Contacts of the helix formed by residues 44 - 56 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A CYS 3.3 26.0 - - - +
564A ALA* 4.5 4.9 - - + -
686A VAL* 5.5 1.8 - - + -
687A ARG* 4.5 6.9 + - - +
692A ILE* 3.4 29.6 - - + -
37B ARG* 4.6 1.1 - - - +
42B ASN 4.9 0.2 - - - +
43B PRO* 1.3 75.1 - - - +
45B GLU* 1.3 56.6 + - - +
46B ALA* 3.6 7.4 + - - +
47B GLU* 2.6 65.5 + - - +
48B LEU* 2.8 13.0 + - - +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A GLY* 6.2 4.0 - - - -
691A HIS* 6.0 5.8 - - + +
692A ILE* 5.6 0.4 - - - +
29B THR* 5.0 7.6 + - - +
30B LYS* 6.1 0.9 - - - -
37B ARG* 3.6 14.2 + - - +
43B PRO 4.0 0.4 + - - -
44B THR* 1.3 72.6 - - - +
46B ALA* 1.3 63.6 + - - +
48B LEU* 3.0 37.2 + - - +
49B GLN* 3.2 16.2 + - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A ARG* 3.5 51.0 + - + +
688A GLY* 5.7 1.3 - - - -
44B THR* 3.2 6.9 + - - +
45B GLU* 1.3 78.7 - - - +
47B GLU* 1.3 61.3 + - - +
49B GLN* 3.6 8.5 + - - +
50B ASP* 3.1 28.0 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A THR* 4.0 20.1 + - - +
536A ARG* 2.8 51.4 + - - +
564A ALA 4.1 4.3 - - - +
687A ARG* 3.7 21.1 + - - +
43B PRO* 3.3 7.1 - - + +
44B THR* 2.6 54.8 + - - +
46B ALA* 1.3 72.6 - - - +
48B LEU* 1.3 65.9 + - - +
50B ASP* 3.0 21.2 + - - +
51B MET* 3.0 19.7 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.6 24.9 - - - +
30B LYS* 5.6 0.2 - - - -
32B LEU* 3.8 11.9 - - + +
33B GLY* 3.6 35.0 - - - +
36B MET* 4.4 0.9 - - - -
37B ARG* 4.0 10.5 - - - +
43B PRO* 3.9 11.2 - - + -
44B THR 2.8 11.4 + - - +
45B GLU* 3.0 39.0 + - - +
47B GLU* 1.3 77.3 - - - +
49B GLN* 1.3 56.5 + - - +
51B MET* 3.3 25.6 + - + +
52B ILE* 3.0 31.4 + - - +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 3.0 40.5 + - + +
45B GLU 3.2 12.1 + - - +
46B ALA* 3.9 10.1 - - - +
47B GLU 3.3 0.2 - - - -
48B LEU* 1.3 76.4 - - - +
50B ASP* 1.3 57.4 + - - +
52B ILE* 3.7 2.7 - - - +
53B ASN* 2.7 61.3 + - - +
61B GLY 5.3 2.1 + - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A THR* 5.3 6.1 - - + -
535A SER* 5.7 0.7 + - - -
687A ARG* 3.1 28.4 + - - -
46B ALA 3.1 16.6 + - - +
47B GLU* 3.0 16.7 + - - +
49B GLN* 1.3 77.7 - - - +
51B MET* 1.3 53.5 + - + +
53B ASN* 3.0 11.8 + - - +
54B GLU* 2.8 49.0 + - + +
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Residues in contact with MET 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A LEU* 3.5 28.5 - - + -
532A THR* 3.5 24.0 - - + -
32B LEU* 3.7 10.8 - - + -
36B MET* 3.4 26.2 - - - +
43B PRO* 3.5 24.5 - - + -
47B GLU 3.0 8.3 + - - +
48B LEU* 3.3 47.8 + - + +
50B ASP* 1.3 76.0 - - - +
52B ILE* 1.3 62.4 + - - +
54B GLU* 3.1 21.7 + - - +
55B VAL* 3.3 19.3 - - - +
63B ILE* 5.0 0.4 - - - -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.9 11.0 - - + +
28B THR 3.7 9.9 - - - +
29B THR* 3.1 47.6 - - + +
32B LEU* 3.9 14.8 - - + -
48B LEU 3.0 16.0 + - - +
49B GLN* 3.7 7.2 - - - +
51B MET* 1.3 74.7 - - - +
53B ASN* 1.3 63.2 + - - +
55B VAL 3.5 0.2 + - - -
56B ASP* 2.9 32.9 + - + +
61B GLY 3.5 26.5 - - - +
62B THR* 4.2 9.9 - - - -
63B ILE* 4.0 19.6 - - + +
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN* 2.7 53.7 + - - +
50B ASP* 3.4 10.3 + - - +
52B ILE* 1.3 76.8 - - - +
54B GLU* 1.3 61.9 + - + +
56B ASP* 3.7 25.4 - - - +
61B GLY* 5.9 2.3 - - - -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A LEU* 4.5 10.3 - - + +
531A LYS* 2.9 49.8 + - - +
532A THR* 4.7 5.0 - - - +
50B ASP* 2.8 40.2 + - + +
51B MET* 3.1 18.9 + - - +
53B ASN* 1.3 74.3 - - + +
55B VAL* 1.3 65.8 + - + +
56B ASP 4.9 1.0 - - - -
57B ALA* 5.9 0.2 - - - -
71B MET* 5.8 2.2 - - + +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A PHE* 4.5 5.2 - - + -
528A LEU* 4.2 14.1 - - + -
51B MET 3.3 16.9 + - - +
54B GLU* 1.3 76.5 - - + +
56B ASP* 1.3 59.0 + - - +
57B ALA* 3.0 12.4 + - - +
63B ILE* 3.5 27.8 - - + -
67B GLU* 3.2 41.2 - - - +
68B PHE* 4.4 2.7 - - - +
70B THR* 5.9 0.9 - - - +
71B MET* 3.9 36.6 - - + -
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 2.9 24.3 + - + +
53B ASN* 3.7 20.8 - - - +
54B GLU 3.4 1.9 - - - -
55B VAL* 1.3 73.0 - - - +
57B ALA* 1.3 60.4 + - - +
58B ASP* 2.9 9.2 - - - +
59B GLY* 2.9 30.1 + - - -
60B ASN* 3.1 5.3 + - - +
61B GLY* 3.5 9.3 + - - -
62B THR 2.8 27.2 - - - +
63B ILE* 4.4 1.1 - - - +
67B GLU* 4.0 7.0 - - - -
202B CA 2.8 11.4 - - - -
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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