Contacts of the helix formed by residues 41 - 58 (chain D) in PDB entry 3QOQ
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 SER 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ARG* 1.3 77.5 - - - +
42D MSE 1.3 61.2 + - - +
43D ASN* 3.2 17.4 + - - +
44D SER* 3.2 21.2 + - - -
45D GLU* 2.9 27.2 + - - +
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Residues in contact with MSE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.5 51.1 - - + -
23D LEU* 5.2 2.5 - - + -
28D ARG* 4.6 35.2 - - + +
31D ILE* 3.8 36.3 - - + +
32D ALA* 4.3 17.0 - - + -
35D ALA* 4.1 10.2 - - + +
40D ARG 3.7 1.0 + - - -
41D SER* 1.3 72.5 + - - +
43D ASN* 1.3 58.4 + - - +
45D GLU* 3.2 4.0 + - - +
46D ILE* 2.9 45.6 + - + +
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.8 20.3 - - + -
20C VAL 4.3 0.8 - - - +
21C VAL* 3.6 9.3 - - - +
22C ARG* 2.7 48.0 + - - +
41D SER* 3.2 8.6 + - - +
42D MSE 1.3 79.1 - - - +
44D SER* 1.3 60.9 + - - +
46D ILE* 3.3 3.9 + - - +
47D ILE* 2.9 46.3 + - - +
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 4.0 15.3 - - - -
41D SER* 3.2 30.7 + - - -
43D ASN* 1.3 83.0 + - - +
45D GLU* 1.3 57.9 + - - +
47D ILE* 3.4 3.6 + - - +
48D ALA* 2.8 34.2 + - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 4.4 11.4 - - + +
34D VAL* 3.2 9.8 - - + +
35D ALA* 3.6 25.8 - - + +
38D HIS* 3.4 15.0 - - - +
40D ARG* 2.8 41.1 + - - +
41D SER 2.9 14.4 + - - +
42D MSE 3.2 9.2 + - - +
44D SER* 1.3 76.5 - - - +
46D ILE* 1.3 62.1 + - - +
48D ALA* 3.3 2.3 + - - +
49D ARG* 2.4 68.1 + - - +
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.7 33.0 - - + -
21C VAL* 3.9 22.9 - - + -
46C ILE* 5.4 1.1 - - + -
50C LEU* 3.9 21.6 - - + +
21D VAL* 5.9 1.6 - - + -
23D LEU* 4.9 5.4 - - + -
31D ILE* 4.1 26.9 - - + -
42D MSE 2.9 29.0 + - + +
43D ASN* 3.7 4.3 - - - +
45D GLU* 1.3 74.8 - - - +
47D ILE* 1.3 59.3 - - - +
49D ARG* 3.2 4.3 + - - +
50D LEU* 2.8 48.5 + - + +
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.1 14.4 - - + -
22C ARG 2.8 30.7 - - - +
23C LEU* 4.8 0.2 - - - -
24C PRO* 3.6 25.1 - - + -
27C MSE 3.9 18.6 - - + -
43D ASN* 2.9 31.3 + - - +
44D SER* 3.9 3.8 - - - +
46D ILE* 1.3 73.0 - - - +
48D ALA* 1.3 58.1 + - - +
49D ARG 3.0 0.2 + - - -
50D LEU* 3.1 7.3 + - + +
51D GLU* 2.7 37.0 + - + +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.4 32.5 - - - +
44D SER 2.8 22.3 + - - +
45D GLU 3.6 4.3 - - - +
47D ILE* 1.3 74.6 - - - +
49D ARG* 1.3 60.6 + - + +
51D GLU* 3.5 7.4 - - - +
52D GLN* 3.3 23.2 + - - +
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG 6.1 0.2 - - - -
50C LEU* 4.0 18.2 - - + -
53C SER* 3.0 36.2 + - - +
54C LEU* 3.5 28.9 - - - +
57C GLU* 2.7 45.2 + - - +
31D ILE* 6.2 2.5 - - - -
34D VAL* 3.3 9.7 - - - +
38D HIS* 3.9 4.4 + - - -
40D ARG* 4.4 3.7 - - - +
45D GLU* 2.4 58.1 + - - +
46D ILE* 3.6 3.6 - - - +
