Contacts of the helix formed by residues 424 - 436 (chain A) in PDB entry 2EZT
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 VAL 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A MET* 3.9 17.7 - - + +
71A LYS* 5.2 1.8 - - - +
96A ASP* 4.3 9.0 - - - +
391A SER* 3.4 4.3 + - - -
392A ILE 3.4 21.5 - - - +
393A ASP* 3.4 7.6 + - - -
394A VAL* 4.3 1.3 - - + -
415A THR* 4.0 3.4 - - - +
416A SER* 3.9 24.9 - - - +
421A THR* 3.5 38.8 - - + +
422A MET 3.4 0.4 - - - -
423A GLY* 1.3 75.4 - - - +
425A GLY* 1.3 59.3 + - - +
426A ILE 3.4 0.2 - - - -
427A PRO* 3.5 6.9 - - - +
428A GLY* 2.9 29.2 + - - -
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A SER* 2.7 24.0 + - - -
392A ILE 4.3 0.2 - - - -
393A ASP* 3.1 27.4 + - - -
424A VAL* 1.3 79.2 - - - +
426A ILE* 1.3 61.7 + - - +
429A ALA* 3.1 12.6 + - - +
443A ASN* 3.1 24.4 - - - +
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Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP* 4.7 1.0 + - - +
423A GLY 3.9 1.0 + - - -
425A GLY* 1.3 74.4 - - - +
427A PRO* 1.4 72.3 - - + +
429A ALA* 3.3 5.1 + - - +
430A ILE* 3.0 25.7 + - + +
443A ASN* 3.4 22.6 + - - +
450A ALA* 4.0 14.8 - - + +
453A THR* 3.4 33.6 + - - +
454A MET* 3.9 11.7 - - - +
456A ASP* 3.8 37.2 - - + +
457A LEU* 3.9 21.8 - - + -
460A GLN* 4.0 8.0 + - - +
469A ASN* 4.5 0.4 - - - +
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Residues in contact with PRO 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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61A VAL* 3.4 38.1 - - + +
64A MET* 3.6 23.1 - - + -
65A ALA* 3.6 14.8 - - + +
423A GLY 3.0 29.2 - - - +
424A VAL 3.5 7.6 - - - +
426A ILE* 1.4 88.7 - - + +
428A GLY* 1.3 55.3 + - - +
430A ILE* 3.2 9.5 + - + +
431A ALA* 2.9 29.6 + - - +
453A THR* 4.2 4.7 - - - +
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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
----------------------------------------------------------
64A MET 5.0 0.6 + - - -
68A ALA* 3.6 21.2 - - - +
391A SER* 3.2 17.9 - - - -
414A ILE* 3.9 11.2 - - - +
424A VAL* 2.9 17.6 + - - -
427A PRO* 1.3 74.2 - - - +
429A ALA* 1.3 55.9 + - - +
431A ALA* 3.6 2.3 + - - +
432A ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A SER* 3.3 8.4 + - - -
425A GLY 3.1 18.2 + - - +
426A ILE 3.6 4.5 - - - +
428A GLY* 1.3 73.2 - - - +
430A ILE* 1.3 60.8 + - - +
432A ALA* 3.6 0.9 - - - +
433A LYS* 2.9 31.7 + - - +
441A VAL* 3.6 14.9 - - + +
442A PHE 4.2 0.2 - - - +
443A ASN* 3.8 9.0 - - + -
460A GLN* 4.6 0.9 - - - +
467A VAL* 3.6 33.3 - - + +
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Residues in contact with ILE 430 (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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30A TYR* 4.2 14.6 - - + -
54A ILE* 5.0 1.1 - - + -
56A VAL* 5.8 1.6 - - + -
61A VAL* 4.5 5.4 - - + -
65A ALA* 4.8 2.2 - - + -
426A ILE* 3.0 28.0 + - + +
427A PRO* 3.2 12.5 + - + +
429A ALA* 1.3 78.0 - - - +
431A ALA* 1.3 56.9 + - - +
433A LYS* 3.4 0.9 + - - -
434A LEU* 3.0 47.2 + - + +
456A ASP* 3.7 27.8 - - + +
459A THR* 3.8 23.1 - - + -
