Contacts of the helix formed by residues 54 - 62 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G PHE* 1.3 83.7 - - - +
55G PHE* 1.3 63.5 + - - +
56G ASP* 3.0 9.5 + - + +
57G ILE* 3.4 14.9 + - + +
132G VAL* 2.7 23.9 + - + +
135G LYS* 3.8 11.4 - - + +
137G THR* 3.4 35.7 - - + +
208G GLU* 4.0 7.6 - - - +
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Residues in contact with PHE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G CYS* 4.7 1.3 - - - -
43G ILE* 3.6 24.9 - - + -
45G VAL* 4.4 5.6 - - + -
51G LEU* 3.7 23.8 - - + -
53G PHE* 3.3 6.3 + - - -
54G ALA* 1.3 71.9 - - - +
56G ASP* 1.3 62.6 + - - +
57G ILE 3.1 0.4 - - - -
58G LEU* 3.0 34.7 + - + +
59G ALA* 3.6 3.5 + - - -
62G PHE* 3.5 27.6 - + - -
201G ARG* 3.8 12.8 - - - +
208G GLU* 3.3 42.2 + - + +
211G VAL* 3.6 31.9 - - + -
213G GLN* 3.8 15.7 - - - -
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Residues in contact with ASP 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ALA* 3.0 3.5 - - + -
55G PHE* 1.3 80.3 - - - +
57G ILE* 1.3 57.0 + - - +
59G ALA* 3.1 20.9 + - - +
60G THR 4.7 0.7 + - - -
137G THR* 2.6 28.7 + - - +
138G LEU 3.9 0.5 + - - -
139G GLY* 3.0 34.2 + - - -
140G TRP* 3.1 27.2 + - - +
162G LEU* 3.5 22.6 - - + +
201G ARG* 3.2 23.7 + - - +
208G GLU* 5.7 0.6 - - - +
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Residues in contact with ILE 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G VAL* 4.1 9.9 - - + -
53G PHE* 3.9 22.9 - - + -
54G ALA* 3.5 15.3 - - + +
55G PHE 3.1 1.4 + - - -
56G ASP* 1.3 76.8 - - - +
58G LEU* 1.3 63.3 + - + +
59G ALA 3.4 0.2 - - - -
60G THR* 4.5 8.3 + - - -
61G SER* 4.9 0.5 + - - -
96G TYR* 3.4 32.2 + - + +
102G LEU* 3.8 33.1 - - + +
126G PHE* 3.8 23.6 - - + -
132G VAL* 3.7 37.0 - - + -
140G TRP* 4.5 0.7 - - - -
162G LEU* 4.9 4.7 - - + -
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Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G MET* 4.7 5.4 - - - -
19G VAL* 4.6 0.4 - - + -
24G PHE* 3.7 34.5 - - + -
26G CYS* 5.0 1.1 - - - -
51G LEU* 4.0 6.3 - - + -
53G PHE* 3.6 35.0 - - + -
55G PHE* 3.0 33.7 + - + +
57G ILE* 1.3 84.9 - - + +
59G ALA* 1.3 65.1 + - - +
60G THR 3.3 2.9 - - - -
61G SER* 2.9 25.2 + - - -
62G PHE* 3.2 20.1 - - + -
102G LEU* 4.4 2.5 - - + -
121G ILE* 4.0 21.3 - - + -
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G PHE* 3.6 4.4 + - + +
56G ASP* 3.1 24.2 + - - +
57G ILE 3.4 0.2 - - - -
58G LEU* 1.3 79.1 - - - +
60G THR* 1.3 57.5 + - + +
61G SER 3.1 4.2 + - - -
62G PHE* 3.5 4.0 + - - -
63G NRQ 3.2 10.0 - - - +
140G TRP* 3.9 14.6 - - + +
199G LEU* 3.9 17.0 - - + -
213G GLN* 2.9 40.1 + - - +
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Residues in contact with THR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ASP 4.7 0.6 + - - -
57G ILE 4.5 9.0 + - - -
59G ALA* 1.3 78.6 - - + +
61G SER* 1.3 62.3 + - - +
62G PHE 3.5 0.7 - - - -
63G NRQ 2.9 61.3 + - + -
92G ARG* 2.9 32.5 + - - -
94G THR* 4.9 4.0 + - - -
102G LEU* 6.0 1.0 - - - +
140G TRP* 5.3 7.4 - - + +
160G MET* 3.8 24.9 - - + -
174G LEU* 4.3 7.5 - - + +
199G LEU* 4.9 2.0 - - + -
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Residues in contact with SER 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 4.3 0.3 - - - +
15G MET* 3.6 8.5 - - - -
57G ILE 4.9 0.2 + - - -
58G LEU* 2.9 16.2 + - - -
60G THR* 1.3 83.4 + - - +
62G PHE* 1.3 62.4 + - - +
63G NRQ 3.5 2.5 - - - +
90G TRP* 3.8 15.0 - - - -
92G ARG* 5.0 1.0 + - - -
102G LEU* 4.4 7.4 - - - +
104G ALA* 4.0 9.9 - - - +
106G GLN* 4.8 0.9 + - - +
119G VAL* 3.6 25.9 - - - +
121G ILE* 3.2 33.7 - - - +
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Residues in contact with PHE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 3.5 37.7 - - + -
15G MET* 3.7 22.2 - - + -
26G CYS* 4.0 11.0 - - + -
28G SER* 3.9 2.7 - - - -
41G MET* 4.0 17.0 - - - +
43G ILE* 3.7 44.9 - - + -
55G PHE* 3.5 22.0 - + - -
58G LEU* 3.2 32.5 - - + -
59G ALA* 4.0 4.5 - - - +
60G THR 3.5 0.2 - - - -
61G SER* 1.3 80.9 - - - +
63G NRQ 1.3 74.3 + - + +
66G SER* 3.8 7.8 - - - -
106G GLN* 5.3 0.3 + - - -
117G TYR* 4.0 11.4 - - - -
213G GLN* 4.1 10.5 - - - +
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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