Contacts of the helix formed by residues 45 - 57 (chain H) in PDB entry 3Q2K
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 ASN 45 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43H ASP* 3.1 14.8 - - - +
44H THR* 1.3 82.1 - - - +
46H PRO* 1.3 61.6 - - - +
47H GLU* 3.6 29.1 + - - +
48H ALA* 3.1 27.9 + - + +
49H LEU* 2.7 37.8 + - - +
500H NAI 3.8 11.9 - - - +
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Residues in contact with PRO 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H THR 3.5 9.6 - - - +
45H ASN* 1.3 88.7 - - - +
47H GLU* 1.3 62.0 + - + +
49H LEU* 3.1 8.2 + - + +
50H GLN* 2.6 51.2 + - - +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H ASN* 3.3 26.2 + - - +
46H PRO* 1.3 83.9 - - + +
48H ALA* 1.3 61.3 + - - +
50H GLN* 3.5 12.0 - - - +
51H ALA* 3.0 26.2 + - - +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H CYS* 3.9 14.4 - - - +
19H GLY* 5.8 0.7 - - - -
43H ASP* 4.1 14.8 - - - +
45H ASN* 3.1 19.8 + - + +
47H GLU* 1.3 74.6 - - - +
49H LEU* 1.3 67.7 + - - +
51H ALA* 3.6 6.5 - - - +
52H ALA* 3.0 26.3 + - - +
500H NAI 4.2 10.5 - - - +
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H CYS* 4.7 1.1 - - - -
41H ILE* 4.0 23.6 - - + +
42H CYS 4.4 1.3 - - - +
43H ASP* 3.8 27.4 - - + +
45H ASN 2.7 20.2 + - - +
46H PRO* 3.1 8.7 - - + +
48H ALA* 1.3 80.3 - - - +
50H GLN* 1.3 68.6 + - - +
52H ALA* 3.1 6.7 + - - -
53H GLU* 3.3 11.5 + - - +
60H PRO* 4.1 20.0 - - + -
61H PHE 3.5 33.4 - - - +
62H SER* 3.9 11.4 - - - -
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Residues in contact with GLN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H PRO* 2.6 31.2 + - - +
47H GLU* 3.5 16.6 - - - +
49H LEU* 1.3 72.0 - - - +
51H ALA* 1.3 64.5 + - - +
53H GLU* 2.7 38.4 - - - +
54H ALA* 2.8 10.7 + - + +
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Residues in contact with ALA 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H GLU 3.0 15.2 + - - +
48H ALA* 3.6 8.1 - - - +
50H GLN* 1.3 79.4 - - - +
52H ALA* 1.3 57.0 + - - +
54H ALA* 3.4 10.0 - - - +
55H ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H CYS* 3.6 31.4 - - + +
22H SER* 6.1 0.9 - - - +
26H ILE* 5.3 10.5 - - + -
41H ILE* 3.6 11.7 - - + -
48H ALA 3.0 18.2 + - - +
49H LEU 3.9 0.2 - - - +
50H GLN 3.0 0.2 + - - -
51H ALA* 1.3 74.6 - - - +
53H GLU* 1.3 62.0 + - - +
55H ALA* 3.1 8.2 + - - +
56H THR* 2.9 31.1 + - - +
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Residues in contact with GLU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ILE* 3.3 16.9 - - + +
49H LEU* 3.3 11.1 + - - +
50H GLN* 2.7 37.9 + - - +
52H ALA* 1.3 72.7 - - - +
54H ALA* 1.3 69.0 + - - +
55H ALA 2.9 1.7 + - - -
56H THR* 4.0 3.4 - - - -
57H GLY* 2.6 31.1 + - - +
58H ALA 3.7 13.2 - - - +
60H PRO* 3.6 30.9 - - + +
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H GLN 2.8 13.1 + - - +
51H ALA* 3.4 15.9 - - - +
53H GLU* 1.3 79.5 + - - +
55H ALA* 1.3 58.3 + - - +
57H GLY 4.8 0.5 + - - -
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ILE* 5.7 3.1 - - + -
51H ALA 3.0 17.8 + - - +
52H ALA* 3.5 8.1 - - - +
53H GLU 2.9 1.2 - - - -
54H ALA* 1.3 79.3 - - - +
56H THR* 1.3 66.1 + - + +
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Residues in contact with THR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ILE* 3.6 44.9 - - + -
38H LEU* 4.2 16.8 - - + +
41H ILE* 4.5 3.8 - - + +
52H ALA 2.9 17.7 + - - +
53H GLU* 2.9 1.3 + - - -
55H ALA* 1.3 85.2 - - + +
57H GLY* 1.3 65.7 + - - +
58H ALA* 3.3 18.1 + - - +
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Residues in contact with GLY 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H LEU 5.6 0.2 - - - -
53H GLU* 2.6 23.4 + - - -
54H ALA 4.8 0.6 + - - -
56H THR* 1.3 72.3 + - - +
58H ALA* 1.3 63.0 + - - +
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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