Contacts of the helix formed by residues 52 - 64 (chain A) in PDB entry 1BRW
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 1.3 73.4 - - - +
53A GLU* 1.3 60.3 + - - +
55A THR* 3.4 3.1 + - - -
56A ALA* 3.1 23.6 + - - +
216A ARG 5.1 0.5 - - - +
219A ARG* 3.8 28.8 + - - +
220A VAL* 3.5 46.6 + - + +
223A ASP* 3.6 30.9 - - - +
227A ARG* 4.8 4.2 + - - +
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Residues in contact with GLU 53 (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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51A THR* 3.1 8.2 + - - +
52A GLU* 1.3 78.0 - - - +
54A GLU* 1.3 63.2 + - + +
56A ALA* 3.4 4.1 + - - +
57A ALA* 3.2 22.2 + - - +
227A ARG* 4.2 26.2 + - - +
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Residues in contact with GLU 54 (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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10A LYS* 3.1 24.6 + - - -
15A ALA* 3.8 10.4 - - + +
16A LEU* 2.7 49.3 + - - +
21A ILE* 3.5 18.3 - - + +
50A MET* 3.4 24.1 - - + +
51A THR* 3.1 41.5 + - - +
53A GLU* 1.3 76.9 - - + +
55A THR* 1.3 58.5 + - - +
57A ALA* 3.4 1.5 + - - -
58A LEU* 3.0 25.6 + - - +
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Residues in contact with THR 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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50A MET* 3.6 17.3 + - - +
51A THR 2.9 17.9 + - - -
52A GLU* 3.7 5.1 - - - -
53A GLU 3.3 0.2 - - - -
54A GLU* 1.3 77.3 - - - +
56A ALA* 1.3 56.8 + - - +
58A LEU* 3.4 6.3 + - - +
59A THR* 2.8 33.5 + - - -
177A ILE* 6.1 0.6 - - + +
178A PRO* 3.7 34.7 - - + +
181A ALA* 4.0 18.2 - - + -
182A SER* 4.4 2.9 - - - +
220A VAL* 4.0 14.1 - - + +
224A ILE* 4.1 8.1 - - + -
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Residues in contact with ALA 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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52A GLU 3.1 17.1 + - - +
53A GLU 3.6 6.1 - - - +
54A GLU 3.2 0.2 - - - -
55A THR* 1.3 76.7 - - - +
57A ALA* 1.3 57.0 + - - +
59A THR* 3.2 5.4 + - - -
60A MET* 3.0 37.2 + - + +
223A ASP* 5.1 0.2 - - - +
224A ILE* 4.2 16.5 - - + +
227A ARG* 3.8 38.1 - - - +
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Residues in contact with ALA 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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18A LYS* 3.9 34.8 - - + -
21A ILE* 4.0 17.7 - - + +
22A GLU* 5.1 2.9 - - - +
53A GLU 3.2 10.9 + - - +
54A GLU* 3.7 8.1 - - - +
56A ALA* 1.3 76.5 - - - +
58A LEU* 1.3 66.1 + - - +
60A MET* 3.5 6.1 + - - +
61A ALA* 3.0 25.6 + - - +
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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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21A ILE* 3.6 15.6 - - + +
24A ILE* 6.5 0.2 - - + -
25A VAL* 4.0 21.1 - - + -
38A MET* 6.0 3.6 - - + -
45A ILE* 5.4 2.2 - - + -
50A MET* 4.1 24.2 - - + -
54A GLU 3.0 17.2 + - - +
55A THR* 3.7 6.3 - - - +
56A ALA 3.3 0.2 - - - -
57A ALA* 1.3 76.2 - - - +
59A THR* 1.3 62.3 + - - +
61A ALA* 3.5 1.6 + - - +
62A MET* 3.2 32.0 + - + +
164A LEU* 5.4 7.4 - - + -
178A PRO 4.3 4.0 - - - +
179A LEU* 4.0 22.7 - - + -
182A SER* 3.5 24.7 - - - +
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Residues in contact with THR 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 THR 2.8 19.3 + - - -
56A ALA 3.4 8.7 - - - -
58A LEU* 1.3 75.7 - - - +
60A MET* 1.3 66.4 + - - +
62A MET* 3.2 8.3 + - - +
63A VAL* 3.1 25.8 + - + +
182A SER* 3.3 22.3 - - - +
185A MET* 4.0 3.6 - - + -
186A SER* 3.6 29.1 - - - +
189A ILE* 4.4 7.9 - - + -
224A ILE* 3.5 31.5 - - + +
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Residues in contact with MET 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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18A LYS* 6.2 3.8 - - - -
56A ALA* 3.0 23.6 + - + +
57A ALA* 4.0 6.7 - - - +
59A THR* 1.3 78.0 - - + +
61A ALA* 1.3 56.9 + - - +
63A VAL* 3.1 12.3 + - - +
64A GLN* 3.0 45.4 + - + +
189A ILE* 4.1 15.0 - - + -
224A ILE* 3.9 33.4 - - + +
227A ARG* 4.9 6.3 - - + -
228A VAL* 3.6 33.7 - - + -
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Residues in contact with ALA 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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21A ILE* 4.4 2.0 - - + +
22A GLU* 4.2 21.5 - - + -
25A VAL* 3.6 39.8 - - + +
57A ALA 3.0 18.6 + - - +
58A LEU 3.8 2.0 - - - +
60A MET* 1.3 76.9 - - - +
62A MET* 1.3 60.6 + - - +
64A GLN* 3.6 18.4 + - - +
65A SER* 3.5 14.4 + - - -
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Residues in contact with MET 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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25A VAL* 4.3 11.4 - - + -
58A LEU* 3.2 26.4 + - + +
59A THR* 3.2 7.2 + - - +
61A ALA* 1.3 75.8 - - - +
63A VAL* 1.3 63.8 + - - +
65A SER* 2.8 23.9 + - - -
158A THR* 3.3 14.9 - - + +
160A ALA* 4.0 16.6 - - + -
161A ASP* 4.1 29.8 - - - +
164A LEU* 4.7 17.7 - - + -
182A SER* 3.1 51.8 - - - +
183A SER* 4.3 0.9 - - - +
186A SER* 4.0 7.9 - - - +
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Residues in contact with VAL 63 (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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59A THR* 3.1 22.9 + - + +
60A MET* 3.1 16.4 + - - +
62A MET* 1.3 75.3 - - - +
64A GLN* 1.3 64.7 + - + +
66A GLY* 3.2 20.8 + - - +
67A GLU 4.9 2.4 - - - +
68A MET* 3.8 32.3 - - + +
158A THR* 3.9 8.8 - - - +
186A SER* 3.7 28.0 - - - +
189A ILE* 4.2 18.8 - - + -
190A ALA* 4.7 6.0 - - + +
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Residues in contact with GLN 64 (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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18A LYS* 5.6 1.0 - - - +
22A GLU* 2.8 34.5 + - - +
26A ARG* 5.3 4.0 + - - -
60A MET* 3.0 41.0 + - + +
61A ALA* 3.6 15.1 - - - +
62A MET 3.2 0.2 - - - -
63A VAL* 1.3 78.7 - - + +
65A SER* 1.3 59.2 + - - +
66A GLY 3.1 7.8 + - - +
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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