Contacts of the helix formed by residues 29 - 42 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D THR* 5.6 4.0 - - + -
126D MET* 3.6 26.3 - - + +
129D ILE* 5.4 2.5 - - + -
27E GLY 3.9 0.2 - - - -
28E GLU* 1.3 85.5 - - + +
30E PRO* 1.3 75.4 - - - +
31E LEU 3.5 2.9 + - - -
32E ASN* 2.6 40.6 + - - +
33E ALA* 2.9 23.4 + - - +
153F LEU* 3.4 7.2 - - - +
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Residues in contact with PRO 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D MET* 6.1 0.2 - - + -
29E THR* 1.3 86.7 - - - +
31E LEU* 1.3 58.4 + - - +
33E ALA* 3.3 2.7 + - + +
34E PHE* 3.0 22.9 + - - +
81F ILE* 3.5 39.7 - - + +
153F LEU* 3.9 16.8 - - + -
7005F MRD 4.1 7.0 - - + +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D MET* 3.5 26.6 - - - +
109D GLU* 3.6 45.8 - - + +
126D MET* 3.7 15.5 - - + +
7015D AG2 3.6 19.5 - - - +
29E THR* 3.2 1.0 + - - -
30E PRO* 1.3 77.4 - - - +
32E ASN* 1.3 60.1 + - - +
34E PHE* 3.3 8.9 + - + +
35E ASP* 2.9 28.2 + - - +
7005F MRD 3.7 41.9 - - + +
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Residues in contact with ASN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D MET* 3.4 12.5 - - - +
126D MET* 3.0 39.6 - - - +
129D ILE* 3.7 26.4 - - + +
130D GLY* 4.0 3.8 + - - -
133D MET* 3.7 13.2 - - - +
27E GLY* 4.3 2.2 - - - -
28E GLU 4.2 7.2 - - - +
29E THR* 2.6 48.2 + - - +
31E LEU* 1.3 73.9 - - - +
33E ALA* 1.3 60.6 + - - +
35E ASP* 3.5 5.9 + - - +
36E GLY* 2.9 24.3 + - - -
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Residues in contact with ALA 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E SER* 3.9 9.0 - - - +
26E GLU 3.9 3.8 - - - -
27E GLY* 3.8 23.3 - - - +
29E THR 2.9 16.7 + - - +
30E PRO* 3.5 8.5 - - + +
32E ASN* 1.3 75.1 - - - +
34E PHE* 1.3 58.6 + - - +
36E GLY* 3.2 1.6 + - - -
37E ALA* 2.9 28.9 + - - +
81F ILE* 5.0 1.1 - - + -
153F LEU* 4.3 9.0 - - + +
154F GLY 4.5 2.5 - - - -
155F CYS* 3.8 19.4 - - + +
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Residues in contact with PHE 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER* 3.4 23.3 - - - -
7015D AG2 3.9 11.7 - - - -
30E PRO 3.0 13.9 + - - +
31E LEU* 3.5 11.0 - - + +
33E ALA* 1.3 73.6 - - - +
35E ASP* 1.3 67.2 + - - +
37E ALA* 3.0 4.9 + - - +
38E LEU* 3.0 44.5 + - + +
48E LEU* 4.9 0.9 - - + -
77F TYR* 4.0 16.6 - + - -
79F TYR* 3.8 36.6 - + - -
81F ILE* 4.4 0.2 - - + -
155F CYS* 3.9 16.5 - - - +
157F PHE* 4.0 14.4 - + - -
7005F MRD 3.6 41.7 - - + -
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Residues in contact with ASP 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.9 2.0 - - - +
108D MET* 3.9 11.7 - - + +
130D GLY* 4.0 5.5 - - - -
133D MET* 5.0 3.2 - - - +
134D ARG* 2.8 36.3 + - - -
7015D AG2 2.9 47.6 + - + +
31E LEU 2.9 17.5 + - - +
32E ASN* 3.5 9.6 - - - +
34E PHE* 1.3 74.6 - - - +
36E GLY* 1.3 63.3 + - - +
38E LEU* 3.2 5.3 + - - +
39E LEU* 3.0 26.4 + - - +
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D MET* 3.6 26.2 - - - +
25E SER* 3.4 12.8 - - - -
32E ASN 2.9 11.3 + - - -
33E ALA 3.6 4.0 - - - -
35E ASP* 1.3 77.8 - - - +
37E ALA* 1.3 56.0 + - - +
39E LEU* 3.3 9.3 + - - +
40E ASN* 2.9 28.4 + - - +
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY* 3.7 8.6 - - - +
24E SER* 3.9 5.8 - - - -
25E SER* 3.4 6.8 - - - -
33E ALA 2.9 13.1 + - - +
34E PHE 3.0 8.0 + - - +
36E GLY* 1.3 73.0 - - - +
38E LEU* 1.3 61.4 + - - +
40E ASN* 3.2 3.5 + - - +
41E ALA* 2.9 27.7 + - - +
155F CYS* 3.8 33.2 - - - +
157F PHE* 3.9 16.2 - - + -
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER 4.0 0.2 - - - +
7015D AG2 3.3 38.8 - - - +
34E PHE* 3.0 37.2 + - + +
35E ASP 3.5 6.3 - - - +
37E ALA* 1.3 73.1 - - - +
39E LEU* 1.3 65.0 + - - +
41E ALA* 3.1 4.4 + - - +
42E GLY 3.0 5.2 + - - -
43E ILE* 2.9 36.0 + - + +
44E GLY* 3.6 12.6 - - - -
48E LEU* 3.7 20.4 - - + -
157F PHE* 3.4 41.7 - - + -
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D MET* 4.6 16.6 - - + +
134D ARG* 3.9 49.6 - - + +
35E ASP* 3.0 25.3 + - - +
36E GLY* 3.5 11.2 - - - +
38E LEU* 1.3 77.2 - - - +
40E ASN* 1.3 60.4 + - - +
42E GLY* 3.1 14.2 + - - -
44E GLY* 3.8 23.8 - - - +
45E ASN* 4.2 8.5 - - - +
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Residues in contact with ASN 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA 4.3 2.6 - - - +
23E GLY* 3.2 8.3 - - - -
24E SER* 3.0 36.9 + - - +
25E SER* 5.1 0.4 - - - -
36E GLY 2.9 17.2 + - - +
37E ALA 3.5 5.6 - - - +
38E LEU 3.2 0.2 - - - -
39E LEU* 1.3 76.4 - - - +
41E ALA* 1.3 59.7 + - - +
42E GLY* 3.2 0.9 + - - -
146F VAL* 5.6 0.3 - - - +
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 3.6 26.0 - - + +
22E ALA 3.5 34.5 + - - +
23E GLY* 3.8 1.3 - - - +
37E ALA 2.9 16.9 + - - +
38E LEU 3.1 5.8 + - - +
40E ASN* 1.3 76.6 - - - +
42E GLY* 1.3 60.0 + - - +
43E ILE* 3.4 1.8 - - + -
64F LEU* 4.6 1.2 - - - +
157F PHE* 4.0 18.4 - - + -
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Residues in contact with GLY 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU 3.0 2.4 + - - -
39E LEU 3.1 13.1 + - - -
40E ASN 3.2 1.6 + - - -
41E ALA* 1.3 79.6 - - - +
43E ILE* 1.3 59.1 + - - +
44E GLY 3.7 2.2 - - - -
64F LEU* 3.3 20.7 - - - +
67F LEU* 5.5 0.9 - - - +
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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
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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