Contacts of the helix formed by residues 25 - 34 (chain A) in PDB entry 1QMR
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS 2.9 18.3 + - - +
21A ALA 3.3 8.3 + - - +
23A ILE 3.4 0.2 - - - -
24A LEU* 1.3 78.8 - - - +
26A GLY* 1.3 63.5 + - - +
27A ASP* 3.2 3.8 - - - -
28A THR* 3.2 20.5 + - - +
29A LEU* 3.1 21.2 + - + +
158A TYR* 2.6 39.7 + - - +
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Residues in contact with GLY 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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21A ALA 3.3 6.3 + - - -
22A PHE 3.8 10.5 - - - -
23A ILE 3.6 6.9 + - - -
24A LEU 3.5 3.8 - - - -
25A ASP* 1.3 76.8 - - - +
27A ASP* 1.3 59.2 + - - +
29A LEU* 4.5 1.3 - - - -
30A PHE* 3.0 64.0 + - - +
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Residues in contact with ASP 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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23A ILE 5.4 1.6 - - - +
24A LEU 5.3 5.1 - - - +
25A ASP 4.9 0.7 - - - -
26A GLY* 1.3 78.8 + - - +
28A THR* 1.3 67.3 + - + +
30A PHE* 5.7 0.7 - - - -
31A PRO* 3.6 16.3 - - - +
41A VAL* 3.8 36.3 + - + +
43A ASN* 5.2 2.4 - - - +
54A LYS* 2.7 47.6 + - - +
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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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25A ASP* 3.2 29.0 + - - +
27A ASP* 1.3 85.2 - - + +
29A LEU* 1.3 70.9 + - - +
30A PHE 3.8 0.2 - - - -
31A PRO* 3.7 6.9 - - - +
32A GLN* 2.9 30.6 + - - +
158A TYR* 4.4 1.4 + - - -
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Residues in contact with LEU 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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21A ALA* 3.7 28.3 - - + +
25A ASP 3.1 12.3 + - - +
26A GLY* 4.4 2.7 - - - +
28A THR* 1.3 86.9 + - - +
30A PHE* 1.3 66.5 + - - +
32A GLN* 2.9 15.4 + - - +
33A VAL* 2.9 37.6 + - + +
147A VAL* 4.7 13.5 - - + -
150A TYR* 4.0 36.6 - - + +
158A TYR* 3.8 31.6 - - + +
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Residues in contact with PHE 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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22A PHE* 3.6 48.0 - + - -
26A GLY* 3.0 38.6 + - - +
27A ASP* 5.1 2.0 - - - -
29A LEU* 1.3 71.3 - - - +
31A PRO* 1.3 65.0 - - + +
33A VAL* 4.1 4.9 - - + -
34A ALA* 2.8 35.8 + - - +
38A ILE* 4.1 22.4 - - + -
41A VAL* 5.2 5.8 - - + -
56A ILE* 6.4 2.0 - - + -
143A LEU* 4.1 33.2 - - + -
147A VAL* 3.9 20.4 - - + -
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Residues in contact with PRO 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 ASP 3.6 20.6 - - - +
28A THR* 3.7 11.2 - - - +
29A LEU 3.6 1.1 - - - -
30A PHE* 1.3 94.2 - - + +
32A GLN* 1.3 63.1 + - + +
34A ALA 4.5 0.2 - - - -
35A PRO* 3.9 18.0 - - - +
38A ILE* 3.5 15.7 - - + +
39A SER 3.8 24.3 - - - +
40A SER* 4.4 7.2 - - - -
41A VAL* 4.5 8.3 - - + +
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Residues in contact with GLN 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* 2.9 29.7 + - - +
29A LEU* 2.9 17.9 + - - +
31A PRO* 1.3 83.0 - - + +
33A VAL* 1.3 68.1 + - + +
35A PRO* 3.5 12.0 - - - +
150A TYR* 5.8 3.9 - - - -
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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 LEU* 2.9 34.1 + - + +
30A PHE* 4.0 6.3 - - + +
32A GLN* 1.3 79.0 - - + +
34A ALA* 1.3 61.3 + - + +
35A PRO* 3.4 6.0 - - - +
146A ALA* 3.5 38.8 - - + +
147A VAL* 4.1 12.8 - - + +
150A TYR* 3.8 37.0 - - + -
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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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30A PHE 2.8 16.4 + - - +
33A VAL* 1.3 80.8 - - + +
35A PRO* 1.3 59.5 - - - +
36A GLN* 3.1 3.6 - - - +
37A ALA* 2.9 23.0 + - + -
38A ILE 3.0 11.3 + - - +
142A THR* 5.1 6.3 - - + -
143A LEU* 3.9 26.2 - - + -
146A ALA* 4.0 13.2 - - + -
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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