31.7 + - - +
409A ILE* 4.0 21.1 - - + +
426A ILE* 3.2 32.5 - - + -
427A PHE* 4.2 11.4 - + - -
430A ILE* 3.8 20.6 - - + -
445A LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 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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221A PHE* 3.6 20.6 - - + -
224A LEU* 4.0 31.6 - - + +
225A ALA* 3.7 30.7 - - + +
387A THR* 2.9 24.1 + - + +
388A ASP* 3.2 15.7 + - - +
390A PHE* 1.3 75.4 - - - +
392A LYS* 1.3 62.6 + - + +
394A ASP* 3.4 16.3 + - + +
395A ASP* 4.8 3.8 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASP* 3.0 18.2 + - - +
389A ALA 3.2 4.2 + - - +
391A LEU* 1.3 76.2 - - + +
393A ALA* 1.3 57.6 + - - +
394A ASP 3.5 0.2 - - - -
395A ASP* 5.2 0.4 - - - -
396A TYR* 3.6 21.7 - - - -
437A LYS 4.6 2.6 - - - +
440A ASP* 4.0 24.9 + - + +
441A ALA* 4.1 17.0 + - - +
444A ILE* 3.5 32.1 - - + +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 2.9 16.1 + - - +
390A PHE 3.2 3.3 + - - +
392A LYS* 1.3 76.7 - - - +
394A ASP* 1.3 58.8 + - - +
395A ASP 3.3 2.5 - - - -
396A TYR* 2.9 22.8 + - - +
397A ILE* 3.2 18.3 + - + +
409A ILE* 4.4 1.6 - - + -
430A ILE* 3.6 25.1 - - + -
438A LEU* 3.6 24.5 - - + -
441A ALA* 3.7 4.5 - - + -
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Residues in contact with ASP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 4.1 6.7 - - + -
225A ALA* 4.4 5.4 - - - +
390A PHE 2.9 15.2 + - - +
391A LEU* 3.4 16.1 + - + +
393A ALA* 1.3 77.5 - - - +
395A ASP* 1.3 60.9 + - - +
396A TYR 3.4 0.5 + - - -
397A ILE 4.2 3.8 + - - +
408A ARG* 3.1 41.7 + - - +
409A ILE* 3.1 20.7 + - - +
410A SER* 2.4 51.2 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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