Contacts of the helix formed by residues 33 - 49 (chain H) in PDB entry 3DEG
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 ASN 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31H GLY 4.7 1.4 - - - +
32H VAL* 1.3 77.3 - - - +
34H ILE* 1.3 66.0 + - - +
35H MET* 3.2 3.1 - - + +
36H GLU* 3.0 34.5 + - + +
37H PHE* 3.0 10.7 + - - +
64H ARG* 2.8 51.9 + - - +
65H SER* 4.5 2.8 - - - +
66H PHE* 3.3 15.5 - - + -
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Residues in contact with ILE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASN* 3.2 39.7 - - - +
23H VAL* 4.9 2.2 - - + -
24H GLY* 3.4 38.8 - - - +
27H LEU* 3.5 30.7 - - + -
28H GLY* 4.2 7.6 - - - +
32H VAL 3.3 7.9 + - - +
33H ASN* 1.3 71.5 - - - +
35H MET* 1.3 63.2 - - - +
37H PHE* 3.2 6.9 + - + -
38H CYS* 2.9 25.6 + - + -
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Residues in contact with MET 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASN* 4.7 2.7 + - - -
33H ASN* 3.2 1.9 - - + -
34H ILE* 1.3 79.5 - - - +
36H GLU* 1.3 70.7 + - + +
38H CYS* 2.8 28.3 - - - -
39H LYS* 3.5 28.8 + - - +
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 3.0 26.0 + - + +
35H MET* 1.3 92.4 - - + +
37H PHE* 1.3 58.3 + - - +
39H LYS* 3.8 6.4 - - - +
40H ALA* 2.8 36.2 + - + +
65H SER* 5.0 5.4 + - - -
66H PHE* 3.3 29.2 - - + +
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Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 4.6 7.6 - - + -
12H VAL* 4.9 7.2 - - + -
17H ALA* 5.7 3.4 - - + -
23H VAL* 5.3 7.0 - - + -
27H LEU* 4.1 18.6 - - + -
32H VAL* 4.8 3.1 - - + -
33H ASN 3.0 7.4 + - - +
34H ILE* 3.8 9.9 - - + +
36H GLU* 1.3 74.5 - - - +
38H CYS* 1.3 61.4 + - - +
40H ALA* 4.1 2.2 - - - -
41H PHE* 2.6 53.9 + + + +
56H VAL* 3.6 15.5 - - + -
58H ILE* 3.5 35.7 - - + -
66H PHE* 3.5 32.2 - + + -
68H PHE* 3.6 33.7 - + - -
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Residues in contact with CYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ALA* 3.9 20.2 - - + +
18H ASN* 3.8 33.4 - - + +
34H ILE* 2.9 19.3 + - + +
35H MET* 2.8 34.8 - - - -
37H PHE* 1.3 78.1 - - + +
39H LYS* 1.3 65.5 + - - +
41H PHE* 4.1 0.8 - - - +
42H ASN* 2.5 35.4 + - - +
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Residues in contact with LYS 39 (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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35H MET* 3.5 33.7 + - - +
36H GLU* 4.0 5.4 - - - +
37H PHE 3.2 0.2 - - - -
38H CYS* 1.3 82.8 - - - +
40H ALA* 1.3 65.8 + - - +
42H ASN* 4.5 2.9 - - - +
43H ALA* 3.2 22.6 + - + +
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Residues in contact with ALA 40 (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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36H GLU* 2.8 27.9 + - + +
37H PHE* 3.6 4.5 - - - +
39H LYS* 1.3 76.2 - - - +
41H PHE* 1.3 65.9 + - - +
43H ALA* 3.1 18.0 - - - +
44H LYS* 3.7 5.4 + - - +
66H PHE* 5.6 0.7 - - + -
68H PHE* 3.9 24.8 - - + -
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Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.3 23.3 - - + -
13H ALA 3.1 27.1 - - - -
14H ALA 3.3 3.1 - - - -
17H ALA* 4.9 5.8 - - + -
37H PHE* 2.6 43.4 + + + +
38H CYS* 4.1 2.9 - - - +
40H ALA* 1.3 69.3 - - - +
42H ASN* 1.3 77.3 + - - +
43H ALA 2.8 5.8 + - - -
44H LYS* 3.1 5.5 + - - +
45H THR* 2.7 52.6 + - + -
54H ILE* 4.0 14.1 - - + -
