Contacts of the helix formed by residues 58 - 74 (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 HIS 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.9 3.8 - - - -
56A VAL* 3.1 17.4 - - - +
57A ARG* 1.3 82.0 - - - +
59A GLU* 1.3 65.9 + - - +
60A GLU* 3.0 51.6 + - + +
61A VAL* 3.2 12.4 + - + +
89A HIS* 3.2 50.5 + + - -
455A GLN* 3.4 22.9 - - + +
456A ASP* 3.5 2.4 + - - +
1514A NA 4.2 16.8 - - - -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 5.6 0.7 - - - -
32A ILE* 3.7 41.6 - - + +
56A VAL* 4.2 6.1 - - - -
58A HIS* 1.3 72.6 + - - +
60A GLU* 1.3 63.3 - - - +
62A GLY* 3.2 2.5 + - - -
63A ALA 3.1 18.0 + - - -
80A PHE 4.2 12.1 - - - +
81A GLY* 4.3 2.5 - - - -
82A SER* 4.5 3.8 + - - -
86A GLY* 3.3 41.0 - - - +
89A HIS* 2.7 36.9 + - + -
90A LEU* 3.5 17.8 - - + +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 3.0 33.2 + - + +
59A GLU* 1.3 76.7 - - - +
61A VAL* 1.3 62.9 - - + +
63A ALA* 3.3 3.0 + - - +
64A MET* 2.8 64.4 + - + +
89A HIS 3.0 23.4 + - - +
90A LEU* 4.4 3.4 - - - +
92A ASN* 3.9 18.5 + - + +
93A GLY* 4.4 0.3 - - - -
422A MET 4.9 1.4 - - - +
452A MET* 4.0 19.2 - - - +
453A THR* 4.2 8.4 - - + +
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Residues in contact with VAL 61 (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 VAL* 4.1 8.5 - - + -
58A HIS 3.2 10.2 + - - +
60A GLU* 1.3 78.2 - - + +
62A GLY* 1.3 57.6 + - - +
64A MET* 4.4 1.6 - - - -
65A ALA* 2.8 30.7 + - + +
427A PRO* 3.4 25.6 - - + +
430A ILE* 4.5 5.8 - - + -
453A THR* 3.7 33.2 - - + -
455A GLN* 3.8 8.1 - - - +
456A ASP* 3.2 45.3 - - + +
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Residues in contact with GLY 62 (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* 3.4 35.2 - - - -
31A GLY* 5.4 0.7 - - - -
56A VAL* 3.8 11.5 - - - +
58A HIS 3.6 4.4 + - - -
59A GLU* 3.2 7.5 + - - -
61A VAL* 1.3 79.2 - - - +
63A ALA* 1.3 56.2 + - - +
66A ALA* 3.0 24.9 + - - +
79A CYS* 3.6 8.7 - - - +
90A LEU* 5.6 0.2 - - - -
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Residues in contact with ALA 63 (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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59A GLU 3.1 12.0 + - - +
60A GLU 3.6 5.8 - - - +
62A GLY* 1.3 74.2 - - - +
64A MET* 1.3 59.2 + - - +
66A ALA* 3.4 3.1 + - - +
67A ALA* 3.1 27.0 + - - +
79A CYS* 3.7 16.3 - - - +
90A LEU* 3.2 40.8 - - + +
93A GLY* 3.7 12.1 - - - +
94A LEU* 4.1 2.5 - - + +
104A VAL* 5.2 2.8 - - - +
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Residues in contact with MET 64 (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 GLU* 2.8 48.9 + - + +
63A ALA* 1.3 68.9 - - - +
65A ALA* 1.3 61.2 + - - +
67A ALA* 3.4 6.0 + - - +
68A ALA* 3.0 28.6 + - - +
92A ASN* 3.9 7.9 - - + -
93A GLY* 3.8 15.0 - - - -
96A ASP* 5.0 3.3 - - - +
421A THR* 3.5 32.1 - - + +
422A MET 3.5 12.8 - - - +
423A GLY* 3.8 12.3 - - - +
424A VAL* 3.9 17.1 - - + +
427A PRO* 3.6 31.2 - - + -
428A GLY 5.0 0.3 + - - -
453A THR* 4.3 7.2 - - - -
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Residues in contact with ALA 65 (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* 3.4 34.3 - - + +
61A VAL* 2.8 23.5 + - + +
62A GLY 3.9 1.6 - - - +
64A MET* 1.3 69.9 - - - +
66A ALA* 1.3 60.4 + - - +
68A ALA* 3.2 0.7 + - - -
69A ASP* 2.8 28.2 + - - -
427A PRO* 3.6 26.1 - - + +
430A ILE* 4.8 3.1 - - + -
431A ALA* 3.4 9.1 - - + +
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Residues in contact with ALA 66 (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* 3.5 8.8 - - + -
62A GLY 3.0 18.7 + - - +
63A ALA 3.6 5.2 - - - +
65A ALA* 1.3 75.8 - - - +
67A ALA* 1.3 63.0 + - - +
69A ASP* 3.4 4.4 - - - +
70A ALA* 3.3 12.0 + - - +
77A GLY* 3.2 22.9 + - - -
78A VAL 3.6 34.3 - - - +
79A CYS* 4.1 4.9 - - + -
104A VAL* 4.0 10.2 - - + +
