Contacts of the helix formed by residues 23 - 31 (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 LEU 23 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LYS* 5.8 2.2 - - + -
22E GLN* 1.3 79.0 - - + +
24E ASP* 1.3 67.0 + - - +
25E LYS* 4.2 6.1 - - + +
26E ASP* 2.8 44.3 + - - +
27E ARG* 3.0 12.2 + - - +
47E LYS* 4.9 1.6 - - - +
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Residues in contact with ASP 24 (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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159D PHE 3.6 21.6 - - - +
160D GLU* 4.4 8.0 - - + -
22E GLN 3.5 2.0 + - - +
23E LEU* 1.3 71.1 - - - +
25E LYS* 1.3 63.7 + - + +
27E ARG* 3.2 8.1 + - - +
28E ASN* 3.0 27.4 + - - +
45E ARG* 4.9 7.0 + - - +
47E LYS* 3.3 37.3 + - - +
48E VAL* 5.2 0.2 - - - -
49E PHE* 3.3 30.9 + - - +
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Residues in contact with LYS 25 (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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160D GLU* 3.5 44.4 + - + +
23E LEU* 3.2 6.4 - - + +
24E ASP* 1.3 76.9 - - + +
26E ASP* 1.3 65.2 + - - +
28E ASN* 3.3 1.4 + - - +
29E SER* 3.1 24.8 + - - -
484E ARG* 5.8 6.3 - - - +
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Residues in contact with ASP 26 (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* 5.4 1.7 - - + +
126D LYS* 3.6 31.6 - - - +
127D GLY* 3.1 25.6 + - - -
21E ILE* 3.8 17.1 - - + +
22E GLN 5.0 0.5 + - - -
23E LEU* 2.8 41.5 + - + +
25E LYS* 1.3 79.4 - - - +
27E ARG* 1.3 63.4 + - - +
29E SER* 2.9 23.8 - - - -
30E VAL* 3.0 14.6 + - + +
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Residues in contact with ARG 27 (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* 3.2 34.0 + - - +
19E SER* 4.2 3.4 - - - +
21E ILE* 3.1 26.9 + - + +
22E GLN* 4.2 11.3 + - - +
23E LEU 3.0 16.0 + - - +
24E ASP* 3.5 10.8 - - - +
26E ASP* 1.3 75.6 - - - +
28E ASN* 1.4 58.0 + - - +
30E VAL* 3.3 11.0 + - - +
31E SER* 3.0 27.5 + - - -
41E GLU* 2.9 39.9 + - - +
44E CYS* 3.5 21.1 + - - -
45E ARG* 3.3 48.2 - - + +
46E ARG* 5.2 2.9 - - - +
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Residues in contact with ASN 28 (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* 2.8 62.4 + - + +
159D PHE* 4.4 3.5 - - - +
160D GLU* 3.0 31.8 + - - +
24E ASP 3.0 12.3 + - - +
25E LYS 3.9 0.2 - - - +
26E ASP 3.3 0.2 - - - -
27E ARG* 1.4 71.6 - - - +
29E SER* 1.3 66.3 + - - +
31E SER* 2.4 20.2 + - - -
32E LEU* 3.2 11.0 + - + +
45E ARG* 3.1 27.9 + - - +
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Residues in contact with SER 29 (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* 5.8 1.3 - - - -
128D LYS 2.8 27.5 + - - -
129D THR* 4.2 0.3 - - - -
130D PRO* 3.9 19.3 - - - +
133D ILE* 4.5 7.4 - - - -
25E LYS 3.1 10.9 + - - -
26E ASP* 2.9 19.3 - - - -
28E ASN* 1.3 75.8 - - - +
30E VAL* 1.3 53.4 + - - +
32E LEU* 2.8 28.1 + - - +
33E VAL* 3.5 10.7 + - - +
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Residues in contact with VAL 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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125D ILE* 3.6 31.0 - - + -
133D ILE* 5.1 0.2 - - - -
18E PHE* 4.0 23.8 - - + -
21E ILE* 5.0 10.8 - - + -
26E ASP 3.0 17.7 + - - +
27E ARG* 3.3 11.6 + - - +
29E SER* 1.3 71.8 - - - +
31E SER* 1.3 60.9 + - - +
32E LEU 2.9 10.6 + - - -
33E VAL* 3.0 21.7 + - - +
37E TRP* 3.4 26.1 - - + +
41E GLU* 3.3 28.0 - - + -
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Residues in contact with SER 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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143D PHE* 3.6 6.2 - - - -
151D VAL* 4.4 0.3 - - - +
155D ASN* 2.8 18.5 + - - -
27E ARG 3.0 12.3 + - - -
28E ASN* 2.4 26.9 + - - -
30E VAL* 1.3 76.1 - - - +
32E LEU* 1.3 61.6 + - - +
33E VAL 3.3 0.6 + - - -
38E TYR* 3.5 41.0 + - - +
41E GLU* 3.6 20.0 - - - -
64E ARG* 3.6 15.9 + - - -
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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