Contacts of the helix formed by residues 38 - 52 (chain A) in PDB entry 1WMA
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 5.7 0.4 + - - +
36A ALA* 3.3 7.8 - - - +
37A ARG* 1.3 78.5 - - + +
39A VAL* 1.3 58.6 + - - +
40A THR* 2.8 24.8 + - - -
41A ARG* 2.9 47.0 + - + +
42A GLY 2.9 24.8 + - - -
309A NDP 4.6 8.0 + - - +
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Residues in contact with VAL 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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36A ALA 4.8 0.2 + - - -
37A ARG 3.8 4.4 + - - -
38A ASP* 1.3 72.5 + - - +
40A THR* 1.3 66.1 + - - +
43A GLN* 2.9 51.6 + - - +
58A PHE* 3.9 25.5 - - + -
60A GLN* 4.8 12.5 - - + +
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Residues in contact with THR 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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38A ASP* 2.8 10.5 + - - -
39A VAL* 1.3 86.5 - - - +
41A ARG* 1.3 63.7 + - + +
43A GLN* 3.5 12.0 + - - +
44A ALA* 3.0 24.7 + - + +
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Residues in contact with ARG 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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13A ASN* 3.7 30.3 - - - +
14A LYS* 6.1 2.6 - - - +
38A ASP* 2.9 41.6 + - + +
40A THR* 1.3 77.3 - - + +
42A GLY* 1.3 61.6 + - - +
44A ALA* 3.4 6.8 + - - +
45A ALA* 3.0 23.7 + - - +
309A NDP 4.1 15.7 + - - -
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Residues in contact with GLY 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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13A ASN* 4.1 4.3 - - - -
34A LEU* 4.0 3.0 - - - +
36A ALA* 3.6 14.0 - - - +
38A ASP 2.9 12.0 + - - -
41A ARG* 1.3 77.8 - - - +
43A GLN* 1.3 60.8 + - - +
45A ALA* 3.2 4.2 + - - +
46A VAL* 3.0 25.8 + - - +
58A PHE* 3.5 27.1 - - - -
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Residues in contact with GLN 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 VAL* 2.9 46.0 + - + +
40A THR* 4.0 12.2 + - - +
42A GLY* 1.3 74.9 - - - +
44A ALA* 1.3 58.3 + - - +
46A VAL* 3.3 9.2 + - - +
47A GLN* 2.9 35.1 + - + +
58A PHE* 4.3 13.2 - - + -
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Residues in contact with ALA 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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40A THR* 3.0 19.0 + - + +
41A ARG* 3.7 9.0 - - - +
43A GLN* 1.3 76.2 - - - +
45A ALA* 1.3 58.3 + - - +
47A GLN* 3.3 8.1 + - - +
48A GLN* 3.0 27.4 + - - +
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Residues in contact with ALA 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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13A ASN* 3.5 35.2 - - - +
18A LEU* 4.1 6.6 - - + +
34A LEU* 3.9 13.2 - - + -
41A ARG 3.0 14.7 + - - +
42A GLY 3.2 5.1 + - - +
44A ALA* 1.3 75.8 - - - +
46A VAL* 1.3 63.5 + - - +
48A GLN* 3.2 14.1 + - - +
49A LEU* 3.0 25.5 + - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.2 16.2 - - + -
42A GLY 3.0 14.0 + - - +
43A GLN* 3.3 9.6 + - - +
45A ALA* 1.3 74.6 - - - +
47A GLN* 1.4 61.3 + - - +
49A LEU* 3.2 2.9 + - - +
50A GLN* 2.8 50.0 + - - +
56A PRO* 3.9 30.9 - - + +
57A ARG 4.3 2.2 - - - +
58A PHE* 4.0 29.6 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLN* 2.9 21.9 + - + +
44A ALA* 3.6 10.8 - - - +
45A ALA 3.2 0.2 - - - -
46A VAL* 1.4 79.2 - - - +
48A GLN* 1.3 61.9 + - - +
50A GLN* 3.2 31.9 + - - +
51A ALA* 2.9 23.6 + - - +
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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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18A LEU* 3.8 29.5 - - - +
22A ARG* 4.0 7.4 - - - +
44A ALA 3.0 12.4 + - - +
45A ALA* 3.2 13.7 + - - +
47A GLN* 1.3 76.3 - - - +
49A LEU* 1.3 61.9 + - + +
51A ALA* 3.1 18.3 + - - +
52A GLU* 3.2 33.6 + - - +
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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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18A LEU* 3.8 23.3 - - + -
21A VAL* 3.6 31.6 - - + -
22A ARG* 3.7 32.5 - - + +
25A CYS* 4.8 1.8 - - - -
34A LEU* 4.2 4.9 - - + -
45A ALA 3.0 13.3 + - - +
46A VAL 3.8 5.8 - - - +
48A GLN* 1.3 77.7 - - + +
50A GLN* 1.3 62.3 + - - +
52A GLU* 3.0 35.9 + - - +
53A GLY 3.3 0.2 + - - -
54A LEU* 3.0 26.8 + - + +
56A PRO* 4.0 22.4 - - + -
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Residues in contact with GLN 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 VAL* 2.8 37.2 + - + +
47A GLN* 3.2 36.5 + - - +
49A LEU* 1.3 77.7 - - - +
51A ALA* 1.3 56.9 + - - +
53A GLY* 2.9 20.6 + - - -
54A LEU 3.2 18.8 - - - +
55A SER* 4.9 3.0 - - - -
56A PRO* 4.7 7.2 - - + +
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Residues in contact with ALA 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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47A GLN 2.9 12.6 + - - +
48A GLN* 3.1 11.6 + - - +
50A GLN* 1.3 75.3 - - - +
52A GLU* 1.3 59.9 + - + +
53A GLY 3.3 1.0 + - - -
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Residues in contact with GLU 52 (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 ARG* 2.8 48.5 + - - +
26A ARG* 3.9 19.8 + - - +
48A GLN* 3.5 28.3 + - + +
49A LEU* 3.0 18.6 + - - +
51A ALA* 1.3 78.0 - - + +
53A GLY* 1.3 59.4 + - - +
54A LEU* 3.6 6.6 - - + +
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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