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Residues in contact with ALA 67 (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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63A ALA 3.1 14.2 + - - +
64A MET* 3.6 8.7 - - - +
66A ALA* 1.3 75.8 - - - +
68A ALA* 1.3 58.5 + - - +
70A ALA* 3.1 6.4 + - - +
71A LYS* 2.9 35.5 + - - +
93A GLY 4.0 12.1 - - - +
96A ASP* 3.8 20.6 - - - +
97A ALA* 4.1 14.1 - - + +
102A VAL* 3.8 2.8 - - + +
104A VAL* 3.8 10.9 - - + +
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Residues in contact with ALA 68 (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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64A MET 3.0 16.8 + - - +
65A ALA 3.2 4.7 + - - +
67A ALA* 1.3 73.8 - - - +
69A ASP* 1.3 65.7 + - - +
71A LYS* 3.1 15.2 + - + +
72A LEU* 2.8 27.9 + - - +
414A ILE* 3.7 12.1 - - + -
428A GLY* 3.6 29.6 - - - -
431A ALA* 3.8 7.4 - - + -
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Residues in contact with ASP 69 (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* 2.7 25.6 + - - +
30A TYR* 2.9 38.1 + - - -
65A ALA 2.8 12.5 + - - -
66A ALA* 3.4 11.0 - - - +
68A ALA* 1.3 72.5 - - - +
70A ALA* 1.3 57.7 + - - +
72A LEU* 3.7 1.7 - - - +
73A THR* 2.9 37.6 + - - +
75A LYS* 4.1 2.9 - - + +
76A ILE 5.3 0.7 - - - +
77A GLY* 4.4 10.8 - - - -
78A VAL 5.2 0.2 + - - -
431A ALA* 3.5 5.0 - - - +
435A ASN* 2.7 33.4 + - - +
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Residues in contact with ALA 70 (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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66A ALA 3.3 5.7 + - - +
67A ALA* 3.1 9.9 + - - +
69A ASP* 1.3 75.6 - - - +
71A LYS* 1.3 61.9 + - - +
74A GLY* 2.8 29.3 + - - +
75A LYS 3.2 19.3 + - - +
77A GLY 4.0 0.2 - - - +
102A VAL* 3.8 20.9 - - + +
103A PRO* 3.3 33.0 - - + +
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Residues in contact with LYS 71 (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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67A ALA* 2.9 25.7 + - - +
68A ALA* 3.4 15.5 - - + +
70A ALA* 1.3 76.0 - - - +
72A LEU* 1.3 59.9 + - - +
74A GLY 4.8 0.3 + - - -
96A ASP* 2.7 31.4 + - - -
100A ASP* 3.1 26.3 + - + +
102A VAL* 4.0 20.1 - - + +
224A ARG* 4.8 6.2 + - - +
412A ARG* 2.8 20.1 + - - -
414A ILE* 3.9 23.1 - - + +
415A THR 2.9 31.5 + - - +
416A SER* 3.8 0.4 - - - +
424A VAL* 5.2 2.2 - - - +
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Residues in contact with LEU 72 (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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68A ALA 2.8 19.6 + - - +
69A ASP 3.7 2.7 - - - +
71A LYS* 1.3 79.8 - - - +
73A THR* 1.3 62.9 + - + +
389A ILE* 4.0 21.5 - - + -
412A ARG* 2.7 40.2 + - + +
414A ILE* 4.1 31.0 - - + -
428A GLY 4.3 0.4 - - - +
431A ALA 4.1 4.5 - - - -
432A ALA* 3.5 39.3 - - + +
435A ASN* 4.2 4.9 - - - +
436A TYR* 3.1 25.8 + - + -
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Residues in contact with THR 73 (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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69A ASP* 2.9 24.3 + - - +
72A LEU* 1.3 78.2 - - + +
74A GLY* 1.3 60.1 + - - +
75A LYS* 3.1 26.2 + - - +
435A ASN* 3.6 36.1 + - + +
436A TYR* 3.7 15.5 - - + +
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Residues in contact with GLY 74 (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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70A ALA* 2.8 18.9 + - - -
71A LYS 4.8 0.4 + - - -
72A LEU 3.7 1.0 - - - -
73A THR* 1.3 75.5 - - - +
75A LYS* 1.3 59.6 + - - +
103A PRO* 4.4 7.6 - - - +
158A TYR* 3.4 19.9 - - - -
161A GLN* 5.9 0.2 + - - -
189A TYR* 5.2 1.6 + - - -
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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
------------------------------------------------------------
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