48D ALA* 1.3 75.6 - - + +
50D LEU* 1.3 65.7 + - - +
51D GLU 3.1 1.7 + - - -
52D GLN* 3.4 6.0 + - - +
53D SER* 3.0 25.7 + - - -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 5.1 7.9 - - + -
23C LEU* 5.2 1.6 - - + -
27C MSE 3.9 16.2 - - + -
31C ILE* 4.2 23.1 - - + -
46C ILE* 4.0 48.7 - - + +
49C ARG* 4.3 18.6 - - + -
50C LEU* 4.5 6.9 - - + +
46D ILE* 2.8 41.6 + - + +
47D ILE* 3.7 5.6 - - + +
49D ARG* 1.3 73.1 - - - +
51D GLU* 1.3 60.4 + - - +
53D SER* 3.6 4.8 + - - -
54D LEU* 3.2 29.4 + - + +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PRO* 5.5 2.1 - - - +
27C MSE 3.3 26.1 - - + +
30C GLN* 5.2 6.0 + - - +
47D ILE* 2.7 23.9 + - + +
48D ALA* 3.5 9.2 - - - +
49D ARG 3.1 0.2 - - - -
50D LEU* 1.3 70.5 - - - +
52D GLN* 1.3 64.1 + - - +
54D LEU* 3.1 15.9 + - - +
55D LEU* 3.2 37.9 + - + +
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Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C SER* 5.6 1.4 + - - -
56C GLN* 5.3 4.0 - - - +
48D ALA 3.3 13.5 + - - +
49D ARG* 4.1 5.0 - - - +
51D GLU* 1.3 80.1 - - - +
53D SER* 1.3 57.0 + - - +
55D LEU* 4.2 13.8 - - + +
56D GLN* 2.9 54.4 + - - +
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 3.2 47.9 + - - +
52C GLN* 5.3 5.0 + - - -
53C SER* 5.7 3.6 - - - -
49D ARG 3.0 18.0 + - - -
50D LEU* 3.7 6.1 - - - -
52D GLN* 1.3 77.8 - - - +
54D LEU* 1.3 63.0 + - - +
56D GLN* 3.7 5.0 + - - +
57D GLU* 3.5 22.0 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MSE 4.7 11.4 - - + -
30C GLN* 3.6 43.5 - - + +
31C ILE* 4.1 21.1 - - + -
34C VAL* 3.8 32.1 - - + -
49C ARG* 3.9 20.0 - - - +
50D LEU* 3.2 19.7 + - + +
51D GLU* 3.1 8.3 + - - +
53D SER* 1.3 73.1 - - - +
55D LEU* 1.3 58.7 + - - +
56D GLN 3.1 4.8 + - - -
57D GLU* 3.3 11.3 + - - +
58D GLY* 2.8 25.5 + - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 3.2 38.7 + - + +
52D GLN* 4.2 15.5 - - + +
54D LEU* 1.3 77.3 - - - +
56D GLN* 1.3 69.1 + - - +
58D GLY* 3.7 6.6 - - - +
59D ALA* 3.1 27.0 + - - +
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLN* 4.9 8.1 - - - +
52D GLN* 2.9 44.5 + - - +
53D SER* 3.7 8.1 - - - +
54D LEU 3.1 0.4 - - - -
55D LEU* 1.3 88.3 + - - +
57D GLU* 1.3 59.7 + - - +
59D ALA* 3.5 19.9 + - - +
60D LEU* 4.2 4.9 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.6 19.7 - - - +
38C HIS* 3.7 13.2 + - - -
49C ARG* 2.9 32.8 + - - +
53D SER 3.6 3.8 - - - +
54D LEU* 3.4 12.5 - - - +
56D GLN* 1.3 75.2 - - - +
58D GLY* 1.3 73.3 + - - +
59D ALA 3.1 5.2 - - - -
60D LEU* 3.1 42.6 + - + +
61D GLN* 5.3 0.3 - - - +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LEU 2.8 17.7 + - - -
55D LEU* 3.8 6.7 - - - -
57D GLU* 1.3 82.8 + - - +
59D ALA* 1.3 56.1 + - - +
60D LEU 3.2 1.6 - - - -
61D GLN* 3.5 27.0 + - - +
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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