Contacts of the helix formed by residues 54 - 62 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C PHE* 1.3 88.1 - - - +
55C PHE* 1.3 63.9 + - - +
56C ASP* 4.2 5.6 - - + +
57C ILE* 3.3 13.1 - - + +
132C VAL* 2.7 24.3 + - + +
135C LYS* 4.0 12.3 - - - +
137C THR* 3.3 37.5 - - + +
208C GLU* 4.1 7.9 - - - +
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C CYS* 4.8 1.3 - - - -
43C ILE* 3.7 18.6 - - + -
45C VAL* 4.3 12.1 - - + -
51C LEU* 4.2 17.0 - - + -
53C PHE* 3.3 3.1 + - - -
54C ALA* 1.3 68.3 - - - +
56C ASP* 1.3 55.0 + - - +
57C ILE 3.0 2.9 - - - -
58C LEU* 2.7 39.3 + - + +
59C ALA* 3.6 2.9 + - + -
62C PHE* 3.3 41.7 - + - -
201C ARG* 3.4 21.3 - - - +
208C GLU* 3.3 41.0 + - + +
211C VAL* 3.9 30.3 - - + -
213C GLN* 4.2 9.2 - - - -
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Residues in contact with ASP 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 3.2 2.0 - - + -
55C PHE* 1.3 76.8 - - - +
57C ILE* 1.3 56.0 + - + +
58C LEU 3.1 0.2 - - - -
59C ALA* 3.1 18.9 + - - +
60C THR 4.7 0.5 + - - -
137C THR* 2.7 30.5 + - - +
139C GLY* 2.7 41.7 + - - -
140C TRP* 2.7 35.9 + - + +
162C LEU* 3.8 9.0 - - + -
201C ARG* 3.2 25.2 + - - +
208C GLU* 5.6 1.3 - - - +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.3 7.0 - - + -
53C PHE* 3.6 26.0 - - + -
54C ALA* 3.3 19.1 - - + +
55C PHE 2.9 2.0 + - - -
56C ASP* 1.3 75.5 - - - +
58C LEU* 1.3 61.3 + - + +
59C ALA 3.4 0.4 - - - -
60C THR* 5.0 5.4 + - - -
61C SER* 4.9 1.2 + - - -
96C TYR* 3.4 33.4 + - + +
102C LEU* 3.8 39.4 - - + +
126C PHE* 4.1 9.6 - - + -
132C VAL* 3.5 43.1 - - + -
140C TRP* 4.2 1.3 - - - -
162C LEU* 4.6 5.8 - - + -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C MET* 4.6 5.8 - - - -
19C VAL* 4.7 0.9 - - + -
24C PHE* 3.6 39.5 - - + -
26C CYS* 5.1 0.9 - - - -
51C LEU* 4.4 10.8 - - + -
53C PHE* 3.7 27.6 - - + -
55C PHE* 2.7 24.0 + - + +
57C ILE* 1.3 84.0 - - + +
59C ALA* 1.3 65.0 + - - +
60C THR 3.4 1.8 - - - -
61C SER* 3.0 24.3 + - - -
62C PHE* 3.3 21.4 - - + -
102C LEU* 4.3 7.9 - - + -
121C ILE* 4.1 26.7 - - + -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C PHE* 3.6 4.7 + - + +
56C ASP* 3.1 24.3 + - - +
57C ILE 3.4 0.2 - - - -
58C LEU* 1.3 79.2 - - - +
60C THR* 1.3 56.7 + - - +
61C SER 3.1 4.3 + - - -
62C PHE* 3.4 4.4 + - - -
63C NRQ 3.3 11.8 - - - +
140C TRP* 3.9 11.9 - - + +
199C LEU* 3.7 17.2 - - + +
201C ARG* 6.1 0.2 - - - +
213C GLN* 3.3 40.6 + - - +
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ASP 4.7 0.4 + - - -
57C ILE 5.0 5.2 + - - -
58C LEU 3.4 0.2 - - - -
59C ALA* 1.3 74.1 - - + +
61C SER* 1.3 61.6 + - - +
63C NRQ 2.8 58.5 - - + -
92C ARG* 2.9 19.7 + - - -
94C THR* 5.0 3.1 + - - +
140C TRP* 5.2 9.9 - - + -
160C MET* 3.7 36.3 - - + -
174C LEU* 4.4 9.8 - - + +
199C LEU* 4.3 3.4 - - + -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.2 0.2 - - - +
15C MET* 3.8 6.1 - - - -
57C ILE 4.9 0.7 + - - -
58C LEU* 3.0 16.1 + - - -
60C THR* 1.3 82.0 + - - +
62C PHE* 1.3 64.3 + - - +
63C NRQ 3.4 9.4 - - - +
90C TRP* 3.6 21.2 - - - -
92C ARG* 4.9 1.0 + - - -
102C LEU* 4.5 7.4 - - - +
104C ALA* 4.0 9.2 - - - +
106C GLN* 4.8 0.2 - - - +
119C VAL* 3.8 16.1 - - - +
121C ILE* 3.4 31.8 - - - +
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Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.5 47.0 - - + +
15C MET* 3.7 23.3 - - + -
26C CYS* 4.1 10.1 - - + -
28C SER* 4.2 0.4 - - - -
41C MET* 3.1 30.4 - - + +
43C ILE* 3.4 40.2 - - + -
55C PHE* 3.3 27.4 - + - -
58C LEU* 3.3 31.4 - - + -
59C ALA 3.4 1.0 + - - -
61C SER* 1.3 79.2 - - - +
63C NRQ 1.3 49.6 + - - +
66C SER* 3.8 1.0 - - - -
117C TYR* 3.7 18.0 - - - -
213C GLN* 3.3 21.8 - - - +
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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