Contacts of the helix formed by residues 54 - 62 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 1.3 81.8 - - - +
55H PHE* 1.3 67.0 + - - +
56H ASP* 3.0 5.6 + - + +
57H ILE* 3.3 13.5 + - + +
132H VAL* 2.7 25.4 + - + +
135H LYS* 3.7 19.1 - - + +
137H THR* 3.8 35.9 - - + +
208H GLU* 4.0 1.3 - - - +
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Residues in contact with PHE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H CYS* 4.7 1.6 - - - -
43H ILE* 3.7 22.9 - - + -
45H VAL* 4.6 11.7 - - + -
51H LEU* 4.0 22.4 - - + -
53H PHE* 3.4 4.7 + - - -
54H ALA* 1.3 71.0 - - - +
56H ASP* 1.3 59.6 + - - +
58H LEU* 2.8 34.2 + - + +
59H ALA 3.7 1.7 + - - -
62H PHE* 3.5 33.9 - + - -
201H ARG* 3.8 8.7 - - - +
208H GLU* 2.9 42.5 + - + +
209H THR 6.3 1.1 - - - -
211H VAL* 3.8 30.1 - - + -
213H GLN* 3.8 20.6 - - - -
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Residues in contact with ASP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA* 3.0 8.0 + - + +
55H PHE* 1.3 77.2 + - - +
57H ILE* 1.3 62.5 + - + +
59H ALA* 3.1 17.0 + - - +
60H THR 4.6 0.9 + - - -
137H THR* 2.3 36.6 + - - +
138H LEU 4.6 0.3 - - - -
139H GLY* 3.5 25.5 + - - -
140H TRP* 3.1 28.8 + - - +
162H LEU* 3.7 17.7 - - + -
201H ARG* 2.9 32.0 + - - +
208H GLU* 4.5 1.6 - - - +
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Residues in contact with ILE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H VAL* 3.8 17.3 - - + -
53H PHE* 3.6 27.4 - - + -
54H ALA* 3.5 14.4 - - + +
55H PHE 3.0 0.6 + - - -
56H ASP* 1.3 76.7 - - + +
58H LEU* 1.3 60.3 + - + +
60H THR* 4.8 6.3 + - - -
61H SER* 5.1 0.5 + - - -
96H TYR* 3.4 36.3 + - + +
102H LEU* 3.7 43.4 - - + +
126H PHE* 4.0 6.3 - - + -
132H VAL* 3.6 35.2 - - + -
140H TRP* 4.6 1.3 - - + -
162H LEU* 5.5 2.7 - - + -
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Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H MET* 4.6 5.8 - - - -
19H VAL* 4.6 0.9 - - + -
24H PHE* 3.6 35.0 - - + -
26H CYS* 4.8 1.1 - - - -
51H LEU* 4.1 12.6 - - + -
53H PHE* 3.7 28.7 - - + -
55H PHE* 2.8 21.0 + - + +
57H ILE* 1.3 87.3 - - + +
59H ALA* 1.3 63.4 + - - +
60H THR 3.3 2.5 - - - -
61H SER* 2.9 25.6 + - - -
62H PHE* 3.4 19.4 - - + -
102H LEU* 4.4 3.1 - - + -
121H ILE* 3.6 32.3 - - + -
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Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H PHE* 3.7 5.2 + - + +
56H ASP* 3.1 21.7 + - - +
58H LEU* 1.3 77.6 - - - +
60H THR* 1.3 58.8 + - + +
61H SER 3.1 4.0 + - - -
62H PHE* 3.4 12.5 + - - -
63H NRQ 3.6 5.7 - - - +
140H TRP* 4.0 11.0 - - + +
199H LEU* 3.8 15.3 - - + -
201H ARG* 6.2 0.7 - - - +
213H GLN* 2.9 45.0 + - - +
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Residues in contact with THR 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ASP 4.6 0.4 + - - -
57H ILE 4.8 6.2 + - - -
58H LEU 3.1 0.4 + - - -
59H ALA* 1.3 75.9 - - + +
61H SER* 1.3 57.9 + - - +
62H PHE 3.5 0.7 - - - -
63H NRQ 2.8 60.0 + - + -
92H ARG* 3.1 22.2 + - - -
94H THR* 4.8 4.3 + - - +
102H LEU* 6.0 1.6 - - - +
140H TRP* 5.0 11.0 - - + +
160H MET* 3.7 37.5 - - + -
174H LEU* 4.6 7.0 - - + +
199H LEU* 5.4 1.3 - - + -
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 4.1 0.7 - - - +
15H MET* 3.7 16.6 - - - -
57H ILE 5.1 0.2 + - - -
58H LEU 2.9 14.4 + - - -
60H THR* 1.3 80.5 + - - +
62H PHE* 1.3 61.9 + - - +
63H NRQ 3.6 4.0 - - - +
90H TRP* 3.8 17.7 - - - -
92H ARG* 4.8 1.2 + - - -
102H LEU* 4.6 7.3 - - - +
104H ALA* 3.9 16.1 - - - +
106H GLN* 4.7 1.0 + - - +
119H VAL* 3.6 25.7 - - - +
121H ILE* 3.5 18.0 - - - +
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Residues in contact with PHE 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.5 36.1 - - + -
15H MET* 3.6 22.9 - - + -
26H CYS* 4.3 7.0 - - + -
28H SER* 4.0 6.5 - - - -
41H MET* 3.6 26.3 - - + +
43H ILE* 3.5 48.2 - - + -
55H PHE* 3.5 24.7 - + - -
58H LEU* 3.4 26.5 - - + -
59H ALA* 3.4 12.4 + - - +
61H SER* 1.3 78.9 - - - +
63H NRQ 1.3 52.0 + - + +
66H SER* 3.6 15.0 + - - -
117H TYR* 3.8 11.8 - - - -
213H GLN* 4.2 5.2 - - - +
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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