Contacts of the helix formed by residues 27 - 46 (chain H) in PDB entry 1NTZ
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 LEU 27 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLN* 3.6 12.3 + - + +
24H CYS* 3.2 13.1 + - - +
26H GLN* 1.3 89.3 - - + +
28H GLU* 1.3 65.5 + - + +
29H LYS* 3.0 4.4 + - + +
30H CYS* 2.8 33.3 + - - +
31H VAL* 3.8 1.6 - - - -
68H CYS* 6.0 4.5 - - - -
72H LYS* 4.6 17.0 - - - +
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Residues in contact with GLU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 1.3 80.9 - - + +
29H LYS* 1.3 74.5 + - + +
31H VAL* 3.1 21.8 + - + +
32H LYS* 3.1 28.7 + - + +
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Residues in contact with LYS 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 3.0 4.7 + - + +
28H GLU* 1.3 83.8 + - + +
30H CYS* 1.3 60.1 + - - +
32H LYS* 3.7 6.4 + - - +
33H ALA* 3.2 25.1 + - - +
64H ALA* 4.1 23.3 - - + +
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Residues in contact with CYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H CYS 3.8 13.9 - - - -
25H GLU 3.0 20.9 - - - +
26H GLN 4.1 0.4 - - - -
27H LEU* 2.8 15.7 + - - +
29H LYS* 1.3 73.7 - - - +
31H VAL* 1.3 63.1 + - - +
32H LYS 3.2 0.2 - - - -
33H ALA* 4.3 5.6 - - - +
34H ARG* 2.9 27.0 + - - +
61H PHE* 3.6 15.4 - - + -
64H ALA* 3.8 11.9 - - - -
65H ARG* 3.5 37.7 - - - -
68H CYS* 5.9 1.3 - - - -
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLU 5.0 0.4 - - - -
26H GLN 2.9 26.8 + - - +
27H LEU* 3.2 12.6 + - - -
28H GLU* 3.1 12.9 + - - +
30H CYS* 1.3 75.6 - - - +
32H LYS* 1.3 63.3 + - + +
34H ARG* 3.4 4.3 + - - +
35H GLU* 2.9 34.7 + - - +
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Residues in contact with LYS 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H GLU* 3.1 24.6 + - + +
29H LYS* 3.8 6.5 - - - +
31H VAL* 1.3 82.0 - - + +
33H ALA* 1.3 65.1 + - - +
35H GLU* 3.2 29.6 + - - +
36H ARG* 3.2 15.1 + - - +
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Residues in contact with ALA 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H LYS 3.2 15.7 + - - +
30H CYS* 4.0 3.1 - - - +
31H VAL 3.4 0.2 - - - -
32H LYS* 1.3 77.6 - - - +
34H ARG* 1.3 58.3 + - - +
36H ARG* 3.1 13.1 + - - +
37H LEU* 2.9 26.8 + - - +
57H GLU* 4.6 3.7 - - - +
60H ASP* 4.4 10.1 - - + +
61H PHE* 3.7 33.4 - - + +
64H ALA* 5.6 1.3 - - + -
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Residues in contact with ARG 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLU* 2.5 35.4 + - - +
30H CYS 2.9 18.3 + - - +
31H VAL* 3.8 4.7 - - - +
33H ALA* 1.3 72.9 - - - +
35H GLU* 1.3 66.4 + - - +
37H LEU* 3.0 26.9 - - + +
38H GLU* 2.9 46.2 + - - +
61H PHE* 3.6 24.8 - - + -
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 2.9 19.2 + - - +
32H LYS* 3.2 25.1 - - - +
33H ALA 3.1 0.2 - - - -
34H ARG* 1.3 78.1 - - - +
36H ARG* 1.3 52.6 + - + +
38H GLU* 3.2 13.4 + - - +
39H LEU* 2.8 52.9 + - + +
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Residues in contact with ARG 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LYS* 3.2 12.1 + - - +
33H ALA* 3.1 12.0 + - - +
35H GLU* 1.3 73.3 - - + +
37H LEU* 1.3 61.0 + - - +
39H LEU* 3.6 15.3 - - + +
40H CYS* 2.8 32.9 + - - +
