Contacts of the helix formed by residues 34 - 45 (chain E) in PDB entry 2P1N
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 CYS 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D ILE* 3.9 26.0 - - + -
140D LYS 4.5 1.6 - - - +
142D ASP* 3.1 22.0 - - - +
143D PHE* 3.5 12.3 - - - -
31E SER 4.3 0.5 - - - +
33E VAL* 1.3 75.8 - - - +
35E LYS* 1.4 58.5 + - - +
36E SER* 2.9 15.8 + - - +
37E TRP* 3.2 39.4 + - - +
38E TYR* 2.9 28.4 + - - +
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Residues in contact with LYS 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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142D ASP* 3.3 38.4 + - - +
143D PHE* 3.9 26.9 - - + -
147D GLU* 5.1 15.7 + - - +
34E CYS* 1.4 73.7 - - - +
36E SER* 1.3 56.0 + - - +
38E TYR* 3.7 12.3 - - - +
39E GLU* 3.0 47.0 + - - +
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Residues in contact with SER 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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142D ASP* 4.9 1.3 + - - -
14E LEU* 5.5 2.6 - - - +
34E CYS* 3.6 15.3 - - - -
35E LYS* 1.3 77.1 - - - +
37E TRP* 1.3 66.9 + - - +
39E GLU* 3.3 6.1 + - - +
40E ILE* 2.9 40.3 + - - +
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Residues in contact with TRP 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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125D ILE* 4.2 13.2 - - + -
133D ILE* 3.8 27.1 - - + -
137D PHE* 4.0 27.1 - + - -
139D ILE* 3.7 28.2 - - + +
8E SER* 6.2 1.0 - - - -
9E PHE* 5.5 1.8 - + - -
14E LEU* 3.2 37.6 - - + +
18E PHE* 3.6 27.6 - + + -
30E VAL* 3.4 24.0 - - + +
33E VAL* 3.6 19.1 - - + -
34E CYS* 3.2 21.9 + - - +
36E SER* 1.3 80.4 - - - +
38E TYR* 1.3 60.8 + - - +
40E ILE* 4.3 5.8 - - + +
41E GLU* 2.8 34.1 + - - +
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Residues in contact with TYR 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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143D PHE* 4.0 10.5 - + + -
151D VAL* 4.0 25.8 - - + +
154D GLU* 4.8 1.6 + - - -
31E SER* 3.5 29.5 + - - +
34E CYS 2.9 14.9 + - - +
35E LYS* 3.7 13.7 - - - +
36E SER 3.3 0.2 - - - -
37E TRP* 1.3 79.2 - - - +
39E GLU* 1.3 77.2 + - + +
41E GLU* 3.5 1.9 - - - +
42E ARG* 2.9 45.2 + - + +
64E ARG* 3.3 55.1 + - - +
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Residues in contact with GLU 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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35E LYS* 3.0 30.1 + - - +
36E SER* 3.3 6.5 + - - +
38E TYR* 1.3 83.6 - - + +
40E ILE* 1.3 69.8 + - + +
42E ARG* 2.7 45.3 + - - +
43E TRP* 3.3 26.9 + - + -
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Residues in contact with ILE 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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11E GLU* 3.8 31.9 - - + +
14E LEU* 3.8 26.9 - - + -
15E GLU* 3.7 33.2 - - + +
18E PHE* 3.9 16.8 - - + -
36E SER* 2.9 28.1 + - - +
37E TRP* 4.5 0.9 - - - -
39E GLU* 1.3 74.0 - - + +
41E GLU* 1.3 67.1 + - - +
43E TRP* 3.5 8.4 + - - +
44E CYS* 3.4 14.2 + - - +
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Residues in contact with GLU 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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18E PHE* 3.6 16.4 - - + -
27E ARG* 2.9 47.1 + - - +
30E VAL* 3.3 25.6 - - + -
31E SER* 3.6 16.5 - - - +
37E TRP 2.8 19.7 + - - +
38E TYR 3.5 1.0 - - - +
40E ILE* 1.3 70.9 - - - +
42E ARG* 1.3 68.7 + - - +
43E TRP 2.8 1.9 + - - -
44E CYS* 3.0 8.1 + - - -
45E ARG* 2.7 48.0 + - - +
64E ARG* 4.3 0.9 + - - -
65E PHE* 3.7 7.3 - - - -
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Residues in contact with ARG 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 TYR* 2.9 39.1 + - + +
39E GLU* 2.7 50.0 + - - +
41E GLU* 1.3 73.8 + - - +
43E TRP* 1.3 85.9 + - - +
44E CYS 3.3 1.2 + - - -
45E ARG* 3.4 9.7 + - - +
63E ARG* 3.1 25.9 + - - +
64E ARG* 2.8 27.7 + - + +
65E PHE* 3.7 27.0 - - + -
66E PRO* 3.8 15.4 - - + +
67E LYS 4.7 0.9 + - - -
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Residues in contact with TRP 43 (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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15E GLU* 5.1 4.4 - - - +
39E GLU* 3.3 26.5 + - + +
40E ILE* 3.5 4.6 + - - +
41E GLU 2.8 1.6 + - - -
42E ARG* 1.3 109.8 - - - +
44E CYS* 1.3 59.2 + - - +
66E PRO* 3.5 41.7 - - + -
67E LYS* 3.6 44.4 - - + +
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Residues in contact with CYS 44 (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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15E GLU* 4.1 32.3 - - + +
18E PHE* 3.7 28.3 - - - -
19E SER 5.2 0.7 - - - -
27E ARG* 3.5 28.0 + - - -
40E ILE 3.4 20.1 + - - +
41E GLU 3.0 2.8 + - - -
43E TRP* 1.3 81.2 - - - +
45E ARG* 1.3 62.8 + - - +
46E ARG* 3.5 11.8 + - - +
67E LYS* 5.2 1.6 - - - -
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Residues in contact with ARG 45 (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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155D ASN* 4.9 0.4 + - - -
159D PHE* 4.3 12.3 + - - +
24E ASP* 4.5 10.3 + - - +
27E ARG* 3.3 32.3 + - + +
28E ASN* 3.1 30.5 + - - +
41E GLU* 2.7 47.6 + - - +
42E ARG 3.4 4.2 + - - +
44E CYS* 1.3 75.6 - - - +
46E ARG* 1.3 64.9 + - - +
47E LYS 3.5 22.1 + - - +
48E VAL* 4.1 6.5 - - + +
64E ARG* 4.3 5.7 - - - +
65E PHE* 3.1 54.0 - - + +
67E LYS* 3.9 7.3 + - - +
68E VAL* 3.7 19.7 + - + +
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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