Contacts of the helix formed by residues 47 - 61 (chain A) in PDB entry 2DHY
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 ALA 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.3 3.6 + - - +
44A ASN* 4.4 10.1 - - + +
45A SER 3.6 5.4 - - - +
46A GLY* 1.3 77.5 - - - +
48A VAL* 1.3 55.9 + - - +
49A ASP* 3.4 3.1 - - + +
50A ALA* 3.1 18.6 + - + +
51A THR* 2.4 47.0 + - - -
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Residues in contact with VAL 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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17A GLU* 4.6 7.6 - - + +
21A ALA* 4.1 26.0 - - + -
24A ASP* 4.9 6.5 - - - +
25A PHE* 3.9 12.3 - - + -
41A LEU* 4.9 2.7 - - + -
47A ALA* 1.3 67.8 - - - +
49A ASP* 1.3 65.0 + - - +
50A ALA 2.7 2.0 + - - -
51A THR* 4.0 6.5 - - - -
52A ILE* 2.6 63.1 + - + +
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Residues in contact with ASP 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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47A ALA* 5.1 2.0 - - + -
48A VAL* 1.3 81.2 - - - +
50A ALA* 1.3 60.4 + - + +
52A ILE* 3.8 11.1 - - - +
53A ASP* 3.7 15.8 + - - +
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Residues in contact with ALA 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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44A ASN* 3.2 23.6 - - + +
47A ALA* 3.1 20.9 + - + +
48A VAL 2.7 3.8 + - - -
49A ASP* 1.3 74.5 - - + +
51A THR* 1.3 55.6 + - - +
52A ILE 2.5 17.4 + - - -
53A ASP* 2.8 17.5 + - - +
54A GLN* 2.9 11.1 + - - +
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Residues in contact with THR 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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25A PHE* 3.5 24.9 - - + -
37A ILE 3.9 3.4 - - - +
40A VAL* 3.7 19.5 - - + -
41A LEU* 3.4 50.9 + - + +
44A ASN* 4.0 6.0 + - - +
47A ALA 2.4 32.2 + - - -
48A VAL 3.7 0.2 - - - -
50A ALA* 1.3 71.8 - - - +
52A ILE* 1.3 63.3 + - - +
54A GLN* 3.3 2.3 - - - +
55A LEU* 3.2 25.0 + - + +
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Residues in contact with ILE 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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24A ASP* 4.9 2.9 - - - +
25A PHE* 3.9 7.4 - - + -
28A MET* 3.8 28.9 - - + -
29A PHE* 4.2 2.4 - - - -
48A VAL* 2.6 46.6 + - + +
49A ASP* 3.8 11.0 - - - +
50A ALA 2.5 4.4 + - - -
51A THR* 1.3 66.3 - - - +
53A ASP* 1.3 70.7 + - + +
54A GLN 2.7 1.9 + - - -
55A LEU* 2.9 4.3 + - - +
56A LEU* 2.6 48.8 + - + +
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Residues in contact with ASP 53 (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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49A ASP 3.7 8.6 + - - +
50A ALA* 2.8 10.6 + - - +
52A ILE* 1.3 79.0 - - - +
54A GLN* 1.3 65.7 + - + +
56A LEU* 3.3 18.4 - - + +
57A GLN* 2.9 45.0 + - - +
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Residues in contact with GLN 54 (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 VAL* 3.2 37.7 - - + +
43A ALA* 5.6 2.0 - - - +
44A ASN* 3.6 21.4 + - - +
50A ALA 2.9 7.9 + - - +
51A THR 3.3 4.5 - - - +
52A ILE 2.7 3.8 + - - -
53A ASP* 1.3 78.3 - - + +
55A LEU* 1.3 64.6 + - - +
57A GLN* 3.3 6.5 + - - +
58A MET* 3.0 40.0 + - - +
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Residues in contact with LEU 55 (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 PHE* 4.1 15.0 - - + -
29A PHE* 3.4 42.5 - - + -
32A MET* 3.6 27.9 - - + +
36A ILE* 4.1 5.2 - - + -
37A ILE* 3.8 27.1 - - + -
40A VAL* 3.7 25.4 - - + -
51A THR* 3.4 17.0 - - + +
52A ILE 2.9 3.4 + - - -
54A GLN* 1.3 74.6 - - - +
56A LEU* 1.3 68.8 + - - +
58A MET* 3.1 12.9 + - + +
59A ASN* 2.7 22.2 + - - +
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Residues in contact with LEU 56 (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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28A MET* 5.6 1.6 - - + -
29A PHE* 3.4 17.1 - - + -
52A ILE* 2.6 48.4 + - + +
53A ASP* 3.3 19.5 - - - +
55A LEU* 1.3 76.5 - - - +
57A GLN* 1.3 63.9 + - + +
59A ASN* 3.1 4.5 + - - +
60A LEU* 2.9 36.5 + - + +
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Residues in contact with GLN 57 (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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53A ASP* 2.9 41.9 + - - +
54A GLN* 3.8 5.0 + - - +
56A LEU* 1.3 74.0 - - + +
58A MET* 1.3 56.9 + - + +
60A LEU* 2.5 37.4 + - + +
61A GLU* 2.7 14.6 + - - -
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Residues in contact with MET 58 (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 MET* 3.5 18.8 - - + -
36A ILE* 4.1 12.8 - - + -
40A VAL* 3.9 16.6 - - + -
54A GLN* 3.0 25.8 + - - +
55A LEU* 3.2 32.3 - - + +
57A GLN* 1.3 77.4 - - - +
59A ASN* 1.3 63.4 + - - +
61A GLU* 3.5 22.8 - - - +
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Residues in contact with ASN 59 (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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28A MET 5.5 0.2 + - - -
29A PHE* 3.5 31.9 - - + +
30A PRO* 5.4 2.2 - - - +
31A ASN* 4.5 15.3 - - - +
32A MET* 3.9 14.1 - - - +
55A LEU 2.7 13.8 + - - +
56A LEU 3.4 9.4 - - - +
58A MET* 1.3 72.0 - - - +
60A LEU* 1.3 68.3 + - + +
61A GLU* 4.1 2.8 - - - +
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Residues in contact with LEU 60 (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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56A LEU* 2.9 43.1 + - + +
57A GLN* 2.5 22.7 + - + +
59A ASN* 1.3 75.1 - - + +
61A GLU* 1.3 76.9 + - - +
63A GLY* 5.4 0.2 - - - -
64A PRO* 4.7 15.8 - - - +
65A SER* 5.0 9.6 - - - +
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Residues in contact with GLU 61 (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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57A GLN 2.7 15.6 + - - -
58A MET* 3.5 17.7 - - - +
59A ASN 4.1 2.2 - - - +
60A LEU* 1.3 89.8 - - - +
62A SER* 1.3 71.5 + - - +
63A GLY* 2.7 8.3 + - - -
64A PRO* 5.2 1.2 - - - +
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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