Contacts of the helix formed by residues 38 - 50 (chain A) in PDB entry 1WZ3
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 PHE 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP 3.8 0.8 + - - -
37A LYS* 1.3 70.9 - - - +
39A ALA* 1.3 60.6 - - - +
40A ASN 3.0 0.4 - - - -
41A VAL* 3.0 34.4 + - + +
42A ILE* 3.1 36.6 + - + +
56A VAL* 3.8 23.8 - - + -
58A VAL* 4.7 2.2 - - + -
64B PRO* 3.6 40.2 - - + -
65B ASN 3.8 11.7 - - - +
66B PRO 3.4 0.6 + - - -
68B GLU 2.7 19.6 + - - +
70B VAL* 4.7 6.5 - - + +
73B LEU* 3.4 27.8 - - + -
83B LEU* 4.6 7.4 - - + -
85B VAL* 3.9 27.8 - - + -
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Residues in contact with ALA 39 (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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37A LYS* 2.8 8.2 + - + +
38A PHE* 1.3 79.5 - - - +
40A ASN* 1.3 61.6 + - - +
42A ILE* 3.6 8.3 - - - +
43A ASP* 2.9 32.1 + - - +
66B PRO* 3.0 34.1 + - + +
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Residues in contact with ASN 40 (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* 5.8 2.5 - - + -
36A ASP* 3.3 32.2 - - + +
37A LYS* 2.9 20.8 + - - +
39A ALA* 1.3 84.2 - - - +
41A VAL* 1.3 59.1 + - + +
43A ASP* 3.8 5.9 - - - +
44A PHE* 3.0 28.6 + - - +
47A ARG* 4.7 3.3 + - - -
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Residues in contact with VAL 41 (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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14A VAL* 4.9 13.9 - - + -
16A LEU* 4.1 25.6 - - + -
32A VAL* 5.5 5.6 - - + -
38A PHE* 3.0 42.5 + - + +
40A ASN* 1.3 77.0 - - + +
42A ILE* 1.3 66.1 + - - +
44A PHE* 3.2 7.7 + - + +
45A LEU* 3.1 25.7 + - + +
56A VAL* 4.9 0.2 - - + -
70B VAL* 4.7 13.5 - - + -
83B LEU* 6.3 0.2 - - + -
85B VAL* 4.1 12.3 - - + -
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Residues in contact with ILE 42 (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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38A PHE* 3.1 38.7 + - + +
39A ALA* 3.6 8.3 - - - +
41A VAL* 1.3 77.2 - - - +
43A ASP* 1.3 58.3 + - - +
45A LEU* 3.4 2.6 + - - +
46A ARG* 3.0 29.1 + - + +
54A LEU* 5.3 0.7 - - + +
56A VAL* 4.6 25.1 - - + +
64B PRO 4.4 6.3 - - - +
66B PRO* 4.1 28.7 - - + -
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Residues in contact with ASP 43 (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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39A ALA 2.9 19.7 + - - +
40A ASN* 3.8 6.3 - - - +
41A VAL 3.2 0.2 - - - -
42A ILE* 1.3 76.7 - - - +
44A PHE* 1.3 63.9 + - - +
46A ARG* 3.4 8.5 + - - +
47A ARG* 2.9 62.5 + - - +
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Residues in contact with PHE 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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16A LEU* 3.7 25.6 - - + -
25A LEU* 4.5 4.7 - - + -
27A GLN* 5.0 1.3 - - + -
30A PHE* 3.4 40.6 - + - -
40A ASN 3.0 18.1 + - - +
41A VAL* 3.2 8.7 + - + +
43A ASP* 1.3 75.7 - - - +
45A LEU* 1.3 61.6 + - + +
47A ARG* 3.2 30.2 + - - +
48A GLN* 2.9 66.7 + - + +
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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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16A LEU* 3.7 39.5 - - + -
25A LEU* 4.0 15.0 - - + -
41A VAL* 3.1 12.4 + - + +
42A ILE 3.8 5.4 - - - +
44A PHE* 1.3 78.1 - - + +
46A ARG* 1.3 67.2 + - - +
48A GLN* 4.4 2.0 - - - +
49A LEU* 2.9 26.0 + - + +
54A LEU* 3.5 19.8 - - + +
56A VAL* 3.8 33.7 - - + -
85B VAL* 4.4 2.2 - - + -
87B TYR* 3.9 36.6 - - + -
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Residues in contact with ARG 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 ILE* 3.0 20.8 + - + +
43A ASP* 3.7 12.6 - - - +
44A PHE 3.3 0.2 - - - -
45A LEU* 1.3 75.5 - - - +
47A ARG* 1.3 58.9 + - + +
50A HIS* 2.9 23.2 + - - -
51A SER 3.1 30.5 + - - +
52A ASP* 5.0 9.2 - - - +
54A LEU* 3.8 7.8 - - + +
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Residues in contact with ARG 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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40A ASN 4.7 2.2 + - - -
43A ASP* 2.9 40.4 + - - +
44A PHE* 3.6 42.0 + - - +
46A ARG* 1.3 77.4 - - + +
48A GLN* 1.3 73.4 + - - +
49A LEU 3.5 0.2 + - - -
50A HIS* 3.5 25.4 + - - +
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Residues in contact with GLN 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* 4.1 31.9 - - + +
44A PHE* 2.9 60.2 + - + +
45A LEU* 3.2 4.2 + - - +
47A ARG* 1.3 87.7 + - - +
49A LEU* 1.3 63.6 - - + +
50A HIS* 3.9 10.7 + - - -
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Residues in contact with LEU 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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23A PRO* 3.6 41.7 - - + +
25A LEU* 4.3 12.3 - - + -
45A LEU* 2.9 18.0 + - + +
48A GLN* 1.3 82.7 - - + +
50A HIS* 1.3 74.1 + - - +
51A SER* 4.3 2.9 - - - +
54A LEU* 3.5 41.5 - - + -
87B TYR* 3.6 28.5 - - + -
89B CYS* 4.3 10.1 - - - -
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Residues in contact with HIS 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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46A ARG 2.9 11.6 + - - -
47A ARG* 3.5 15.9 + - - +
48A GLN 3.4 13.8 + - - -
49A LEU* 1.3 80.0 - - - +
51A SER* 1.3 59.2 + - - +
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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