Contacts of the helix formed by residues 43 - 48 (chain A) in PDB entry 1QGI
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 TRP 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASN* 3.4 33.8 - - + +
7A PHE* 4.2 13.9 - + - -
27A ASN* 2.8 31.3 + - - -
30A MET* 3.5 32.8 - - + +
31A LYS* 4.0 12.6 - - + -
34A ASN* 3.5 35.0 - - + +
41A LEU 2.9 18.1 + - - +
42A ASN* 1.3 67.5 - - - +
44A ILE* 1.3 67.4 + - + +
45A LYS 3.1 2.9 - - - -
46A TYR* 2.9 18.9 + - - +
47A TYR* 3.4 28.9 - + - -
63A LEU* 3.5 31.4 - - + +
141A TRP* 4.0 14.8 - + - -
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Residues in contact with ILE 44 (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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5A ASP 5.9 0.2 - - - +
6A ASN* 3.5 57.0 - - + +
42A ASN* 3.4 17.0 - - - +
43A TRP* 1.3 88.7 - - + +
45A LYS* 1.3 83.6 + - - +
46A TYR 3.1 1.2 + - - -
47A TYR* 3.2 30.4 + - + -
131A GLN* 3.4 10.4 - - - +
132A ASN* 5.3 0.9 - - - +
137A ARG* 4.7 13.2 - - - +
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Residues in contact with LYS 45 (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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40A ASP* 5.2 2.7 - - - +
42A ASN* 3.1 43.1 - - + +
43A TRP 3.1 0.6 - - - -
44A ILE* 1.3 102.7 - - - +
46A TYR* 1.3 72.7 + - + +
47A TYR 3.4 1.2 + - - -
48A GLY* 3.6 9.9 + - - -
49A TYR* 4.0 4.0 + - - -
128A LYS* 4.9 8.1 + - - +
131A GLN* 2.6 51.2 + - - +
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Residues in contact with TYR 46 (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 ASN* 3.4 30.1 - - - +
38A GLN* 3.6 44.2 + - + +
40A ASP* 2.9 34.2 + - - +
42A ASN 3.7 9.9 - - - -
43A TRP 2.9 14.0 + - - +
45A LYS* 1.3 84.2 - - + +
47A TYR* 1.3 64.4 + - - +
48A GLY 3.0 1.8 - - - -
49A TYR* 3.1 35.4 + + + +
62A GLY 3.2 23.0 - - - +
63A LEU* 3.7 13.7 - - + -
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Residues in contact with TYR 47 (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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6A ASN 2.6 30.3 + - - -
7A PHE* 3.8 4.9 - - - -
43A TRP* 3.4 16.2 - + - -
44A ILE* 3.2 29.5 + - + +
46A TYR* 1.3 77.7 - - - +
48A GLY* 1.3 55.3 - - - +
49A TYR 3.8 0.3 + - - -
62A GLY* 4.1 2.6 + - - -
63A LEU* 3.8 19.3 - - + +
127A ILE* 4.7 0.3 - - - +
131A GLN* 3.8 17.9 - - - +
136A TRP* 2.8 32.2 + + + -
137A ARG* 3.6 50.7 - - + -
140A MET* 3.4 24.0 - - + +
141A TRP* 2.9 33.3 + + - -
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Residues in contact with GLY 48 (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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45A LYS 3.6 10.0 + - - -
46A TYR 3.0 0.2 - - - -
47A TYR* 1.3 80.3 - - - +
49A TYR* 1.3 63.4 + - - -
50A CYS* 3.3 4.2 + - - +
127A ILE* 3.7 24.0 - - - +
128A LYS* 3.7 36.3 + - - +
131A GLN* 4.3 7.7 - - - +
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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