Contacts of the helix formed by residues 50 - 61 (chain D) in PDB entry 4B8Z
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 ASP 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D ASP* 3.0 16.4 + - - +
49D THR* 1.4 77.6 + - - +
51D THR* 1.3 61.1 + - - +
52D ALA* 3.2 14.8 + - - +
53D GLN* 2.9 53.1 + - + +
54D THR* 2.7 32.4 + - - -
96D ASN* 3.7 1.1 - - - -
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Residues in contact with THR 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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49D THR 4.5 1.7 + - - -
50D ASP* 1.3 72.0 + - - +
52D ALA* 1.4 58.4 + - - +
54D THR* 3.6 1.9 + - - -
55D ARG* 3.1 30.4 + - + +
92D HIS* 6.1 0.9 - - - -
96D ASN* 3.1 31.2 + - + +
100D SER* 5.0 1.2 + - - -
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Residues in contact with ALA 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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50D ASP* 3.2 10.3 + - - +
51D THR* 1.4 75.5 - - - +
53D GLN* 1.4 63.3 + - + +
55D ARG* 3.6 6.3 + - - +
56D ALA* 3.1 24.3 + - - +
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Residues in contact with GLN 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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43D SER 4.9 0.7 - - - +
46D ALA* 3.6 19.1 - - + +
47D ASP* 2.8 51.6 + - - +
50D ASP* 2.9 37.4 + - - +
51D THR 3.4 0.2 - - - -
52D ALA* 1.4 72.0 - - + +
54D THR* 1.4 57.9 + - - +
56D ALA* 3.6 7.2 + - - +
57D LEU* 3.2 20.6 + - - +
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Residues in contact with THR 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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47D ASP 4.6 0.2 + - - -
48D LEU* 3.4 44.8 + - + -
50D ASP 2.7 22.6 + - - -
51D THR 3.9 4.0 - - - -
53D GLN* 1.4 74.5 - - - +
55D ARG* 1.4 64.3 + - - +
57D LEU* 3.2 4.6 + - - +
58D PHE* 3.0 41.5 + - + -
96D ASN* 3.4 36.7 - - + +
97D VAL 4.0 1.1 - - - +
100D SER* 3.7 4.3 - - - +
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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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51D THR* 3.1 20.3 + - + +
52D ALA* 3.8 7.0 - - - +
54D THR* 1.4 75.0 - - - +
56D ALA* 1.4 57.0 + - - +
58D PHE* 3.5 2.3 + - - +
59D GLU* 3.0 30.8 + - - +
100D SER* 3.9 14.7 + - - +
103D GLU* 4.8 9.9 - - - +
104D VAL* 5.4 1.2 - - - +
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Residues in contact with ALA 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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52D ALA 3.1 17.8 + - - +
53D GLN* 3.6 8.3 - - - +
55D ARG* 1.4 73.9 - - - +
57D LEU* 1.4 58.3 + - - +
59D GLU* 3.8 5.9 - - - +
60D LYS* 3.0 31.0 + - - +
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Residues in contact with LEU 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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11D LEU* 5.4 7.4 - - + +
45D ASP* 5.3 3.4 - - + +
46D ALA* 4.0 17.7 - - + -
48D LEU* 5.6 2.2 - - + -
53D GLN 3.2 13.9 + - - +
54D THR* 3.2 10.3 + - - +
56D ALA* 1.4 76.2 - - - +
58D PHE* 1.3 63.0 + - + +
60D LYS* 4.0 3.4 - - - +
61D VAL* 2.9 34.8 + - - +
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Residues in contact with PHE 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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11D LEU* 3.5 29.6 - - + -
13D THR* 4.7 3.1 - - + -
48D LEU* 5.2 2.7 - - + -
54D THR* 3.0 42.4 + - + +
55D ARG* 3.9 3.8 - - - +
57D LEU* 1.3 78.2 - - + +
59D GLU* 1.3 59.2 + - - +
61D VAL 2.9 18.9 - - - +
62D GLN* 3.6 1.0 - - - +
63D PRO* 3.9 14.5 - - + +
66D VAL* 3.9 12.6 - - + -
97D VAL* 3.6 33.7 - - + -
100D SER* 3.6 15.9 - - - -
101D ALA* 3.7 36.1 - - + -
104D VAL* 3.4 31.9 - - + +
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Residues in contact with GLU 59 (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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55D ARG 3.0 18.3 + - - +
56D ALA* 3.8 7.0 - - - +
57D LEU 3.3 0.2 - - - -
58D PHE* 1.3 76.9 - - - +
60D LYS* 1.4 63.7 + - - +
62D GLN* 4.3 9.2 + - - +
104D VAL* 4.4 7.4 - - + +
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Residues in contact with LYS 60 (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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56D ALA 3.0 18.1 + - - +
57D LEU* 4.1 4.3 - - - +
59D GLU* 1.4 79.0 - - - +
61D VAL* 1.3 56.8 + - + +
62D GLN* 3.5 4.7 + - - +
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Residues in contact with VAL 61 (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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11D LEU* 4.3 22.3 - - + +
39D VAL* 4.7 16.8 - - + -
57D LEU 2.9 17.9 + - - +
58D PHE* 2.9 18.7 - - - +
60D LYS* 1.3 70.5 - - + +
62D GLN* 1.4 59.2 + - - +
63D PRO* 3.0 14.1 - - + +
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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