56H VAL* 4.0 20.6 - - + -
68H PHE* 3.8 23.7 - + - -
70H THR* 4.2 14.4 - - + -
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Residues in contact with ASN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ALA 3.1 8.6 - - - +
15H GLY* 4.0 7.6 - - - -
16H MET* 2.6 34.9 + - - +
17H ALA* 3.7 19.0 + - - +
38H CYS* 2.5 26.6 + - - +
39H LYS* 4.5 3.4 - - - +
41H PHE* 1.3 84.0 - - - +
43H ALA* 1.3 58.8 + - - +
45H THR* 3.9 7.2 - - - -
46H ASP* 2.5 38.2 + - - +
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Residues in contact with ALA 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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39H LYS* 3.2 16.1 + - + +
40H ALA* 3.1 17.0 - - - +
41H PHE 2.8 1.0 + - - -
42H ASN* 1.3 81.0 - - - +
44H LYS* 1.3 60.5 + - + +
46H ASP* 3.9 12.1 + - - +
47H SER* 4.3 3.8 + - - -
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Residues in contact with LYS 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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40H ALA 3.7 4.4 + - - +
41H PHE 3.1 5.1 + - - +
43H ALA* 1.3 77.4 - - + +
45H THR* 1.3 65.0 + - - +
46H ASP 3.2 0.9 - - - -
47H SER* 3.3 9.2 + - - +
48H ILE* 3.0 43.7 + - + +
68H PHE* 6.0 4.7 - - + -
70H THR* 5.2 9.7 - - - +
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Residues in contact with THR 45 (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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14H ALA* 3.0 43.7 - - - +
41H PHE* 2.7 51.1 + - + -
42H ASN* 3.9 3.4 - - - -
43H ALA 3.4 0.2 - - - -
44H LYS* 1.3 75.5 - - - +
46H ASP* 1.3 59.3 + - - +
48H ILE* 4.3 8.0 - - - +
49H GLU 2.9 42.0 + - - +
54H ILE* 4.2 11.9 - - + -
70H THR* 5.0 3.0 + - + +
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Residues in contact with ASP 46 (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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15H GLY* 3.9 12.8 - - - -
42H ASN* 2.5 29.1 + - - +
43H ALA* 3.9 8.0 - - - +
45H THR* 1.3 79.4 - - - +
47H SER* 1.3 63.2 + - - +
49H GLU* 3.7 4.3 + - - -
50H LYS* 3.2 48.9 + - + +
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Residues in contact with SER 47 (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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43H ALA 4.3 3.2 + - - -
44H LYS* 3.3 15.1 + - - -
45H THR 3.3 0.2 - - - -
46H ASP* 1.3 79.2 - - - +
48H ILE* 1.3 69.4 + - - +
49H GLU* 4.4 0.2 - - - -
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LYS* 3.0 46.5 + - + +
45H THR* 3.3 6.0 + - - +
47H SER* 1.3 79.1 - - - +
49H GLU* 1.3 88.8 + - + +
54H ILE* 4.1 6.1 - - + -
70H THR* 3.5 36.8 - - + +
71H LYS 5.4 1.8 - - - +
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Residues in contact with GLU 49 (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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14H ALA* 3.4 12.3 - - - +
45H THR* 2.9 24.7 + - - +
46H ASP 4.2 2.9 - - - -
47H SER 3.4 1.7 - - - -
48H ILE* 1.3 91.4 - - + +
50H LYS* 1.3 59.9 + - - +
52H LEU* 3.2 36.5 - - + +
54H ILE* 3.4 26.2 - - + +
71H LYS 4.3 7.6 - - - +
72H THR* 5.2 5.9 - - - +
73H PRO* 4.9 6.9 - - - +
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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
------------------------------------------------------------
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