Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 1BJW
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 GLU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR 3.7 1.2 + - - -
46A PRO* 1.3 73.0 - - - +
48A HIS* 1.3 57.6 + - - +
50A LYS* 3.3 18.8 + - + +
51A GLU* 2.8 23.9 + - - +
54A ARG* 3.1 36.4 + - - -
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 3.6 29.5 - - + +
47A GLU* 1.3 77.7 - - - +
49A VAL* 1.3 73.4 + - + +
51A GLU* 3.4 6.9 + - - +
52A ALA 3.0 17.7 + - - -
55A ARG* 4.9 0.5 + - - -
236A PHE* 5.9 0.4 - + - -
277A GLU* 3.4 27.4 - - - +
278A ALA* 4.2 3.1 - - - -
281A ASN* 3.9 19.8 + - - +
284A ALA* 3.6 30.9 + - + +
285A SER* 2.9 38.6 + - - -
288A PHE* 5.0 0.2 - - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 4.0 8.5 - - - +
46A PRO* 3.2 23.0 + - + +
48A HIS* 1.3 87.8 - - + +
50A LYS* 1.3 67.0 + - - +
52A ALA* 3.2 3.5 + - - +
53A ALA* 3.1 21.5 + - - +
236A PHE* 5.3 0.9 - - + -
238A MET* 3.8 31.4 - - + -
241A TRP* 4.5 4.3 - - + -
274A ALA* 3.6 23.6 - - + +
277A GLU* 4.3 6.7 - - - -
278A ALA* 3.8 26.0 - - + -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 2.7 32.3 + - - +
45A THR* 3.6 24.1 + - - +
46A PRO 3.3 9.8 + - - +
47A GLU* 3.3 32.3 + - - +
49A VAL* 1.3 77.3 - - - +
51A GLU* 1.3 64.2 + - - +
53A ALA* 3.3 5.1 + - - +
54A ARG* 3.1 38.5 + - - +
241A TRP* 4.5 9.0 - - + -
57B LEU* 2.9 42.3 + - + +
58B ALA* 4.7 4.4 + - - +
60B GLY* 4.3 0.8 - - - +
62B THR* 4.6 9.0 - - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 2.8 19.1 + - - +
48A HIS* 3.7 7.9 - - - +
49A VAL 3.2 0.2 - - - -
50A LYS* 1.3 77.9 - - - +
52A ALA* 1.3 55.2 + - - +
54A ARG* 3.3 32.1 + - - +
55A ARG* 3.0 55.0 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS 3.0 5.4 + - - +
49A VAL 3.2 6.9 + - - +
51A GLU* 1.3 75.1 - - - +
53A ALA* 1.3 61.9 + - - +
55A ARG* 3.4 24.1 + - - +
56A ALA* 3.2 21.7 + - - +
273A TRP* 4.2 6.9 - - - +
274A ALA* 4.2 10.1 - - - -
277A GLU* 3.3 39.7 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL 3.1 7.1 + - - +
50A LYS 3.5 9.4 - - - +
52A ALA* 1.3 74.6 - - - +
54A ARG* 1.3 64.9 + - - +
56A ALA* 3.3 5.0 + - - +
57A LEU* 3.1 26.4 + - - +
241A TRP* 3.7 35.2 - - + -
270A ILE* 3.9 19.5 - - + +
274A ALA* 4.1 6.0 - - + +
57B LEU* 4.4 9.4 - - + -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.1 39.0 + - - -
50A LYS* 3.1 27.3 + - - +
51A GLU* 3.3 37.9 + - - +
53A ALA* 1.3 75.9 - - - +
55A ARG* 1.3 63.0 + - - +
57A LEU* 3.2 12.1 + - - +
58A ALA* 3.0 23.6 + - - +
54B ARG* 4.9 23.9 + - + +
57B LEU* 4.0 24.8 - - + +
58B ALA* 4.7 11.7 - - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS 4.9 0.4 + - - -
51A GLU* 3.0 51.0 + - - +
52A ALA* 3.6 28.5 - - - +
53A ALA 3.2 0.4 - - - -
54A ARG* 1.3 71.8 - - - +
56A ALA* 1.3 59.2 + - - +
58A ALA* 3.2 5.9 + - - +
59A GLN* 2.9 50.1 + - - +
277A GLU* 3.5 25.7 + - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 3.2 11.6 + - - +
53A ALA* 3.3 9.8 + - - +
55A ARG* 1.3 78.4 - - - +
57A LEU* 1.3 60.2 + - - +
59A GLN* 3.3 10.3 + - - -
60A GLY 3.2 4.3 + - - -
61A LYS* 2.9 45.0 + - + +
270A ILE* 4.6 13.2 - - + -
273A TRP* 3.9 24.5 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 3.1 18.1 + - - +
54A ARG* 3.5 11.9 - - - +
55A ARG 3.2 0.2 - - - -
56A ALA* 1.3 78.1 - - - +
58A ALA* 1.3 56.7 + - - +
60A GLY* 3.3 5.2 + - - -
61A LYS 5.1 0.7 - - - +
62A THR* 4.6 8.0 - - + +
270A ILE* 4.6 15.5 - - + -
50B LYS* 2.7 54.9 + - + +
53B ALA* 4.1 19.5 - - + -
54B ARG* 4.3 29.6 - - + +
57B LEU* 5.0 7.0 - - + -
241B TRP* 3.6 35.0 - - + -
270B ILE* 6.3 0.2 - - + -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG 3.0 16.6 + - - +
55A ARG* 3.7 7.0 - - - +
57A LEU* 1.3 76.0 - - - +
59A GLN* 1.3 62.8 + - + +
60A GLY 3.3 0.4 + - - -
50B LYS* 4.8 3.8 + - - +
54B ARG* 4.4 12.3 - - - +
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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