Contacts of the helix formed by residues 48 - 56 (chain D) in PDB entry 3Q37
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 HIS 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ILE* 3.4 27.5 - - + +
86C ASP* 5.0 1.6 + - - -
87C TYR* 4.3 9.5 - + - -
16D ASN 3.9 9.9 + - - -
17D GLY 3.2 34.2 + - - -
18D SER* 4.4 6.2 - - - -
19D GLN 4.5 0.8 + - - -
22D LEU* 3.4 22.4 - - + +
44D PRO* 3.9 13.2 - - + -
45D THR* 3.0 22.0 + - - +
47D LEU* 1.3 80.0 - - - +
49D ILE* 1.3 64.2 + - - +
50D PRO 3.4 1.3 - - - -
51D MET* 3.3 31.1 - - + +
52D THR* 2.9 29.2 + - - +
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Residues in contact with ILE 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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47C LEU* 3.7 22.9 - - + -
44D PRO* 4.0 22.9 - - + +
45D THR 3.1 15.3 + - - +
46D PHE* 3.2 11.4 + - + +
48D HIS* 1.3 76.5 - - - +
50D PRO* 1.3 66.3 - - + +
52D THR* 3.1 2.3 + - - -
53D LYS* 2.8 29.1 + - + +
63D ILE* 4.4 4.7 - - + -
64D ALA 4.1 4.0 - - - +
65D ALA* 4.0 33.7 - - + +
84D LEU* 4.2 6.7 - - + -
87D TYR* 5.1 4.3 - - + -
89D ILE* 3.7 30.1 - - + -
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Residues in contact with PRO 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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47C LEU* 3.4 26.2 - - + +
50C PRO* 3.6 23.8 - - + -
46D PHE 3.4 13.7 - - - +
47D LEU 3.7 6.1 - - - +
48D HIS 3.6 3.1 - - - -
49D ILE* 1.3 93.3 - - + +
51D MET* 1.3 55.2 + - - +
53D LYS* 3.4 3.4 + - + +
54D ALA* 2.9 29.5 + - - +
87D TYR* 3.8 33.2 - - + +
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Residues in contact with MET 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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87C TYR* 3.0 46.7 + - + +
19D GLN* 3.2 44.0 - - + +
22D LEU* 4.6 11.2 - - - -
23D SER 5.4 1.1 - - - -
26D ILE* 5.3 2.2 - - + -
48D HIS* 3.3 27.1 + - + +
50D PRO* 1.3 79.7 - - - +
52D THR* 1.3 68.9 + - - +
54D ALA* 3.4 6.7 + - - +
55D ARG* 3.1 54.8 + - - +
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Residues in contact with THR 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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13D TRP* 4.1 9.2 - - + -
22D LEU* 5.2 0.3 - - - +
26D ILE* 3.8 26.1 - - + +
42D VAL* 4.3 11.2 - - + -
44D PRO* 3.6 27.1 - - + +
48D HIS* 2.9 23.1 + - - +
49D ILE 3.6 3.4 - - - -
51D MET* 1.3 79.6 - - - +
53D LYS* 1.3 58.5 + - - +
56D LEU* 2.8 42.3 + - + +
63D ILE* 3.9 18.8 - - + -
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Residues in contact with LYS 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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49D ILE* 2.8 19.1 + - + +
50D PRO* 3.7 7.0 - - + +
52D THR* 1.3 76.8 - - - +
54D ALA* 1.3 62.0 + - - +
55D ARG 3.4 0.3 + - - -
56D LEU* 4.2 9.5 + - - +
63D ILE* 3.5 20.1 - - + +
87D TYR* 3.7 27.6 - - + +
88D GLY* 3.2 22.0 + - - -
89D ILE* 4.0 18.1 - - + +
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Residues in contact with ALA 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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50D PRO 2.9 18.7 + - - +
51D MET* 3.6 9.6 - - - +
52D THR 3.1 0.2 - - - -
53D LYS* 1.3 78.1 - - - +
55D ARG* 1.3 62.1 + - + +
56D LEU 5.3 0.2 - - - -
57D THR* 5.7 1.6 - - - +
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Residues in contact with ARG 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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19D GLN* 5.4 2.7 + - - +
23D SER* 3.8 29.5 + - - +
26D ILE* 3.8 26.7 - - + -
27D ASP* 5.6 4.2 + - - +
30D ASN* 3.0 20.6 + - - -
51D MET* 3.1 40.5 + - - +
52D THR 4.2 0.4 - - - +
54D ALA* 1.3 84.9 - - + +
56D LEU* 1.3 62.8 + - - +
57D THR* 3.4 9.1 + - - +
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Residues in contact with LEU 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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26D ILE* 3.8 13.6 - - + +
29D PHE* 4.1 25.8 - - + -
30D ASN* 3.6 16.2 - - - +
42D VAL* 3.9 14.6 - - + -
52D THR* 2.8 25.3 + - + +
53D LYS 4.2 7.9 + - - +
54D ALA 3.9 0.2 - - - -
55D ARG* 1.3 71.8 - - - +
57D THR* 1.3 63.3 + - - +
58D ASN* 4.3 7.4 - - + +
61D PHE* 3.7 34.1 - - + +
63D ILE* 3.8 28.9 - - + -
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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