Contacts of the helix formed by residues 24 - 37 (chain A) in PDB entry 6QY3
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 ASP 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.2 3.9 - - + +
23A GLU* 1.3 78.9 - - - +
25A VAL* 1.3 61.6 + - - +
26A SER* 4.5 2.7 - - - +
27A VAL* 3.8 23.4 - - + +
28A PHE* 2.9 30.5 + - - +
208A LEU 4.7 0.6 + - - -
209A ASP 5.5 1.3 - - - +
210A LYS* 4.8 17.7 - - + +
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Residues in contact with VAL 25 (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 GLU 4.1 1.8 + - - -
24A ASP* 1.3 72.5 - - - +
26A SER* 1.3 58.8 + - - +
28A PHE* 3.8 5.7 - - - +
29A ALA* 2.9 31.5 + - - +
171B SER 4.6 10.3 - - - +
172B TYR* 3.7 17.9 - - - +
173B PHE 4.9 2.7 - - - +
174B SER* 4.9 15.9 - - - +
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Residues in contact with SER 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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24A ASP* 3.3 2.6 - - - +
25A VAL* 1.3 79.7 - - - +
27A VAL* 1.3 57.7 + - - +
29A ALA* 4.3 3.4 - - - +
30A GLN* 2.9 32.4 + - - +
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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
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7A LEU* 6.1 4.5 - - + -
22A ILE* 5.1 5.8 - - + -
24A ASP* 3.4 22.7 + - + +
25A VAL 3.4 0.2 - - - -
26A SER* 1.3 77.7 - - - +
28A PHE* 1.3 59.5 + - - +
30A GLN* 4.2 4.4 - - - +
31A LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 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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22A ILE* 4.0 22.6 - - + +
24A ASP 2.9 18.8 + - - +
25A VAL* 3.8 7.2 - - - +
27A VAL* 1.3 75.0 - - - +
29A ALA* 1.3 61.3 + - - +
31A LEU* 3.1 5.6 + - - +
32A VAL* 2.9 29.1 + - - +
196A GLU 5.9 0.7 - - - +
197A PRO* 5.4 9.2 - - + -
171B SER 5.9 2.2 - - - +
172B TYR* 6.0 2.2 - - - -
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Residues in contact with ALA 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 VAL 2.9 17.6 + - - +
26A SER* 4.3 2.9 - - - +
28A PHE* 1.3 76.1 - - - +
30A GLN* 1.3 57.9 + - - +
32A VAL* 3.4 6.3 + - - +
33A LYS* 2.9 28.5 + - - +
144B VAL* 5.0 15.7 + - + +
172B TYR* 3.9 29.3 - - + +
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Residues in contact with GLN 30 (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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26A SER 2.9 21.5 + - - +
27A VAL* 4.2 5.2 - - - +
29A ALA* 1.3 77.4 - - - +
31A LEU* 1.3 57.2 + - - +
33A LYS* 3.7 8.2 - - - +
34A GLU* 2.9 27.0 + - - +
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Residues in contact with LEU 31 (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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27A VAL 2.9 22.3 + - - +
28A PHE* 3.1 8.2 + - - +
30A GLN* 1.3 75.0 - - - +
32A VAL* 1.3 60.8 + - - +
34A GLU* 3.2 8.9 + - - +
35A PHE* 2.9 25.3 + - - +
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Residues in contact with VAL 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 PHE 2.9 15.1 + - - +
29A ALA* 3.9 7.0 - - - +
31A LEU* 1.3 73.0 - - - +
33A LYS* 1.3 61.1 + - - +
35A PHE* 2.9 10.0 + - - +
36A TYR* 2.9 29.3 + - - +
167A VAL* 5.6 10.1 - - + -
144B VAL* 6.4 1.8 - - + -
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Residues in contact with LYS 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 ALA 2.9 17.9 + - - +
30A GLN* 3.7 9.2 - - - +
32A VAL* 1.3 77.4 - - - +
34A GLU* 1.3 56.0 + - - +
36A TYR* 3.9 4.8 - - - +
37A GLN* 2.9 33.7 + - - +
142B CYS 5.4 3.4 - - - +
143B THR* 5.3 14.6 - - - -
144B VAL* 5.4 4.0 - - + +
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Residues in contact with GLU 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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30A GLN 2.9 18.0 + - - +
31A LEU* 3.2 9.8 + - - +
33A LYS* 1.3 76.5 - - - +
35A PHE* 1.3 57.6 + - - +
37A GLN* 3.8 4.0 - - - +
38A TYR* 3.0 28.2 + - - +
41A GLN* 5.3 9.8 - - + +
43A ASN* 5.8 3.6 - - + -
44A LEU* 4.1 29.4 - - + +
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Residues in contact with PHE 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 LEU 2.9 12.8 + - - +
32A VAL* 2.9 13.9 + - - +
34A GLU* 1.3 76.5 - - - +
36A TYR* 1.3 63.7 + - - +
38A TYR* 3.5 17.0 - - - +
61A LEU* 5.4 12.3 - - + +
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Residues in contact with TYR 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 VAL 2.9 13.6 + - - +
33A LYS* 4.2 4.7 - - - +
35A PHE* 1.3 77.4 - - - +
37A GLN* 1.3 57.6 + - - +
38A TYR 3.3 1.4 + - - -
39A ASP* 4.9 2.3 + - - +
66B LEU* 4.3 24.7 - - + +
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Residues in contact with GLN 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 LYS 2.9 19.4 + - - +
34A GLU* 3.8 2.7 - - - -
36A TYR* 1.3 75.0 - - - +
38A TYR* 1.3 50.5 + - - +
39A ASP* 3.1 4.0 - - - -
40A GLU* 2.6 38.7 + - + +
41A GLN* 2.7 26.9 + - + -
140B LYS 4.8 13.5 - - - +
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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