Contacts of the helix formed by residues 40 - 51 (chain B) in PDB entry 1XAH
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 GLU 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE 3.6 0.2 + - - -
39B ASP* 1.3 73.8 + - - +
41B TYR* 1.3 76.9 + - + +
43B ASN* 3.5 5.9 - - - +
44B GLN* 3.4 25.7 + - + +
63B ILE* 3.7 19.0 - - + +
64B ILE 2.9 22.6 + - - +
65B PRO* 4.3 4.0 - - - +
66B ALA* 3.7 24.5 + - + +
69B LYS* 5.8 1.9 - - - +
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP* 3.1 2.4 + - - -
40B GLU* 1.3 91.0 - - + +
42B VAL* 1.3 58.7 + - - +
43B ASN 3.0 1.8 - - - -
44B GLN* 2.7 40.4 + - + +
45B TYR* 3.2 17.2 + - + -
66B ALA* 3.7 23.6 - - + -
69B LYS* 4.4 13.2 + - - -
401B NAD 3.6 34.8 - - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.1 16.4 - - + +
39B ASP* 3.1 31.4 + - + +
41B TYR* 1.3 75.5 - - - +
43B ASN* 1.3 55.3 + - - +
45B TYR* 3.3 5.5 + - - -
46B PHE* 2.9 52.8 + - + +
97B VAL* 4.2 13.0 - - + +
98B GLY* 4.3 5.2 - - - -
124B THR* 4.4 9.6 - - + +
401B NAD 3.4 35.4 + - + +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.7 13.6 - - + +
39B ASP 2.8 19.2 + - - +
40B GLU 3.5 6.1 - - - +
41B TYR 2.9 0.2 + - - -
42B VAL* 1.3 69.6 - - - +
44B GLN* 1.3 74.4 + - - +
47B ALA* 2.8 44.2 + - - +
61B LYS* 2.8 38.7 + - - +
63B ILE* 3.4 28.9 - - + +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 3.4 21.2 + - + +
41B TYR* 2.7 27.7 + - + +
43B ASN* 1.3 88.7 - - - +
45B TYR* 1.3 64.6 + - + +
47B ALA* 4.3 3.2 + - - +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.2 20.9 + - + -
42B VAL* 3.6 2.9 - - - +
44B GLN* 1.3 85.5 - - + +
46B PHE* 1.3 86.6 + + + +
166B THR* 3.4 47.3 + - + -
168B PRO* 4.7 8.9 - - + +
401B NAD 3.5 24.4 - + - -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 2.9 43.2 + - + +
45B TYR* 1.3 93.4 - - + +
47B ALA* 1.3 65.3 + - - +
48B ASN* 2.9 6.4 + - - +
49B LYS* 3.0 34.9 + - + +
50B PHE* 3.2 25.7 - - + -
124B THR* 5.1 0.2 - - - -
162B ASP 5.2 2.5 - - - -
163B PHE* 3.7 35.0 - + + -
166B THR* 3.1 35.2 - - + -
401B NAD 3.5 23.3 - + - -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN* 2.8 46.7 + - - +
44B GLN 4.3 2.8 + - - +
45B TYR 3.9 0.6 - - - -
46B PHE* 1.3 71.3 - - - +
48B ASN* 1.3 63.7 + - - +
50B PHE* 3.4 11.1 + - - +
51B ASP* 2.8 31.0 + - - +
61B LYS* 3.9 10.1 + - - +
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 2.9 2.7 + - - -
47B ALA* 1.3 81.9 + - - +
49B LYS* 1.3 54.5 + - + +
50B PHE 2.7 15.2 + - - -
51B ASP* 3.0 28.5 + - + +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.7 43.1 - - + +
46B PHE* 3.0 39.5 + - + +
48B ASN* 1.3 77.9 - - + +
50B PHE* 1.3 61.5 + - + +
51B ASP 5.4 0.2 - - - -
160B ASP* 4.9 4.6 + - - -
162B ASP* 4.6 19.3 + - - +
163B PHE* 5.1 8.5 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.6 24.5 - - + -
24B ILE* 4.6 12.3 - - + -
36B LEU* 4.4 27.4 - - + -
38B ILE* 3.7 18.2 - - + -
46B PHE* 3.2 33.2 - - + -
47B ALA* 3.4 7.4 + - - +
48B ASN 2.7 2.6 + - - -
49B LYS* 1.3 83.3 - - + +
51B ASP* 1.3 64.8 + - - +
61B LYS* 6.0 2.5 - - + +
97B VAL* 3.3 38.8 - - + -
122B VAL* 4.9 0.9 - - + -
163B PHE* 3.7 20.2 - + - -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA* 2.8 28.5 + - - +
48B ASN* 3.0 24.9 + - - +
49B LYS 5.4 0.2 - - - -
50B PHE* 1.3 80.9 - - - +
61B LYS* 4.3 11.1 + - - -
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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