Contacts of the helix formed by residues 24 - 32 (chain E) in PDB entry 1QVT
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 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E ASN 5.6 2.5 - - - +
22E ALA 4.0 6.2 + - - +
23E THR* 1.3 77.7 - - - +
25E THR* 1.3 65.6 + - - +
26E GLY 3.0 0.3 + - - -
27E GLU* 3.1 25.1 + - - +
28E ILE* 3.1 16.7 + - - +
46E LYS* 4.6 3.8 - - - +
204E SO4 2.8 36.7 + - - +
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Residues in contact with THR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR 4.2 0.8 + - - -
24E THR* 1.3 73.2 - - - +
26E GLY* 1.3 66.7 + - - +
28E ILE* 3.5 14.4 + - - +
29E VAL* 3.0 25.0 + - - +
36E LYS* 3.7 17.7 - - + +
39E LEU* 3.2 25.5 - - - +
40E TYR* 2.9 37.6 + - + +
46E LYS* 4.8 12.4 - - - +
204E SO4 3.5 11.4 - - - +
207E SO4 3.8 10.5 - - - +
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Residues in contact with GLY 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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24E THR 3.0 1.4 - - - -
25E THR* 1.3 84.6 - - - +
27E GLU* 1.3 50.3 + - - +
29E VAL* 3.1 10.4 - - - +
30E LYS* 2.7 34.8 + - - +
36E LYS* 3.8 13.2 - - - -
204E SO4 3.1 23.5 + - - -
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Residues in contact with GLU 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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14E LEU* 3.7 30.6 - - + +
18E ASN* 4.0 13.7 - - - +
22E ALA 4.4 5.5 - - - +
23E THR* 4.5 1.2 - - - -
24E THR* 3.1 29.1 + - - +
26E GLY* 1.3 71.9 - - - +
28E ILE* 1.3 67.1 + - - +
30E LYS* 3.6 6.5 - - + +
31E LEU* 3.1 37.4 + - + +
204E SO4 3.7 1.2 + - - -
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Residues in contact with ILE 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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7E ILE* 3.7 38.8 - - + +
10E VAL* 3.5 5.6 - - + +
11E ALA* 4.1 14.1 - - + +
14E LEU* 3.9 13.7 - - + +
15E PHE* 4.4 7.2 - - + -
23E THR* 4.0 23.6 - - + +
24E THR 3.1 10.0 + - - +
25E THR* 3.5 20.6 - - - +
27E GLU* 1.3 78.1 - - - +
29E VAL* 1.3 62.7 + - - +
32E SER* 2.9 27.2 + - - -
39E LEU* 3.8 6.3 - - + -
46E LYS* 5.5 4.9 - - + -
49E LEU* 3.7 23.3 - - + -
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Residues in contact with VAL 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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7E ILE* 4.8 0.4 - - + -
25E THR 3.0 12.4 + - - +
26E GLY* 3.1 15.7 - - - +
28E ILE* 1.3 79.9 - - - +
30E LYS* 1.3 68.0 + - - +
32E SER* 2.9 15.1 + - - +
34E SER* 3.0 36.9 + - - +
35E SER* 3.0 41.1 - - - +
36E LYS* 3.4 21.3 - - + +
39E LEU* 4.0 15.0 - - + -
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Residues in contact with LYS 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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44A LYS* 5.3 0.7 + - - -
26E GLY 2.7 22.0 + - - +
27E GLU* 3.2 10.9 + - + +
29E VAL* 1.3 74.4 - - + +
31E LEU* 1.3 70.3 + - + +
33E GLU* 3.0 23.0 + - - +
34E SER 5.2 1.1 - - - -
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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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40A TYR* 3.9 3.1 + - - -
41A TYR* 4.1 17.9 - - + +
44A LYS* 3.5 34.4 + - - +
10E VAL* 3.6 20.3 - - + +
14E LEU* 3.9 35.7 - - + -
27E GLU* 3.1 19.5 + - + +
28E ILE 3.9 0.2 - - - -
30E LYS* 1.3 83.6 - - + +
32E SER* 1.3 56.6 + - - +
33E GLU 3.3 2.1 + - - -
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Residues in contact with SER 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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40A TYR* 3.7 10.6 + - - -
3E LEU* 4.0 2.3 - - - +
6E LYS* 3.9 36.1 - - - +
7E ILE* 3.9 12.3 - - - +
10E VAL* 4.0 6.5 - - - -
28E ILE 2.9 23.0 + - - -
29E VAL* 2.9 15.8 + - - -
30E LYS 3.0 0.6 - - - -
31E LEU* 1.3 78.0 - - - +
33E GLU* 1.3 72.6 + - - +
34E SER* 3.1 13.9 + - - -
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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