460A GLN* 3.7 18.8 - - + -
465A LEU* 3.9 18.3 - - + +
467A VAL* 5.0 1.3 - - - -
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Residues in contact with ALA 431 (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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30A TYR* 3.6 13.5 - - - +
65A ALA 3.4 25.8 - - - +
68A ALA* 3.8 10.1 - - + -
69A ASP* 3.5 20.4 - - - +
72A LEU* 4.1 0.7 - - + -
427A PRO 2.9 15.0 + - - +
428A GLY 3.8 0.2 - - - +
430A ILE* 1.3 72.6 - - - +
432A ALA* 1.3 64.7 + - - +
434A LEU* 3.4 2.7 + - - +
435A ASN* 2.8 32.5 + - - -
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Residues in contact with ALA 432 (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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72A LEU* 3.5 14.8 - - + +
389A ILE* 3.7 25.1 - - + -
391A SER* 5.4 1.1 - - - -
414A ILE* 5.5 0.4 - - + -
428A GLY 2.9 19.2 + - - +
429A ALA* 3.6 6.5 - - - +
431A ALA* 1.3 76.5 - - - +
433A LYS* 1.3 56.6 + - - +
435A ASN 3.2 1.0 + - - -
436A TYR* 2.8 36.0 + - - +
441A VAL* 3.7 20.9 - - + -
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Residues in contact with LYS 433 (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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429A ALA 2.9 17.6 + - - +
430A ILE 4.0 2.7 - - - +
432A ALA* 1.3 73.0 - - - +
434A LEU* 1.3 63.5 - - - +
436A TYR 4.1 1.1 - - - +
437A PRO* 3.2 47.7 + - + +
439A ARG 2.7 29.3 + - - -
440A GLN* 4.4 1.8 - - - +
441A VAL* 3.6 19.6 - - + +
465A LEU* 3.8 23.1 - - + +
466A PRO* 3.6 54.3 + - + +
467A VAL* 4.3 3.6 - - + -
533A ALA 5.1 2.8 + - - -
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Residues in contact with LEU 434 (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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27A ASP* 5.0 4.1 - - - +
28A HIS* 3.9 25.3 + - + +
30A TYR* 3.8 18.2 - - + +
54A ILE* 4.0 37.2 - - + -
430A ILE* 3.0 34.3 + - + +
431A ALA 3.8 4.0 - - - +
433A LYS* 1.3 77.7 - - - +
435A ASN* 1.3 59.3 + - - +
437A PRO* 3.9 8.3 - - - +
463A TYR* 5.4 2.0 - - + -
465A LEU* 3.8 25.1 - - + -
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Residues in contact with ASN 435 (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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28A HIS* 3.2 18.7 - - - -
69A ASP* 2.7 38.6 + - - +
72A LEU* 4.2 4.6 - - - +
73A THR* 3.6 23.7 + - + +
431A ALA 2.8 24.4 + - - +
434A LEU* 1.3 76.6 - - - +
436A TYR* 1.3 86.3 + - + +
437A PRO* 3.6 5.6 - - - +
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Residues in contact with TYR 436 (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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72A LEU* 3.1 44.0 + - + +
73A THR* 3.7 11.3 - - + +
389A ILE* 3.3 30.3 - - + -
412A ARG* 4.3 5.7 + - + -
432A ALA* 2.8 19.8 + - - +
433A LYS* 3.5 7.0 - - - +
435A ASN* 1.3 96.4 - - + +
437A PRO* 1.4 61.2 - - - +
438A GLU 3.2 2.7 - - - -
439A ARG* 3.0 62.2 + - + +
441A VAL* 4.5 0.9 - - - +
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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