Contacts of the helix formed by residues 44 - 51 (chain A) in PDB entry 1GXD
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.2 40.2 - - + +
29A TYR* 4.5 10.1 - - + +
31A CYS* 4.9 3.0 - - + +
36A CYS* 3.3 22.7 - - - -
37A ASN* 4.8 5.4 + - - -
38A LEU* 3.4 14.0 - - + +
42A LYS 4.1 0.2 + - - -
43A ASP* 1.3 91.8 + - - +
45A LEU* 1.3 68.5 + - - +
46A LYS* 2.9 4.0 + - - +
47A LYS* 3.1 22.0 + - - +
48A MET* 3.3 8.3 + - - +
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Residues in contact with LEU 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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18A LYS* 4.3 9.4 - - - +
21A ALA* 5.4 5.6 - - + -
25A LEU* 3.5 26.2 - - + -
38A LEU* 3.8 18.4 - - + +
44A THR* 1.3 80.2 - - - +
46A LYS* 1.3 63.5 + - + +
48A MET* 3.0 36.0 - - + +
49A GLN* 3.0 27.0 + - - +
58A GLY 3.8 10.1 - - - +
59A ASP* 2.8 50.7 - - + +
64A THR* 4.5 3.6 - - + -
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Residues in contact with LYS 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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42A LYS* 2.6 46.8 - - - +
43A ASP* 2.6 48.3 + - - +
44A THR 2.9 3.0 + - - +
45A LEU* 1.3 77.9 - - + +
47A LYS* 1.3 58.7 + - + +
49A GLN* 2.9 28.0 + - - +
50A LYS* 2.9 11.0 + - - +
56A GLN* 4.6 17.6 - - - +
58A GLY* 5.5 9.9 - - - -
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Residues in contact with LYS 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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29A TYR* 3.9 14.2 + - + -
43A ASP* 4.2 20.6 - - + +
44A THR* 3.1 13.4 + - - +
46A LYS* 1.3 79.9 - - + +
48A MET* 1.3 61.5 + - - +
50A LYS* 3.1 29.6 - - + +
51A PHE* 3.1 20.8 + - - +
78A VAL* 3.1 37.6 - - + +
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Residues in contact with MET 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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25A LEU* 4.0 9.4 - - + -
29A TYR* 2.8 39.7 + - + +
44A THR 3.3 2.8 + - - -
45A LEU* 3.0 35.7 - - + +
47A LYS* 1.3 80.9 - - - +
49A GLN* 1.3 60.7 + - + +
51A PHE* 2.9 24.1 - - - +
52A PHE* 3.6 16.9 - - - -
64A THR* 3.1 46.7 - - + +
67A THR* 5.3 6.7 - - - -
68A MET* 4.8 19.7 - - + -
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Residues in contact with GLN 49 (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 LEU* 3.3 13.8 - - - +
46A LYS* 2.9 9.8 + - - +
48A MET* 1.3 76.8 - - + +
50A LYS* 1.3 61.1 - - - +
51A PHE 2.7 14.7 - - - +
52A PHE* 5.6 0.7 - - - -
53A GLY 2.8 17.9 - - - +
54A LEU* 3.4 6.4 - - - -
55A PRO* 3.9 12.1 + - + -
56A GLN* 3.5 15.6 - - + +
57A THR 3.3 16.3 + - - -
58A GLY* 2.7 32.1 + - - +
60A LEU* 3.1 26.9 - - - +
64A THR* 3.0 31.8 + - - +
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Residues in contact with LYS 50 (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 TYR* 6.3 0.2 - - - -
46A LYS 2.9 7.5 + - - +
47A LYS* 3.1 32.7 + - + +
49A GLN* 1.3 74.3 - - - +
51A PHE* 1.3 103.0 + - - +
52A PHE 3.5 0.9 + - - -
53A GLY* 3.8 9.9 + - - -
54A LEU* 4.2 6.3 + - - +
56A GLN* 4.5 15.9 - - - +
77A ASP 5.8 0.4 + - - -
78A VAL* 5.0 12.9 - - - +
386A GLN* 3.5 25.1 + - - +
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Residues in contact with PHE 51 (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 TYR* 4.0 8.1 - + - +
47A LYS 3.1 5.2 + - - +
48A MET 2.9 15.6 - - - +
49A GLN* 2.7 23.4 - - - +
50A LYS* 1.3 109.8 - - - +
52A PHE* 1.3 91.6 + + + +
77A ASP* 3.7 36.8 - - + -
78A VAL* 6.0 0.9 - - + -
384A HIS* 4.0 17.0 - - + -
385A SER 3.6 27.4 - - - -
386A GLN* 3.6 23.1 - - + +
394A PRO* 4.0 14.8 - - + -
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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