Contacts of the helix formed by residues 54 - 62 (chain D) in PDB entry 3BXB
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 ALA 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D PHE* 1.3 75.9 - - - +
55D PHE* 1.3 65.1 + - - +
56D ASP* 3.2 7.2 + - + +
57D ILE* 3.4 22.0 + - + +
131D PRO 4.6 1.3 - - - +
132D VAL* 2.9 25.8 + - + +
135D LYS* 4.0 10.8 - - - +
137D THR* 3.4 37.0 - - + +
208D GLU* 4.0 6.3 - - - +
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Residues in contact with PHE 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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26D CYS* 5.0 0.4 - - - -
43D ILE* 3.9 20.2 - - + -
45D VAL* 4.3 11.9 - - + -
51D LEU* 4.5 10.1 - - + -
53D PHE* 3.4 2.9 + - - -
54D ALA* 1.3 71.6 - - - +
56D ASP* 1.3 53.5 + - - +
58D LEU* 2.7 43.9 + - + +
59D ALA 3.5 1.7 + - - -
62D PHE* 3.3 33.9 - + - -
201D ARG* 3.3 24.5 - - - +
208D GLU* 3.1 44.2 + - + +
211D VAL* 3.9 20.0 - - + -
213D GLN* 3.3 28.7 - - - -
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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
----------------------------------------------------------
54D ALA* 3.1 3.5 - - + -
55D PHE* 1.3 77.8 - - - +
57D ILE* 1.3 60.8 + - - +
59D ALA* 3.2 13.7 + - - +
60D THR 4.7 0.3 + - - -
137D THR* 2.6 28.5 + - - +
138D LEU* 3.6 0.7 + - - -
139D GLY* 2.8 38.8 + - - -
140D TRP* 2.8 33.0 + - + +
162D LEU* 3.5 18.3 - - + +
199D LEU* 6.1 0.3 - - - +
201D ARG* 3.4 23.1 + - - +
208D GLU* 5.2 2.1 - - - +
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Residues in contact with ILE 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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19D VAL* 4.1 10.3 - - + -
53D PHE* 3.8 21.5 - - + -
54D ALA* 3.4 17.3 - - + +
55D PHE 2.8 1.8 + - - -
56D ASP* 1.3 78.0 - - - +
58D LEU* 1.3 62.7 + - + +
59D ALA 3.3 0.2 - - - -
60D THR* 4.5 7.7 + - - -
61D SER* 5.0 0.2 + - - -
96D TYR* 3.4 31.7 + - + +
102D LEU* 3.7 40.2 - - + +
126D PHE* 3.9 17.9 - - + -
132D VAL* 3.6 37.9 - - + -
140D TRP* 4.5 0.9 - - - -
162D LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 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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15D MET* 4.4 4.5 - - + -
19D VAL* 4.7 0.7 - - + -
24D PHE* 3.8 33.2 - - + -
26D CYS* 4.9 2.0 - - - -
51D LEU* 3.8 17.9 - - + -
53D PHE* 3.8 28.0 - - + -
55D PHE* 2.7 28.7 + - + +
57D ILE* 1.3 82.0 - - + +
59D ALA* 1.3 54.9 + - - +
60D THR 3.2 2.7 - - - -
61D SER* 2.7 37.3 + - - -
62D PHE* 3.4 23.2 - - + -
102D LEU* 4.3 11.2 - - + -
121D ILE* 4.4 11.4 - - + -
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Residues in contact with ALA 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 PHE 3.5 2.2 + - - -
56D ASP* 3.2 24.2 + - - +
58D LEU* 1.3 77.6 - - - +
60D THR* 1.3 57.6 + - - +
61D SER 3.3 3.1 + - - -
62D PHE* 3.6 3.9 + - - +
63D NRQ 3.4 14.2 - - - +
140D TRP* 3.6 14.4 - - + +
199D LEU* 3.5 17.6 - - + +
213D GLN* 3.3 41.2 - - - +
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Residues in contact with THR 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 ASP 4.7 0.4 + - - -
57D ILE 4.5 8.0 + - - -
59D ALA* 1.3 77.6 - - + +
61D SER* 1.3 63.0 + - - +
62D PHE 3.4 0.9 - - - -
63D NRQ 2.9 56.2 + - + -
92D ARG* 2.9 25.4 + - - -
94D THR* 5.0 4.0 + - - +
102D LEU* 5.9 1.4 - - - +
140D TRP* 5.2 5.8 - - + +
160D MET* 3.8 37.2 - - + -
174D LEU* 4.5 7.4 - - + +
199D LEU* 5.2 0.7 - - + -
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Residues in contact with SER 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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13D LEU* 4.1 0.3 - - - +
15D MET* 3.8 7.0 - - - -
58D LEU* 2.7 19.8 + - - -
60D THR* 1.3 77.5 + - - +
62D PHE* 1.3 63.6 + - - +
63D NRQ 3.7 2.8 - - - +
90D TRP* 3.9 12.5 - - - -
92D ARG* 5.0 1.0 + - - -
102D LEU* 4.3 8.5 - - - +
104D ALA* 3.8 12.8 - - - +
106D GLN* 5.0 0.3 + - - +
119D VAL* 3.7 27.9 - - - +
121D ILE* 3.4 31.8 - - - +
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Residues in contact with PHE 62 (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 LEU* 3.5 40.8 - - + +
15D MET* 3.5 23.1 - - + -
26D CYS* 4.0 12.3 - - + -
28D SER* 4.4 1.8 - - - -
41D MET* 3.3 34.5 - - - +
43D ILE* 3.5 49.1 - - + -
55D PHE* 3.3 26.2 - + - -
58D LEU* 3.4 36.1 - - + -
59D ALA* 3.6 5.1 + - - +
60D THR 3.4 0.4 - - - -
61D SER* 1.3 80.8 - - - +
63D NRQ 1.3 58.1 + - + +
66D SER* 4.0 1.4 - - - -
117D TYR* 3.9 7.4 - - - -
213D GLN* 4.3 2.0 - - - +
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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