Contacts of the helix formed by residues 54 - 62 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 1.3 81.3 - - - +
55A PHE* 1.3 59.8 + - - +
56A ASP* 2.9 10.7 + - + +
57A ILE* 3.2 12.9 + - + +
131A PRO 4.4 1.6 - - - +
132A VAL* 2.9 26.8 + - + +
135A LYS* 3.9 12.5 - - - +
137A THR* 3.3 37.0 - - + +
208A GLU* 4.3 4.5 - - - +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 4.8 1.1 - - - -
43A ILE* 4.0 11.4 - - + -
45A VAL* 4.3 13.9 - - + -
51A LEU* 4.2 16.4 - - + -
53A PHE* 3.2 7.9 + - - -
54A ALA* 1.3 70.9 - - - +
56A ASP* 1.3 56.8 + - - +
57A ILE 3.1 0.2 - - - -
58A LEU* 2.9 34.4 + - + +
59A ALA* 3.6 2.2 + - + -
62A PHE* 3.5 38.4 - + - -
201A ARG* 3.5 16.4 - - - +
208A GLU* 3.2 47.5 + - + +
211A VAL* 3.8 34.1 - - + -
213A GLN* 3.9 13.7 - - - -
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 2.9 3.3 + - + +
55A PHE* 1.3 77.4 - - - +
57A ILE* 1.3 59.9 + - + +
58A LEU 3.1 0.6 + - - -
59A ALA* 3.5 10.4 + - - +
60A THR 5.0 0.7 + - - -
137A THR* 2.8 27.2 + - - +
138A LEU* 3.6 1.6 + - - -
139A GLY* 2.9 31.7 + - - -
140A TRP* 2.7 34.6 + - - +
162A LEU* 3.5 24.8 - - + +
201A ARG* 2.9 25.7 + - - +
208A GLU* 5.6 0.9 - - - -
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.8 22.2 - - + -
53A PHE* 3.6 28.3 - - + -
54A ALA* 3.6 11.4 - - + +
55A PHE 3.1 1.8 + - - -
56A ASP* 1.3 78.2 - - - +
58A LEU* 1.3 62.4 + - + +
60A THR* 4.9 5.8 + - - -
61A SER* 4.8 1.4 + - - -
96A TYR* 3.4 30.2 + - + +
102A LEU* 3.9 35.8 - - + +
126A PHE* 4.2 6.3 - - + -
132A VAL* 3.5 40.4 - - + -
140A TRP* 5.1 0.4 - - - -
162A LEU* 5.0 3.4 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A MET* 4.7 6.1 - - - -
19A VAL* 4.6 2.0 - - + -
24A PHE* 3.7 38.8 - - + -
26A CYS* 5.0 1.6 - - - -
51A LEU* 4.1 13.7 - - + -
53A PHE* 3.8 24.2 - - + -
55A PHE* 2.9 22.5 + - + +
57A ILE* 1.3 91.1 - - + +
59A ALA* 1.3 66.0 + - - +
60A THR 3.2 2.2 - - - -
61A SER* 2.7 21.6 + - - -
62A PHE* 3.3 23.4 - - + -
102A LEU* 4.7 1.1 - - + -
121A ILE* 4.2 24.2 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.6 5.1 + - + +
56A ASP* 3.5 21.4 + - - +
58A LEU* 1.3 75.5 - - - +
60A THR* 1.3 62.4 + - - +
61A SER 3.2 0.5 + - - -
62A PHE* 3.3 11.6 + - - +
63A NRQ 3.4 6.1 - - - +
140A TRP* 3.8 13.5 - - + +
199A LEU* 3.9 15.0 - - + -
201A ARG* 6.0 0.2 - - - +
213A GLN* 2.9 44.9 + - - +
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP 5.0 0.4 + - - -
57A ILE 4.9 5.8 + - - -
58A LEU 3.0 2.0 + - - -
59A ALA* 1.3 76.3 - - + +
61A SER* 1.3 61.5 + - - +
62A PHE 3.2 0.7 - - - -
63A NRQ 2.9 57.2 + - + -
92A ARG* 3.1 26.0 + - - -
94A THR* 5.0 2.6 + - - -
102A LEU* 6.2 0.2 - - - +
140A TRP* 5.1 7.2 - - + +
160A MET* 3.8 35.2 - - + -
174A LEU* 4.7 4.6 - - + +
199A LEU* 4.5 3.6 - - + -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A MET* 3.6 10.1 - - - -
57A ILE 4.8 0.3 + - - -
58A LEU 2.7 21.7 + - - -
60A THR* 1.3 75.9 + - - +
62A PHE* 1.3 57.7 + - - -
63A NRQ 4.0 2.3 - - - +
90A TRP* 3.6 21.5 - - - -
92A ARG* 5.0 0.5 + - - -
102A LEU* 4.1 9.0 - - - +
104A ALA* 3.9 10.6 - - - +
106A GLN* 4.9 0.5 + - - +
119A VAL* 3.6 22.5 - - - +
121A ILE* 3.1 34.5 - - - +
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.7 38.4 - - + +
15A MET* 3.5 29.8 - - + -
26A CYS* 4.1 9.2 - - + -
28A SER* 4.5 2.5 - - - -
41A MET* 3.7 23.1 - - - +
43A ILE* 3.4 49.6 - - + -
55A PHE* 3.5 22.0 - + - -
58A LEU* 3.3 34.3 - - + -
59A ALA* 3.5 13.0 - - - +
60A THR 3.2 0.6 - - - -
61A SER* 1.3 79.9 - - - +
63A NRQ 1.3 49.9 + - + +
66A SER* 4.0 0.3 - - - -
117A TYR* 3.8 14.4 - - - -
213A GLN* 3.9 8.7 - - - +
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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