Contacts of the helix formed by residues 29 - 42 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY 3.2 0.2 - - - -
28A GLU* 1.3 85.1 - - + +
30A PRO* 1.3 76.4 - - - +
31A LEU 3.6 2.7 + - - -
32A ASN* 2.6 38.0 + - - +
33A ALA* 2.9 22.5 + - - +
153B LEU* 3.9 7.6 - - - -
122F THR* 5.8 4.0 - - + -
126F MET* 3.8 25.4 - - + +
129F ILE* 5.1 2.9 - - + -
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Residues in contact with PRO 30 (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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29A THR* 1.3 86.7 - - - +
31A LEU* 1.3 57.2 + - - +
33A ALA* 3.2 2.3 + - - +
34A PHE* 2.9 24.4 + - - +
81B ILE* 3.4 36.7 - - + +
153B LEU* 4.0 23.6 - - + -
7006B MRD 4.0 9.2 - - + +
126F MET* 6.3 0.2 - - + -
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Residues in contact with LEU 31 (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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29A THR* 3.3 1.4 + - - -
30A PRO* 1.3 80.3 - - - +
32A ASN* 1.3 58.7 + - - +
34A PHE* 3.4 4.4 + - + +
35A ASP* 2.9 28.2 + - - +
7006B MRD 3.6 47.0 - - + +
108F MET* 3.4 25.1 - - - +
109F GLU* 3.3 47.6 - - + +
126F MET* 3.6 17.0 - - + +
7016F AG2 3.8 17.9 - - + +
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Residues in contact with ASN 32 (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 GLY* 4.3 1.8 - - - -
28A GLU 4.2 4.7 - - - +
29A THR* 2.6 44.4 + - - +
31A LEU* 1.3 74.6 - - - +
33A ALA* 1.3 60.4 + - - +
35A ASP* 3.4 6.1 + - - +
36A GLY 2.9 22.5 + - - -
108F MET* 3.8 11.1 - - - +
126F MET* 3.1 38.2 - - - +
129F ILE* 3.6 29.0 - - + +
130F GLY* 3.9 5.4 + - - -
133F MET* 3.6 14.9 - - - +
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Residues in contact with ALA 33 (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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25A SER* 3.9 9.0 - - - +
26A GLU 3.8 4.3 - - - -
27A GLY* 3.8 19.0 - - - +
29A THR 2.9 12.6 + - - +
30A PRO 3.5 8.7 - - - +
32A ASN* 1.3 73.0 - - - +
34A PHE* 1.3 61.1 + - - +
36A GLY* 3.2 2.3 + - - -
37A ALA* 2.9 27.5 + - - +
81B ILE* 4.9 0.2 - - + -
153B LEU* 3.6 21.5 - - + -
154B GLY 4.3 0.2 - - - -
155B CYS* 3.7 19.4 - - + +
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Residues in contact with PHE 34 (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 PRO 2.9 16.8 + - - +
31A LEU* 3.5 7.6 - - + +
33A ALA* 1.3 73.0 - - - +
35A ASP* 1.3 64.5 + - - +
37A ALA* 3.1 2.6 + - - +
38A LEU* 3.0 47.1 + - + +
48A LEU* 4.9 0.7 - - + -
77B TYR* 4.0 16.4 - + - -
79B TYR* 3.7 40.6 - + - -
81B ILE* 4.4 0.2 - - + -
155B CYS* 3.8 16.7 - - - +
157B PHE* 3.9 15.0 - + - -
7006B MRD 3.6 40.2 - - + -
52E SER 3.4 23.3 - - - -
7016F AG2 3.7 13.7 - - - -
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Residues in contact with ASP 35 (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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31A LEU 2.9 18.4 + - - +
32A ASN* 3.6 8.9 - - - +
34A PHE* 1.3 75.5 - - - +
36A GLY* 1.3 58.1 + - - +
38A LEU* 3.3 2.9 + - - +
39A LEU* 2.9 30.5 + - - +
106F LEU* 3.8 11.0 - - - +
108F MET* 4.0 5.1 - - + +
130F GLY* 4.1 5.7 - - - -
133F MET* 5.1 3.0 - - - +
134F ARG* 2.7 36.5 + - - -
7016F AG2 2.9 45.0 + - + -
