Contacts of the helix formed by residues 44 - 56 (chain D) in PDB entry 3HR4
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 THR 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536C ARG* 4.6 0.7 - - - +
563C CYS 3.4 18.4 - - - +
564C ALA* 4.6 4.0 - - - -
686C VAL* 4.7 5.8 - - + -
687C ARG* 4.1 9.9 + - + +
688C GLY* 6.0 0.2 - - - -
692C ILE* 3.3 35.7 - - + +
43D PRO* 1.3 75.4 - - - +
45D GLU* 1.3 64.3 + - - +
46D ALA* 3.4 9.2 + - - +
47D GLU* 2.7 42.7 + - - +
48D LEU* 2.9 26.1 + - - +
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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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691C HIS* 4.5 15.9 - - + +
692C ILE* 5.4 1.9 - - - -
693C GLN* 3.8 23.7 + - - +
29D THR* 5.8 0.7 - - - -
37D ARG* 5.0 5.4 + - - -
43D PRO 4.1 5.0 - - - +
44D THR* 1.3 79.4 - - - +
46D ALA* 1.3 57.1 + - - +
48D LEU* 3.7 18.5 - - + +
49D GLN* 3.0 29.8 + - - +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C ARG* 3.3 48.5 + - + +
688C GLY* 5.8 0.7 - - - -
44D THR* 3.1 9.1 + - - +
45D GLU* 1.3 79.1 - - - +
47D GLU* 1.3 58.2 - - - +
49D GLN* 3.6 7.1 + - - +
50D ASP* 3.1 30.4 + - - +
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Residues in contact with GLU 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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532C THR* 4.2 22.3 + - - +
536C ARG* 2.7 47.1 + - - +
564C ALA 4.7 0.3 - - - +
687C ARG* 5.3 9.2 - - - +
43D PRO* 3.5 8.8 - - + +
44D THR* 2.7 46.3 + - - +
46D ALA* 1.3 76.3 - - + +
48D LEU* 1.3 62.5 + - - +
49D GLN 3.2 0.4 - - - -
50D ASP* 3.2 11.9 + - - +
51D MET* 2.8 36.1 + - - +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 3.5 28.9 - - - +
32D LEU* 3.6 28.6 - - + +
33D GLY* 3.7 23.8 - - - +
36D MET* 4.3 0.7 - - - -
37D ARG* 4.7 6.5 - - - +
43D PRO* 4.1 11.9 - - + +
44D THR 2.9 12.0 + - - +
45D GLU* 3.7 29.2 - - + +
47D GLU* 1.3 77.2 - - - +
49D GLN* 1.3 57.0 + - - +
51D MET* 3.0 25.5 + - + +
52D ILE* 2.8 33.9 + - - +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 3.6 26.4 - - + +
45D GLU 3.0 16.8 + - - +
46D ALA* 3.6 8.7 - - - +
48D LEU* 1.3 77.0 - - - +
50D ASP* 1.3 63.8 + - - +
52D ILE* 3.2 4.0 + - - +
53D ASN* 3.0 60.5 + - - +
61D GLY* 4.8 10.3 + - - -
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Residues in contact with ASP 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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532C THR* 5.5 3.4 - - + -
687C ARG* 3.1 33.7 + - - -
46D ALA 3.1 18.3 + - - +
47D GLU* 3.5 15.1 - - + +
48D LEU 3.2 0.2 - - - -
49D GLN* 1.3 75.9 - - - +
51D MET* 1.3 63.5 + - + +
53D ASN* 3.1 14.0 + - - +
54D GLU* 3.1 31.7 + - + +
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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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528C LEU* 3.9 22.5 - - + +
529C MET* 4.3 2.2 - - - +
532C THR* 3.4 27.4 - - + -
32D LEU* 4.1 11.2 - - + -
36D MET* 3.5 26.5 - - - +
43D PRO* 3.4 35.2 - - + -
47D GLU 2.8 27.9 + - - +
48D LEU* 3.4 33.0 - - + +
50D ASP* 1.3 74.9 - - - +
52D ILE* 1.3 63.5 + - - +
54D GLU* 3.2 25.0 + - - +
55D VAL* 3.6 15.1 + - - +
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Residues in contact with ILE 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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27D ILE* 3.6 24.9 - - + +
28D THR* 4.0 1.8 - - - +
29D THR* 3.4 36.8 - - + +
32D LEU* 3.8 16.6 - - + -
48D LEU 2.8 14.9 + - - +
49D GLN* 3.5 10.5 - - - +
51D MET* 1.3 74.5 - - - +
53D ASN* 1.3 58.4 + - - +
55D VAL* 3.4 2.4 + - - +
56D ASP* 2.7 35.1 + - + +
61D GLY 3.4 28.7 - - - +
62D THR* 4.3 3.6 - - - -
63D ILE* 3.6 20.5 - - + +
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Residues in contact with ASN 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 GLN* 3.0 39.4 + - - +
50D ASP* 3.1 13.2 + - - +
52D ILE* 1.3 80.0 - - - +
54D GLU* 1.3 62.2 + - - +
55D VAL 3.0 2.6 + - - -
56D ASP* 3.8 21.6 + - - +
61D GLY* 5.8 1.7 - - - -
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Residues in contact with GLU 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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527C MET 5.4 0.5 - - - +
528C LEU* 4.1 11.6 - - + +
531C LYS* 3.3 51.2 + - - +
532C THR* 4.7 2.3 - - - +
50D ASP* 3.1 20.2 + - + +
51D MET* 3.2 29.9 + - - +
53D ASN* 1.3 76.6 - - - +
55D VAL* 1.3 63.5 + - + +
71D MET* 6.1 0.3 - - - +
74D ARG* 5.3 6.9 + - - -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C PHE* 4.8 2.7 - - + -
528C LEU* 3.8 14.4 - - + -
51D MET 3.8 9.9 - - - +
52D ILE 3.4 1.5 + - - +
54D GLU* 1.3 86.1 - - + +
56D ASP* 1.3 53.1 + - - +
57D ALA* 2.6 20.1 + - - +
63D ILE* 3.6 39.5 - - + -
67D GLU* 3.6 32.1 - - - +
68D PHE* 4.7 2.0 - - - -
71D MET* 3.6 34.5 - - + -
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ILE* 2.7 27.7 + - + +
53D ASN* 3.8 17.7 + - - +
55D VAL* 1.3 67.8 - - - +
57D ALA* 1.3 64.9 + - - +
58D ASP* 2.8 7.3 - - - +
59D GLY* 2.8 26.6 + - - -
60D ASN* 3.1 0.8 - - - +
61D GLY* 2.8 26.7 + - - -
62D THR 2.7 14.1 - - - +
63D ILE* 4.6 0.6 - - - +
67D GLU* 3.7 5.4 - - - -
202D CA 2.4 30.8 - - - -
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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