Contacts of the helix formed by residues 415 - 428 (chain A) in PDB entry 2ZXI
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 SER 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.2 19.5 - - - -
410A LEU* 3.8 14.0 - - - +
411A ARG 3.4 3.4 + - - -
412A ARG 3.6 2.3 - - - +
414A GLU* 1.3 81.4 - - - +
416A TYR* 1.3 62.7 + - - +
417A ILE* 3.6 3.8 + - - +
418A GLY* 3.0 21.8 + - - -
419A VAL* 3.2 21.8 + - - +
446A ILE* 3.7 8.8 - - - +
454A ARG* 3.4 3.8 - - - +
455A LEU* 4.1 19.7 - - - -
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Residues in contact with TYR 416 (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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56A ALA* 4.1 15.8 - - + +
59A ILE* 4.4 22.4 - - + -
60A VAL* 3.8 13.0 - - + -
63A GLU* 2.7 20.9 + - - +
415A SER* 1.3 70.3 - - - +
417A ILE* 1.3 65.7 + - - +
419A VAL* 3.2 10.4 + - + -
420A MET* 3.0 22.3 + - - +
435A LEU* 3.7 24.2 + - + +
436A PHE* 5.7 0.3 - - - -
438A SER* 2.8 45.4 + - - -
440A SER* 4.3 23.8 + - - -
443A ARG* 6.2 2.9 - - + -
446A ILE* 3.7 20.1 - - + +
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Residues in contact with ILE 417 (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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60A VAL* 4.1 14.8 - - + -
63A GLU* 3.1 27.3 + - + +
64A ILE* 4.0 28.5 - - + +
67A LEU* 4.4 17.9 - - + -
389A GLY* 3.5 28.7 - - - +
392A ILE* 4.6 0.4 - - + -
410A LEU* 3.5 21.8 - - + -
415A SER* 3.2 2.2 - - - +
416A TYR* 1.3 77.5 - - - +
418A GLY* 1.3 62.6 + - - +
420A MET* 3.4 9.9 + - + +
421A ILE* 3.0 38.3 + - + +
455A LEU* 5.2 0.7 - - + -
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 3.1 31.8 - - - +
412A ARG* 3.8 8.7 - - - +
415A SER* 3.0 18.3 + - - -
416A TYR 3.1 0.2 - - - -
417A ILE* 1.3 75.8 - - - +
419A VAL* 1.3 58.4 + - - +
421A ILE* 3.4 4.0 + - - +
422A ASP* 2.8 32.9 + - - +
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Residues in contact with VAL 419 (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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412A ARG* 3.2 59.0 - - + +
415A SER 3.2 10.1 + - - +
416A TYR* 3.2 17.0 + - + +
418A GLY* 1.3 75.5 - - - +
420A MET* 1.3 63.0 + - - +
422A ASP* 3.2 2.6 + - - +
423A ASP* 2.9 35.7 + - - +
438A SER* 3.9 18.8 - - - +
439A ARG 4.8 4.7 - - - +
440A SER* 4.3 17.7 - - - +
446A ILE* 4.6 0.4 - - + -
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Residues in contact with MET 420 (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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60A VAL* 5.0 1.1 - - + -
385A GLU 4.9 0.2 - - - +
386A GLU* 3.3 53.8 - - - +
389A GLY* 4.3 8.7 - - - -
390A GLN* 3.9 22.4 - - + +
416A TYR* 3.0 14.2 + - - +
417A ILE* 3.6 18.6 - - + +
419A VAL* 1.3 76.4 - - - +
421A ILE* 1.3 63.7 + - + +
423A ASP* 3.2 4.0 + - - +
424A LEU* 3.0 38.3 + - + +
433A TYR* 3.4 31.5 + - + -
435A LEU* 3.9 18.6 - - + -
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Residues in contact with ILE 421 (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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362A PRO* 3.3 35.0 - - + +
364A LEU* 3.9 34.1 - - + -
390A GLN* 4.5 15.5 - - + -
393A VAL* 3.8 32.3 - - + -
410A LEU* 5.3 6.5 - - + +
417A ILE* 3.0 26.9 + - + +
418A GLY* 4.0 4.7 - - - +
420A MET* 1.3 77.7 - - + +
422A ASP* 1.3 59.9 + - - +
424A LEU* 3.5 7.5 + - + +
425A THR* 2.9 30.7 + - + +