43H ARG* 5.0 3.1 + - - +
57H GLU* 4.0 16.5 - - + +
60H ASP* 5.7 3.0 + - - -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ALA 2.9 7.1 + - - +
34H ARG* 3.0 36.6 - - + +
36H ARG* 1.3 78.7 - - - +
38H GLU* 1.3 53.4 + - + +
40H CYS* 3.5 1.6 - - - +
41H ASP* 2.5 54.2 + - - +
54H CYS* 4.4 4.9 - - + +
57H GLU* 3.3 38.1 - - + +
58H LEU* 3.5 31.9 - - + +
61H PHE* 3.9 17.0 - - + -
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Residues in contact with GLU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ARG* 2.9 43.9 + - + +
35H GLU* 3.6 12.0 - - - +
37H LEU* 1.3 77.9 - - + +
39H LEU* 1.3 62.1 + - + +
41H ASP* 3.2 13.9 - - - +
42H GLU* 2.8 50.5 + - - +
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLU* 2.8 42.9 + - + +
36H ARG* 3.6 16.2 - - + +
37H LEU 3.2 0.2 - - - -
38H GLU* 1.3 77.5 - - + +
40H CYS* 1.3 64.3 + - - +
42H GLU* 3.3 9.6 + - - +
43H ARG* 3.2 34.0 + - - +
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Residues in contact with CYS 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ARG 2.8 21.0 + - - +
37H LEU 3.7 0.9 - - - +
39H LEU* 1.3 74.2 - - - +
41H ASP* 1.4 61.1 + - - +
43H ARG* 3.0 49.3 + - - +
44H VAL* 3.2 19.1 + - - +
52H GLU* 3.4 17.3 - - - -
54H CYS* 3.2 30.1 - - - -
57H GLU* 3.2 26.9 - - - +
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Residues in contact with ASP 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PRO* 5.5 3.5 - - - +
139D THR* 3.0 25.1 + - - +
37H LEU* 2.5 42.3 + - - +
38H GLU* 3.2 14.2 - - - +
40H CYS* 1.4 73.4 - - - +
42H GLU* 1.3 65.8 + - + +
44H VAL* 3.4 4.0 + - - +
45H SER* 3.2 24.7 + - - -
54H CYS* 3.5 9.6 - - - -
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Residues in contact with GLU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H GLU* 2.8 40.8 + - - +
39H LEU* 3.9 9.2 + - - +
41H ASP* 1.3 73.8 - - + +
43H ARG* 1.3 58.2 + - - +
45H SER* 3.7 8.9 + - - +
46H SER* 2.6 33.4 + - - -
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ASN* 4.9 11.5 - - - +
36H ARG* 5.0 3.4 + - - +
39H LEU* 3.2 22.7 + - - +
40H CYS* 3.0 37.7 + - - +
42H GLU* 1.3 76.9 - - - +
44H VAL* 1.3 65.5 + - + +
46H SER* 3.0 23.0 + - - -
47H ARG* 3.8 6.9 + - - +
52H GLU* 3.0 38.5 + - - +
57H GLU* 4.7 4.2 + - - -
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Residues in contact with VAL 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D THR* 3.5 31.0 - - - +
140D GLY* 4.6 3.8 - - - +
40H CYS* 3.2 17.7 + - - +
41H ASP 3.4 1.5 + - - +
43H ARG* 1.3 73.4 - - + +
45H SER* 1.3 65.2 + - - +
47H ARG 3.7 9.0 + - - +
50H THR* 3.9 25.9 - - + +
52H GLU* 3.3 22.2 - - - +
53H ASP* 3.5 23.6 - - - +
54H CYS* 3.7 7.0 - - - -
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 5.5 2.5 - - - +
41H ASP* 3.2 16.0 + - - -
42H GLU* 3.8 12.7 - - - +
43H ARG 3.2 0.6 - - - -
44H VAL* 1.3 76.5 - - - +
46H SER* 1.3 57.2 + - - +
47H ARG 2.8 14.4 + - - +
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Residues in contact with SER 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H GLU* 2.6 22.5 + - - +
43H ARG* 3.0 10.7 + - - -
45H SER* 1.3 73.4 - - - +
47H ARG* 1.3 65.3 + - - +
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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