Contacts of the helix formed by residues 29 - 42 (chain I) in PDB entry 1N13
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 THR 29 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27I GLY 3.9 0.3 - - - -
28I GLU* 1.3 85.2 - - + +
30I PRO* 1.3 75.9 - - - +
31I LEU 3.6 2.7 + - - -
32I ASN* 2.6 39.6 + - - +
33I ALA* 3.0 23.7 + - - +
153J LEU* 3.7 6.0 - - - +
122L THR* 5.7 4.7 - - + -
126L MET* 3.8 26.5 - - + +
129L ILE* 5.0 3.1 - - + -
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Residues in contact with PRO 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I THR* 1.3 88.0 - - - +
31I LEU* 1.3 56.0 + - - +
33I ALA* 3.3 1.4 + - - +
34I PHE* 3.0 23.7 + - - +
81J ILE* 3.4 35.6 - - + +
153J LEU* 4.0 22.2 - - + -
7004J MRD 4.1 9.6 - - + +
126L MET* 6.2 0.2 - - + -
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Residues in contact with LEU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I THR* 3.2 1.4 + - - -
30I PRO* 1.3 77.4 - - - +
32I ASN* 1.3 61.4 + - - +
34I PHE* 3.3 2.6 + - + +
35I ASP* 2.9 28.1 + - - +
7004J MRD 3.5 43.7 - - + +
108L MET* 3.5 22.2 - - - +
109L GLU* 3.5 35.2 - - + +
126L MET* 3.6 17.7 - - + +
7014L AG2 3.6 40.6 - - + +
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Residues in contact with ASN 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I GLY* 4.4 2.0 - - - -
28I GLU 4.2 5.2 - - - +
29I THR* 2.6 47.9 + - - +
31I LEU* 1.3 74.3 - - - +
33I ALA* 1.3 60.0 + - - +
35I ASP* 3.4 6.6 + - - +
36I GLY 2.9 22.3 + - - -
108L MET* 3.8 11.1 - - - +
126L MET* 3.0 35.8 - - - +
129L ILE* 3.6 33.8 - - + +
130L GLY* 3.9 4.5 + - - -
133L MET* 3.6 14.8 - - - +
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Residues in contact with ALA 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 3.9 13.3 - - - +
26I GLU 3.8 4.3 - - - -
27I GLY* 3.8 18.5 - - - +
29I THR 3.0 16.2 + - - +
30I PRO 3.6 4.7 - - - +
32I ASN* 1.3 73.8 - - - +
34I PHE* 1.3 61.7 + - - +
36I GLY* 3.2 1.2 + - - -
37I ALA* 2.9 28.6 + - - +
81J ILE* 5.1 0.2 - - + -
153J LEU* 3.7 20.9 - - + +
155J CYS* 3.7 14.4 - - + +
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Residues in contact with PHE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PRO 3.0 14.3 + - - +
31I LEU* 3.5 7.9 - - + +
33I ALA* 1.3 76.1 - - - +
35I ASP* 1.3 61.3 + - - +
37I ALA* 3.0 3.8 + - - +
38I LEU* 2.9 52.3 + - + +
48I LEU* 4.9 0.7 - - + -
77J TYR* 4.0 15.7 - + - -
79J TYR* 3.9 37.0 - + - -
81J ILE* 4.5 0.4 - - + -
155J CYS* 3.8 16.0 - - - +
157J PHE* 3.9 10.8 - + - -
7004J MRD 3.7 40.2 - - + -
52K SER* 3.4 23.6 - - - -
7014L AG2 3.7 18.2 - - + -
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Residues in contact with ASP 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LEU 2.9 18.2 + - - +
32I ASN* 3.5 8.7 - - - +
34I PHE* 1.3 75.0 - - - +
36I GLY* 1.3 57.9 + - - +
38I LEU* 3.2 2.9 + - - +
39I LEU* 3.0 30.1 + - - +
106L LEU* 3.9 10.6 - - - +
108L MET* 4.0 9.6 - - + +
130L GLY* 4.2 5.5 - - - -
133L MET* 5.1 3.3 - - - +
134L ARG* 2.8 45.3 + - - -
7014L AG2 3.0 34.5 + - + -
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Residues in contact with GLY 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 3.3 22.0 - - - -
32I ASN 2.9 14.9 + - - -
33I ALA 3.6 1.8 - - - -
34I PHE 3.2 0.2 - - - -
35I ASP* 1.3 78.7 - - - +
37I ALA* 1.3 55.0 + - - +
39I LEU* 3.3 10.9 + - - +
40I ASN* 3.0 28.6 + - - +
133L MET* 3.8 12.8 - - - +
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Residues in contact with ALA 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLY* 3.8 7.0 - - - +
24I SER 4.0 5.8 - - - +
25I SER* 3.4 6.7 - - - -
33I ALA 2.9 13.1 + - - +
34I PHE 3.0 8.9 + - - +
36I GLY* 1.3 73.2 - - - +
38I LEU* 1.3 62.2 + - - +
40I ASN* 3.3 3.1 + - - +
41I ALA* 2.9 28.5 + - - +
155J CYS* 3.8 32.3 - - - +
157J PHE* 3.8 17.3 - - + -
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Residues in contact with LEU 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PHE* 2.9 43.9 + - + +
35I ASP 3.6 7.6 - - - +
37I ALA* 1.3 73.5 - - - +
39I LEU* 1.3 65.9 + - - +
41I ALA* 3.1 8.2 + - - +
42I GLY 3.1 4.7 + - - -
43I ILE* 2.9 40.4 + - + +
44I GLY* 3.6 11.9 - - - -
48I LEU* 3.6 19.5 - - + -
157J PHE* 3.7 26.2 - - + -
7014L AG2 3.4 39.3 - - - +
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Residues in contact with LEU 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ASP* 3.0 24.6 + - - +
36I GLY* 3.5 11.9 - - - +
38I LEU* 1.3 77.0 - - - +
40I ASN* 1.3 60.8 + - - +
42I GLY* 3.1 13.9 + - - -
44I GLY* 3.8 21.8 - - - +
45I ASN* 4.2 11.0 - - - +
133L MET* 4.9 14.1 - - + +
134L ARG* 3.8 48.5 - - + +
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Residues in contact with ASN 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ALA 4.3 2.8 - - - +
23I GLY* 3.2 9.0 - - - -
24I SER* 3.1 35.6 + - - +
25I SER* 5.2 0.4 - - - -
36I GLY 3.0 17.2 + - - +
37I ALA 3.6 4.3 - - - +
38I LEU 3.3 0.2 - - - -
39I LEU* 1.3 76.2 - - - +
41I ALA* 1.3 59.6 + - - +
42I GLY* 3.2 1.1 + - - -
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Residues in contact with ALA 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 3.5 29.8 - - + +
22I ALA* 3.4 35.6 + - - +
23I GLY 3.8 0.9 - - - +
37I ALA 2.9 16.9 + - - +
38I LEU* 3.1 6.2 + - - +
40I ASN* 1.3 76.4 - - - +
42I GLY* 1.3 60.0 + - - +
43I ILE* 3.4 2.0 - - + -
64J LEU* 4.4 1.7 - - - +
157J PHE* 4.2 14.1 - - + -
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Residues in contact with GLY 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I LEU 3.1 2.2 + - - -
39I LEU 3.1 12.5 + - - -
40I ASN 3.2 2.0 + - - -
41I ALA* 1.3 79.2 - - - +
43I ILE* 1.3 58.5 + - - +
44I GLY 3.7 2.5 - - - -
64J LEU* 3.4 20.9 - - - +
67J LEU* 5.5 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
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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