Contacts of the helix formed by residues 23 - 38 (chain A) in PDB entry 4QBX
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 PRO 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS 3.2 10.7 - - - +
22A SER* 1.3 82.8 - - - +
24A PRO* 1.3 76.8 - - + +
25A GLY* 4.4 2.5 - - - +
26A GLN* 2.9 44.3 + - + +
27A VAL* 2.9 11.4 + - - +
262A LYS* 5.4 0.7 - - - +
264A VAL* 4.0 18.8 - - + -
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Residues in contact with PRO 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 3.5 3.1 - - - +
23A PRO* 1.3 84.7 - - + +
25A GLY* 1.3 59.3 + - - +
26A GLN 3.2 0.7 + - - -
27A VAL* 3.9 12.0 + - + -
28A THR* 4.5 3.8 + - - -
49A GLN 5.0 5.6 - - - +
50A ASN* 4.6 8.3 - - + -
53A GLU* 3.3 47.3 - - + +
403A CIT 5.2 0.2 - - - +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.1 3.6 - - - +
24A PRO* 1.3 80.7 - - - +
26A GLN* 1.3 63.9 + - - +
28A THR* 5.3 1.3 - - - -
29A GLU* 5.8 0.9 + - - +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 2.9 35.8 + - + +
25A GLY* 1.3 83.8 - - - +
27A VAL* 1.3 61.3 + - - +
28A THR 3.3 2.5 - - - -
29A GLU* 3.4 10.3 + - - +
30A ALA* 3.1 24.6 + - - +
264A VAL* 3.5 31.9 - - + +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 6.0 0.4 - - + -
19A THR* 4.3 8.3 - - + -
22A SER* 3.6 27.8 - - - +
23A PRO 2.9 16.1 + - - +
24A PRO* 3.9 4.9 - - + +
25A GLY 3.9 0.2 - - - -
26A GLN* 1.3 75.8 - - - +
28A THR* 1.3 68.9 + - - +
30A ALA* 4.0 7.9 - - + -
31A VAL* 3.0 31.6 + - + +
50A ASN* 4.2 12.3 - - + +
53A GLU* 3.5 27.6 - - + -
54A VAL* 3.8 25.1 - - + +
264A VAL* 4.9 0.2 - - - +
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO 4.5 3.1 + - - -
25A GLY 5.3 1.3 - - - -
26A GLN 3.3 0.8 - - - +
27A VAL* 1.3 82.0 - - - +
29A GLU* 1.3 57.9 + - - +
32A LYS* 3.0 56.2 + - + +
53A GLU* 2.8 35.2 + - - +
56A VAL* 3.9 23.4 - - + +
57A ALA* 3.3 11.5 - - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 5.9 0.7 - - - +
26A GLN* 3.4 10.7 + - - +
27A VAL 3.3 0.2 - - - -
28A THR* 1.3 79.2 - - - +
30A ALA* 1.3 57.7 + - - +
32A LYS* 4.0 18.9 - - - +
33A VAL* 2.9 49.7 + - + +
266A PRO* 5.4 8.6 - - + +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 5.6 - - + +
26A GLN 3.1 14.5 + - - +
27A VAL* 3.6 16.2 - - + +
28A THR 3.3 0.2 - - - -
29A GLU* 1.3 77.1 - - - +
31A VAL* 1.3 56.8 + - - +
33A VAL* 3.5 0.8 + - - +
34A ALA* 2.9 28.8 + - - +
263A SER 4.0 5.2 - - - +
264A VAL* 4.0 22.2 - - + +
266A PRO* 6.3 1.1 - - - -
269A ILE* 3.7 28.0 - - + +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 21.5 - - + -
19A THR* 4.6 0.4 - - + -
27A VAL* 3.0 29.5 + - + +
30A ALA* 1.3 72.5 - - - +
32A LYS* 1.3 64.8 - - - +
34A ALA* 3.3 1.0 + - - +
35A ILE* 2.9 40.8 + - + +
42A ILE* 4.1 19.1 - - + -
54A VAL* 4.3 19.1 - - + +
57A ALA* 3.5 24.2 - - + -
58A ILE* 4.3 12.6 - - + -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 3.0 39.6 + - + +
29A GLU* 3.7 20.6 - - - +
31A VAL* 1.3 77.5 - - - +
33A VAL* 1.3 61.6 + - - +
35A ILE* 3.4 0.5 + - - -
36A ASP* 3.0 29.3 + - - +
56A VAL* 4.9 3.1 - - - -
57A ALA* 3.8 13.2 - - + +
60A GLU* 3.9 30.1 - - - -
61A LYS* 3.6 29.9 - - - +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 2.9 44.0 + - + +
30A ALA 3.8 3.8 - - - +
32A LYS* 1.3 74.4 - - + +
34A ALA* 1.3 64.4 + - - +
36A ASP* 3.1 11.7 + - - +
37A VAL* 2.9 32.4 + - + +
266A PRO* 4.2 34.3 - - + +
269A ILE* 4.2 17.7 - - + -
270A ALA* 5.8 0.4 - - + -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.8 18.6 - - + -
30A ALA 2.9 20.1 + - - +
31A VAL* 3.6 5.2 - - - +
33A VAL* 1.3 75.2 - - - +
35A ILE* 1.3 61.9 + - - +
37A VAL* 3.2 2.4 + - - -
38A GLY 3.1 6.4 + - - -
39A TYR* 2.9 53.1 + - + -
42A ILE* 4.9 2.7 - - + -
269A ILE* 3.7 13.2 - - + -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 2.9 37.3 + - + +
32A LYS 3.9 3.4 - - - +
34A ALA* 1.3 75.7 - - - +
36A ASP* 1.3 63.7 + - - +
38A GLY* 3.2 3.5 + - - -
39A TYR 3.6 14.8 - - - +
40A ARG* 2.9 24.7 + - - +
42A ILE* 4.8 8.7 - - + -
58A ILE* 4.5 15.5 - - + -
61A LYS* 4.0 28.0 - - + -
66A VAL* 4.0 14.1 - - + +
67A VAL* 3.7 28.0 - - + -
72A LEU* 4.5 18.8 - - + -
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.0 18.8 + - - +
33A VAL* 3.1 12.5 + - - +
35A ILE* 1.3 78.5 - - - +
37A VAL* 1.3 63.6 + - + +
38A GLY 3.7 0.3 + - - -
40A ARG* 5.8 0.3 + - - -
61A LYS* 2.8 36.4 + - - +
66A VAL* 3.9 13.6 - - - +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 2.9 30.0 + - + +
34A ALA* 3.5 9.0 - - - +
36A ASP* 1.3 81.7 - - + +
38A GLY* 1.3 56.4 + - - +
39A TYR* 4.0 19.5 - - + -
269A ILE* 4.2 3.8 - - + -
270A ALA* 4.0 32.3 - - + -
273A PHE* 3.6 17.6 - - + +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.1 1.0 + - - -
35A ILE 3.2 4.2 + - - -
36A ASP 3.4 1.4 + - - -
37A VAL* 1.3 79.0 - - - +
39A TYR* 1.3 66.9 + - - +
40A ARG* 3.4 28.9 + - - +
273A PHE* 3.2 25.0 - - - -
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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