Contacts of the helix formed by residues 54 - 62 (chain B) in PDB entry 3BX9
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 1.3 73.7 - - - +
55B PHE* 1.3 65.1 + - - +
56B ASP* 3.2 4.7 + - + +
57B ILE* 3.3 23.5 + - + +
132B VAL* 2.9 25.5 + - + +
135B LYS* 3.7 14.5 - - - +
137B THR* 3.3 39.0 - - + +
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS* 4.7 0.7 - - - -
43B ILE* 3.8 20.4 - - + -
45B VAL* 4.4 9.2 - - + -
51B LEU* 3.8 20.0 - - + -
53B PHE* 3.3 7.0 + - - +
54B ALA* 1.3 71.0 - - - +
56B ASP* 1.3 54.2 + - - +
58B LEU* 2.8 43.5 + - + +
59B ALA* 3.7 2.4 + - + -
62B PHE* 3.5 35.0 - + - -
135B LYS* 5.7 0.4 - - - +
201B ARG* 3.9 20.8 - - - +
208B GLU* 4.0 24.2 - - + +
211B VAL* 3.8 40.6 - - + -
213B GLN* 4.0 14.1 - - - -
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA* 3.1 2.4 - - + -
55B PHE* 1.3 78.4 - - - +
57B ILE* 1.3 60.3 + - - +
58B LEU 3.1 0.9 - - - -
59B ALA* 3.2 15.0 + - - +
60B THR* 4.8 0.7 + - - +
137B THR* 2.6 28.8 + - - +
138B LEU 3.7 0.7 + - - -
139B GLY* 2.9 37.5 + - - -
140B TRP* 2.8 30.3 + - + +
162B LEU* 3.5 17.8 - - + +
201B ARG* 3.9 24.4 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.9 18.8 - - + -
53B PHE* 3.6 27.6 - - + -
54B ALA* 3.3 16.8 + - + +
55B PHE 3.0 1.8 + - - -
56B ASP* 1.3 75.2 - - - +
58B LEU* 1.3 60.6 + - + +
59B ALA 3.5 0.2 - - - -
60B THR* 4.8 6.5 + - - -
61B SER* 5.0 0.5 + - - -
96B TYR* 3.5 30.4 + - + +
102B LEU* 3.7 40.7 - - + +
126B PHE* 4.2 8.3 - - + -
132B VAL* 3.4 40.2 - - + -
140B TRP* 5.4 0.2 - - - -
162B LEU* 4.9 3.8 - - + -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 4.4 9.2 - - - -
19B VAL* 4.7 0.7 - - + -
24B PHE* 3.7 40.8 - - + -
26B CYS* 4.5 2.7 - - - -
51B LEU* 4.1 16.2 - - + -
53B PHE* 4.0 24.5 - - + -
55B PHE* 2.8 25.2 + - + +
57B ILE* 1.3 88.0 - - + +
59B ALA* 1.3 55.2 + - - -
60B THR 3.3 2.5 - - - -
61B SER* 2.9 27.1 + - - -
62B PHE* 3.3 22.8 - - + -
102B LEU* 4.3 2.5 - - + -
121B ILE* 4.1 22.4 - - + -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE* 3.7 4.7 + - + +
56B ASP* 3.2 21.9 + - - +
57B ILE 3.5 0.2 - - - -
58B LEU* 1.3 78.0 - - - +
60B THR* 1.3 61.4 + - - +
61B SER 3.1 1.4 + - - -
62B PHE* 3.5 3.8 + - - -
63B NRQ 3.5 9.2 - - - +
140B TRP* 3.9 11.2 - - + +
199B LEU* 3.7 19.9 - - + +
213B GLN* 3.0 41.9 + - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP 4.8 0.4 + - - +
57B ILE 4.8 6.3 + - - -
59B ALA* 1.3 76.6 - - + +
61B SER* 1.3 61.9 + - - +
62B PHE 3.4 0.4 - - - -
63B NRQ 2.9 36.9 + - + -
92B ARG* 2.8 40.8 + - - -
94B THR* 5.0 3.3 + - - +
102B LEU* 6.0 1.4 - - - +
140B TRP* 5.3 6.7 - - + +
160B MET* 3.9 30.1 - - + -
174B LEU* 4.5 4.3 - - + +
199B LEU* 3.9 16.4 - - + -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.2 0.3 - - - +
15B MET* 3.7 17.3 - - - -
57B ILE 5.0 0.3 + - - -
58B LEU* 2.9 16.4 + - - -
60B THR* 1.3 81.7 + - - +
62B PHE* 1.3 62.7 + - - +
63B NRQ 3.7 1.3 - - - +
90B TRP* 3.7 17.7 - - - -
92B ARG* 5.0 0.2 + - - -
102B LEU* 4.3 8.8 - - - +
104B ALA* 3.7 10.9 - - - +
106B GLN* 4.8 0.7 + - - +
119B VAL* 3.6 23.7 - - - +
121B ILE* 3.4 26.3 - - - +
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 36.9 - - + +
15B MET* 3.5 28.9 - - + -
26B CYS* 4.0 9.9 - - + -
28B SER* 4.4 0.2 - - - -
41B MET* 2.8 39.3 - - - +
43B ILE* 3.7 45.5 - - + -
55B PHE* 3.5 22.9 - + - -
58B LEU* 3.3 34.8 - - + -
59B ALA* 3.5 4.7 + - - -
60B THR 3.4 0.4 - - - -
61B SER* 1.3 81.2 - - - +
63B NRQ 1.3 48.4 + - - +
66B SER* 3.8 2.8 - - - -
117B TYR* 3.8 7.4 - - - -
213B GLN* 3.7 18.8 - - - +
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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