Contacts of the helix formed by residues 21 - 31 (chain E) in PDB entry 3Q2K
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 ILE 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E ARG* 1.3 74.6 - - - +
22E SER* 1.3 68.3 + - - +
23E LYS 3.1 1.8 - - - -
24E ASN* 3.0 32.2 + - - +
25E HIS* 3.0 20.1 - - - +
79E ALA* 3.5 21.8 - - + +
102E GLU* 3.4 20.2 - - - +
301E HIS* 3.8 14.6 - - + -
500E NAI 3.0 73.3 + - + +
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Residues in contact with SER 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.4 29.6 - - - -
17E GLY 3.5 15.7 - - - -
18E CYS* 2.9 10.8 - - - +
19E GLY 2.3 39.5 + - - +
21E ILE* 1.3 77.8 - - - +
23E LYS* 1.3 62.2 + - - +
25E HIS* 2.9 17.3 + - - +
26E ILE* 3.0 24.6 + - - +
79E ALA* 4.5 0.6 - - - +
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Residues in contact with LYS 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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19E GLY 3.8 13.0 - - - +
20E ARG* 3.2 39.7 - - - +
22E SER* 1.3 77.7 + - - +
24E ASN* 1.3 60.1 + - - +
26E ILE* 4.1 11.1 - - + +
27E GLY* 3.2 22.5 + - - -
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Residues in contact with ASN 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 ARG 4.3 7.7 + - - -
21E ILE* 3.0 26.8 + - + +
23E LYS* 1.3 77.4 - - - +
25E HIS* 1.3 62.6 + - - +
27E GLY* 3.7 2.0 - - - +
28E ALA* 2.8 29.1 + - - +
301E HIS* 3.6 32.7 + - + +
302E PRO* 4.9 1.3 - - + +
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Residues in contact with HIS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 4.2 12.1 - - + -
21E ILE* 3.0 33.3 - - + +
22E SER* 2.9 8.2 + - - +
24E ASN* 1.3 74.4 - - - +
26E ILE* 1.3 60.5 + - - +
28E ALA* 2.9 2.9 + - - +
29E ILE* 2.8 37.8 + - + +
77E VAL* 3.7 18.6 - - + +
79E ALA* 4.4 5.4 - - + +
100E VAL* 5.2 0.7 - - + -
102E GLU* 3.0 39.9 + - + +
129E VAL* 4.2 11.2 - - + -
301E HIS* 3.6 17.0 + + - -
304E TYR* 6.3 0.4 - + - -
305E TYR* 2.8 37.4 + + - +
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Residues in contact with ILE 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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15E LEU* 4.2 12.8 - - + +
22E SER* 3.0 29.7 + - - +
23E LYS* 4.1 9.9 - - + +
25E HIS* 1.3 73.8 - - - +
27E GLY* 1.3 56.0 + - - +
29E ILE* 3.0 7.7 + - + -
30E ALA* 2.8 38.4 + - + +
38E LEU* 4.5 13.7 - - + -
41E ILE* 6.5 0.2 - - + -
52E ALA* 5.5 11.7 - - + -
55E ALA* 6.3 2.7 - - + -
56E THR* 3.3 36.8 - - + -
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Residues in contact with GLY 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 LYS 3.2 15.8 + - - -
24E ASN* 3.9 1.6 - - - -
26E ILE* 1.3 78.5 - - - +
28E ALA* 1.3 61.2 + - - +
30E ALA* 4.5 4.8 - - - +
31E GLN* 3.5 28.5 + - - +
302E PRO* 5.6 1.3 - - - -
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Residues in contact with ALA 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 ASN 2.8 22.7 + - - +
25E HIS 3.4 2.2 - - - +
27E GLY* 1.3 75.1 - - - +
29E ILE* 1.3 58.9 + - - +
31E GLN* 3.2 20.4 - - - +
32E HIS* 3.7 14.4 + - - -
301E HIS* 3.7 2.0 - - + -
302E PRO* 3.6 31.9 - - + +
305E TYR* 3.2 31.6 - - + -
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Residues in contact with ILE 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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13E PHE* 3.8 30.3 - - + -
25E HIS* 2.8 21.0 + - + +
26E ILE* 3.7 4.3 - - + +
28E ALA* 1.3 74.2 - - - +
30E ALA* 1.3 69.5 + - - +
31E GLN 3.1 1.1 - - - -
32E HIS* 2.8 23.6 + - - +
33E GLY 3.7 0.3 + - - -
36E ALA* 4.1 4.6 - - + +
37E GLU* 4.1 14.1 - - - +
38E LEU* 4.0 33.9 - - + +
77E VAL* 5.1 2.9 - - + -
305E TYR* 3.7 44.9 - - + +
309E ILE* 6.1 1.8 - - + -
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Residues in contact with ALA 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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26E ILE* 2.8 22.6 + - + +
27E GLY* 4.5 5.4 - - - +
29E ILE* 1.3 72.0 - - - +
31E GLN* 1.3 53.5 + - - +
32E HIS 2.6 0.9 + - - -
33E GLY* 2.5 34.7 + - - +
36E ALA 5.6 0.7 - - - -
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Residues in contact with GLN 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 GLY 3.5 14.9 + - - +
28E ALA 3.2 15.2 + - - +
29E ILE 3.1 0.8 - - - -
30E ALA* 1.3 75.9 - - - +
32E HIS* 1.3 65.2 + - + +
33E GLY 3.6 0.7 - - - -
34E ASP* 4.4 4.2 - - - +
302E PRO* 3.2 34.5 - - + +
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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