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Residues in contact with GLY 36 (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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25A SER* 3.3 20.4 - - - -
32A ASN 2.9 11.7 + - - -
33A ALA 3.6 3.6 - - - -
34A PHE 3.2 0.2 - - - -
35A ASP* 1.3 77.5 - - - +
37A ALA* 1.3 55.4 + - - +
39A LEU* 3.3 10.2 + - - +
40A ASN* 2.9 28.8 + - - +
133F MET* 3.7 16.8 - - - +
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Residues in contact with ALA 37 (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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23A GLY* 3.8 11.3 - - - +
24A SER* 3.9 12.8 - - - +
25A SER* 3.4 6.7 - - - -
33A ALA 2.9 14.0 + - - +
34A PHE 3.1 8.0 + - - +
36A GLY* 1.3 72.3 - - - +
38A LEU* 1.3 62.2 + - - +
40A ASN* 3.3 3.5 + - - +
41A ALA* 2.9 28.6 + - - +
155B CYS* 3.9 13.5 - - - +
157B PHE* 3.8 25.4 - - + -
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Residues in contact with LEU 38 (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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34A PHE* 3.0 34.5 + - + +
35A ASP 3.6 7.4 - - - +
37A ALA* 1.3 76.0 - - - +
39A LEU* 1.3 61.9 + - - +
41A ALA* 3.2 8.3 + - - +
42A GLY 3.0 4.9 + - - -
43A ILE* 3.0 32.1 + - + +
44A GLY* 3.7 11.7 - - - -
48A LEU* 3.6 21.1 - - + -
157B PHE* 3.5 43.3 - - + -
7016F AG2 3.3 41.1 - - - +
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Residues in contact with LEU 39 (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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35A ASP* 2.9 22.3 + - - +
36A GLY* 3.5 15.5 - - - +
38A LEU* 1.3 76.8 - - - +
40A ASN* 1.3 62.5 + - - +
42A GLY* 3.1 13.7 + - - -
44A GLY* 3.8 20.2 - - - +
45A ASN* 4.1 11.4 - - - +
133F MET* 4.7 14.8 - - + +
134F ARG* 3.9 50.0 - - + +
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Residues in contact with ASN 40 (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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22A ALA 4.3 2.8 - - - +
23A GLY* 3.3 7.3 - - - -
24A SER* 3.0 35.7 + - - +
25A SER* 5.1 0.2 - - - -
36A GLY 2.9 17.2 + - - +
37A ALA 3.3 4.9 + - - +
39A LEU* 1.3 75.9 - - - +
41A ALA* 1.3 59.7 + - - +
42A GLY 3.5 0.5 + - - -
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Residues in contact with ALA 41 (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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21A VAL* 3.5 29.5 - - + +
22A ALA* 3.4 36.3 + - - +
23A GLY 3.8 0.9 - - - +
37A ALA 2.9 16.2 + - - +
38A LEU 3.6 5.4 - - - +
39A LEU 3.2 0.4 - - - -
40A ASN* 1.3 76.6 - - - +
42A GLY* 1.3 59.8 + - - +
43A ILE* 3.5 1.6 - - + -
64B LEU* 4.4 1.2 - - - +
157B PHE* 4.1 14.8 - - + -
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Residues in contact with GLY 42 (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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38A LEU 3.0 3.0 + - - -
39A LEU 3.1 12.6 + - - -
40A ASN 3.3 0.8 + - - -
41A ALA* 1.3 79.4 - - - +
43A ILE* 1.3 60.8 + - - +
44A GLY 3.6 2.9 - - - -
64B LEU* 3.4 18.5 - - - +
67B LEU* 5.5 1.0 - - - +
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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