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Residues in contact with ASP 422 (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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362A PRO* 5.2 6.9 - - + +
410A LEU 5.8 0.4 - - - +
412A ARG* 2.9 35.5 + - + +
418A GLY 2.8 19.1 + - - +
419A VAL 3.5 4.3 - - - +
421A ILE* 1.3 79.1 - - - +
423A ASP* 1.3 57.9 + - - +
425A THR* 3.6 4.0 + - - -
426A THR* 2.9 38.7 + - - -
427A LYS* 6.0 0.5 - - - -
560A GLU* 5.4 0.7 - - - +
594A GLN* 3.6 14.2 + - - +
597A ARG* 3.0 37.6 + - - -
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Residues in contact with ASP 423 (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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412A ARG* 3.1 21.9 + - - -
419A VAL* 2.9 27.7 + - - +
420A MET 3.2 3.6 + - - +
422A ASP* 1.3 77.3 - - - +
424A LEU* 1.3 57.0 + - - +
427A LYS* 2.7 58.4 + - + +
428A GLY 3.2 3.3 + - - +
433A TYR* 3.2 33.9 + - + -
438A SER* 3.7 8.8 - - - -
439A ARG 4.9 0.7 + - - -
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Residues in contact with LEU 424 (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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357A PRO* 3.1 33.3 - - + +
358A THR 3.9 1.2 + - - -
364A LEU* 5.6 1.3 - - + -
379A ASN* 3.8 24.0 - - - +
380A GLY 4.6 0.4 - - - +
381A THR* 3.6 33.9 - - + -
390A GLN* 3.8 11.4 - - + +
420A MET* 3.0 28.6 + - + +
421A ILE* 3.8 10.8 - - + +
422A ASP 3.3 0.2 - - - -
423A ASP* 1.3 75.7 - - - +
425A THR* 1.3 59.9 + - + +
428A GLY* 3.1 23.5 + - - +
429A VAL* 3.8 16.6 - - + -
433A TYR* 3.8 19.7 - - + -
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Residues in contact with THR 425 (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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357A PRO 3.5 21.8 - - - +
358A THR* 3.9 9.6 - - - +
360A LEU* 3.5 23.6 - - + +
361A TYR* 3.5 23.8 - - - +
362A PRO* 4.0 18.3 - - + +
364A LEU* 4.8 3.6 - - + -
367A LYS* 5.0 1.4 + - - -
379A ASN* 5.7 0.2 - - - +
421A ILE* 2.9 22.2 + - + +
422A ASP* 3.6 3.1 + - - -
424A LEU* 1.3 80.2 - - + +
426A THR* 1.3 63.9 + - - +
587A PHE* 3.6 18.7 - - - +
594A GLN* 4.3 4.0 + - - -
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Residues in contact with THR 426 (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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422A ASP* 2.9 24.3 + - - -
425A THR* 1.3 79.9 + - - +
427A LYS* 1.3 63.9 + - + +
587A PHE* 3.0 27.1 - - + -
594A GLN* 2.9 38.2 + - + +
597A ARG* 3.9 18.4 - - + +
598A ILE* 3.8 36.6 - - + +
599A ASP 4.8 1.7 + - - -
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Residues in contact with LYS 427 (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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358A THR* 4.5 3.8 - - - +
412A ARG* 6.0 0.2 - - - +
422A ASP* 6.0 0.7 - - - -
423A ASP* 2.7 46.1 + - + +
426A THR* 1.3 76.2 - - - +
428A GLY* 1.3 63.8 + - - +
587A PHE* 5.2 2.8 - - - -
597A ARG* 3.0 44.6 + - - +
599A ASP* 5.1 13.5 - - + +
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Residues in contact with GLY 428 (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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357A PRO* 4.8 4.0 - - - -
358A THR* 3.6 16.7 - - - +
423A ASP 3.2 2.3 + - - +
424A LEU 3.1 20.9 + - - -
426A THR 3.7 1.0 - - - -
427A LYS* 1.3 89.8 - - - +
429A VAL* 1.3 69.9 + - - +
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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