Contacts of the helix formed by residues 21 - 31 (chain E) in PDB entry 1GN2
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 SER 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E GLU* 3.7 15.0 - - - -
18E PRO 4.5 1.1 + - - -
20E ILE* 1.3 77.7 - - - +
22E GLY* 1.3 65.4 + - - +
23E GLN* 3.2 10.6 + - - +
24E ILE* 3.1 32.7 + - - +
25E ASN* 3.3 10.7 + - - -
168E LEU* 5.7 1.2 - - - +
169E GLN* 2.8 28.7 + - - +
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Residues in contact with GLY 22 (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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13E TYR* 3.5 29.2 - - - +
14E GLY* 4.1 1.1 - - - -
17E GLU* 3.3 22.6 + - - -
20E ILE 3.7 0.2 + - - -
21E SER* 1.3 71.5 - - - +
23E GLN* 1.3 66.4 + - - +
24E ILE 3.1 0.2 + - - -
25E ASN* 3.2 2.1 + - - +
26E GLU* 2.9 26.9 + - - +
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Residues in contact with GLN 23 (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 SER* 3.2 8.1 + - - +
22E GLY* 1.3 75.9 - - - +
24E ILE* 1.3 62.7 + - - +
26E GLU* 3.7 12.4 - - - +
27E LEU* 3.1 35.9 + - + +
168E LEU* 3.9 25.6 - - + +
171F LYS* 4.3 26.5 - - - +
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Residues in contact with ILE 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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20E ILE* 4.1 14.1 - - + -
21E SER* 3.1 20.6 + - - +
22E GLY 3.1 0.8 - - - -
23E GLN* 1.3 77.3 - - - +
25E ASN* 1.3 58.9 + - - +
26E GLU 2.9 0.9 + - - -
27E LEU* 3.0 5.0 + - - +
28E HIS* 2.8 43.5 + - + +
164E HIS 4.2 15.3 - - - +
165E ALA* 3.9 16.8 - - - +
166E PHE* 4.0 22.9 - - - -
168E LEU* 4.2 23.3 - - + +
169E GLN* 3.8 35.4 - - + +
170E TYR* 5.5 1.1 - - + -
177E PHE* 6.2 0.4 - - + -
167F TYR* 6.3 0.2 - - + -
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Residues in contact with ASN 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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11E TRP* 4.0 7.8 - - + -
13E TYR* 3.0 41.0 + - + +
16E LEU* 3.4 30.4 - - - +
20E ILE* 3.5 27.7 + - - +
21E SER 3.3 5.0 + - - +
22E GLY 3.2 3.5 + - - +
24E ILE* 1.3 80.1 - - - +
26E GLU* 1.3 57.1 + - - +
28E HIS* 3.8 6.8 + - - +
29E HIS* 3.0 32.4 + - - +
79E TRP* 5.3 1.6 + - - -
80E TRP* 3.9 18.0 - - + -
83E LEU* 5.2 1.2 - - - +
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Residues in contact with GLU 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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13E TYR* 3.6 36.0 - - + +
22E GLY 2.9 16.4 + - - +
23E GLN* 3.7 13.4 - - - +
24E ILE 2.9 1.0 + - - -
25E ASN* 1.3 76.0 - - - +
27E LEU* 1.3 67.6 + - + +
30E SER* 2.7 39.4 + - - +
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Residues in contact with LEU 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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23E GLN* 3.1 27.2 + - + +
24E ILE* 3.0 5.1 + - - +
26E GLU* 1.3 79.2 - - + +
28E HIS* 1.3 58.7 + - - +
30E SER* 4.1 0.7 - - - -
31E LYS* 2.8 47.4 + - + +
32E HIS* 3.1 6.2 + - - -
168E LEU* 3.7 26.9 - - + -
167F TYR* 3.7 18.6 - - + +
171F LYS* 3.8 26.5 - - + -
172F ASN* 3.3 24.2 - - - +
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Residues in contact with HIS 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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24E ILE* 2.8 29.6 + - + +
25E ASN* 3.8 1.6 + - - +
27E LEU* 1.3 79.5 - - - +
29E HIS* 1.3 57.2 + - - +
32E HIS* 3.3 15.8 - - + +
33E HIS* 2.9 28.8 + - - +
76E HIS* 3.0 14.8 + + - -
79E TRP* 3.5 24.0 + + - -
80E TRP* 3.6 20.1 - + + -
160E ASP* 2.9 19.1 - - - -
164E HIS* 3.0 22.7 + + - +
165E ALA* 4.3 7.1 - - + +
999E FE 2.4 25.7 - - - -
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Residues in contact with HIS 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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6E LEU* 3.8 29.0 - - + +
7E PRO* 2.9 27.6 + - + -
8E ASP* 5.0 4.3 - - - -
9E LEU* 3.4 34.2 - - + +
13E TYR* 2.9 28.0 + + + -
25E ASN 3.0 19.8 + - - +
28E HIS* 1.3 76.1 - - - +
30E SER* 1.3 61.8 + - - +
33E HIS* 3.3 20.2 - - - +
34E ALA 3.3 7.3 + - - -
80E TRP* 3.5 26.2 - + + -
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Residues in contact with SER 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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6E LEU* 4.9 4.0 - - - -
13E TYR* 4.1 12.3 - - - -
26E GLU* 2.7 29.4 + - - +
27E LEU* 4.1 0.5 - - - -
29E HIS* 1.3 81.3 - - - +
31E LYS* 1.3 78.7 + - - +
34E ALA* 3.5 16.8 - - - +
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Residues in contact with LYS 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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27E LEU* 2.8 33.1 + - + +
30E SER* 1.3 93.7 + - - +
32E HIS* 1.3 64.8 - - + +
33E HIS 3.6 0.4 - - - -
34E ALA* 3.9 2.0 - - - +
35E THR* 2.8 30.4 + - - -
172F ASN* 3.5 46.0 - - + +
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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