Contacts of the helix formed by residues 29 - 42 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B THR* 5.7 4.7 - - + -
126B MET* 3.7 25.9 - - + +
129B ILE* 5.3 2.7 - - + -
28C GLU* 1.3 86.7 - - + +
30C PRO* 1.3 76.1 - - - +
31C LEU 3.6 2.6 + - - -
32C ASN* 2.7 36.5 + - - +
33C ALA* 2.9 23.2 + - - +
153D LEU* 4.0 7.0 - - - -
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Residues in contact with PRO 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C THR* 1.3 86.3 - - - +
31C LEU* 1.3 57.1 + - - +
33C ALA* 3.2 3.3 + - - +
34C PHE* 2.9 28.8 + - - +
81D ILE* 3.7 28.4 - - + +
153D LEU* 4.0 25.1 - - + -
7001D MRD 4.1 7.6 - - + +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 3.5 24.0 - - - -
109B GLU* 3.4 48.0 - - + +
126B MET* 3.6 16.8 - - + +
7011B AG2 3.6 18.4 - - - -
29C THR* 3.3 1.6 + - - -
30C PRO* 1.3 79.2 - - - +
32C ASN* 1.3 57.2 + - - +
34C PHE* 3.3 8.3 + - + +
35C ASP* 2.9 29.3 + - - +
7001D MRD 3.7 41.9 - - + +
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 3.6 14.5 - - - +
126B MET* 3.0 39.0 + - - +
129B ILE* 3.6 28.9 - - + +
130B GLY* 3.9 5.9 - - - +
133B MET* 3.6 15.3 - - - +
27C GLY* 4.3 2.0 - - - -
28C GLU 4.2 7.4 - - - +
29C THR* 2.7 41.1 + - - +
31C LEU* 1.3 74.1 - - - +
33C ALA* 1.3 60.6 + - - +
35C ASP* 3.5 4.4 + - - +
36C GLY 2.9 22.2 + - - -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C SER* 3.9 6.6 - - - +
26C GLU 3.8 14.1 - - - -
27C GLY* 3.8 11.4 - - - +
29C THR 2.9 12.4 + - - +
30C PRO 3.5 8.3 - - - +
32C ASN* 1.3 74.8 - - - +
34C PHE* 1.3 61.2 + - - +
36C GLY* 3.2 1.4 + - - -
37C ALA* 2.9 28.4 + - - +
81D ILE* 5.0 0.2 - - + -
153D LEU* 3.8 21.5 - - + +
155D CYS* 3.7 18.6 - - + +
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Residues in contact with PHE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER 3.4 23.8 - - - -
7011B AG2 3.8 11.7 - - - -
30C PRO 2.9 17.2 + - - +
31C LEU* 3.5 8.5 - - + +
33C ALA* 1.3 76.5 - - - +
35C ASP* 1.3 63.9 + - - +
37C ALA* 3.0 3.6 + - - +
38C LEU* 3.0 52.1 + - + +
48C LEU* 4.8 1.1 - - + -
77D TYR* 4.0 14.1 - + - -
79D TYR* 3.8 39.7 - + - -
81D ILE* 4.6 0.4 - - + -
155D CYS* 3.8 16.4 - - - +
157D PHE* 3.9 10.3 - + - -
7001D MRD 3.7 39.9 - - + -
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Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.0 2.6 - - - +
108B MET* 3.9 14.7 - - + +
130B GLY* 4.0 5.9 - - - -
133B MET* 5.1 2.5 - - - +
134B ARG* 2.7 44.3 + - - -
7011B AG2 3.0 39.8 + - + -
31C LEU 2.9 17.1 + - - +
32C ASN* 3.6 7.0 + - - +
34C PHE* 1.3 76.4 - - - +
36C GLY* 1.3 56.6 + - - +
38C LEU* 3.2 3.7 + - - +
39C LEU* 2.9 31.1 + - - +
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 3.7 16.8 - - - +
25C SER* 3.3 22.8 - - - -
32C ASN 2.9 11.9 + - - -
33C ALA 3.2 1.1 + - - -
34C PHE 3.2 0.4 - - - -
35C ASP* 1.3 78.1 - - - +
37C ALA* 1.3 55.1 + - - +
39C LEU* 3.3 9.6 + - - +
40C ASN* 2.9 28.6 + - - +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY* 3.8 12.5 + - - +
24C SER* 3.9 6.1 - - - -
25C SER* 3.4 6.2 - - - -
33C ALA 2.9 13.6 + - - +
34C PHE 3.0 8.0 + - - +
36C GLY* 1.3 72.5 - - - +
38C LEU* 1.3 62.6 + - - +
40C ASN* 3.2 3.3 + - - +
41C ALA* 2.9 29.0 + - - +
155D CYS* 3.9 20.6 - - - +
157D PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7011B AG2 3.4 40.4 - - - +
34C PHE* 3.0 39.1 + - + +
35C ASP 3.6 7.6 - - - +
37C ALA* 1.3 76.0 - - - +
39C LEU* 1.3 64.2 + - - +
41C ALA* 3.0 7.9 + - - +
42C GLY 2.9 18.4 + - - -
43C ILE* 3.0 16.2 + - + +
44C GLY* 3.6 13.5 - - - +
48C LEU* 3.7 20.6 - - + -
157D PHE* 3.6 42.2 - - + -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 4.6 16.6 - - + +
134B ARG* 3.7 52.5 - - + +
35C ASP* 2.9 21.9 + - - +
36C GLY* 3.5 14.4 - - - +
38C LEU* 1.3 75.6 - - - +
40C ASN* 1.3 62.4 + - - +
42C GLY* 3.1 13.9 + - - -
44C GLY* 3.8 21.3 - - - +
45C ASN* 4.0 12.1 - - - +
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Residues in contact with ASN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA 4.1 2.9 - - - +
23C GLY* 3.2 7.8 - - - -
24C SER* 3.0 37.1 + - - +
25C SER* 5.0 0.4 - - - -
36C GLY 2.9 16.9 + - - +
37C ALA 3.2 5.4 + - - +
39C LEU* 1.3 76.6 - - - +
41C ALA* 1.3 60.3 + - - +
146D VAL* 5.5 0.9 - - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 3.6 28.4 - - + +
22C ALA* 3.4 36.9 - - - +
23C GLY 3.7 0.7 - - - +
37C ALA 2.9 16.3 + - - +
38C LEU 3.0 5.1 + - - +
40C ASN* 1.3 76.7 - - - +
42C GLY* 1.3 58.9 + - - +
43C ILE* 3.5 2.0 - - + -
64D LEU* 4.5 1.2 - - - +
157D PHE* 4.1 13.9 - - + -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 2.9 2.8 + - - -
39C LEU 3.1 11.3 + - - -
40C ASN 3.3 0.6 + - - -
41C ALA* 1.3 79.1 - - - +
43C ILE* 1.3 62.5 + - - +
44C GLY 3.6 2.9 + - - -
45C ASN 5.4 0.2 + - - -
64D LEU* 3.5 17.7 - - - +
67D LEU* 5.3 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