Contacts of the strand formed by residues 39 - 48 (chain A) in PDB entry 1BRP
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 ASP 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU 4.0 0.4 - - - -
38A GLN* 1.3 77.2 - - - +
40A ASN* 1.3 88.2 + - - +
41A ILE* 3.2 8.1 + - - +
60A ARG* 3.0 63.1 + - - +
166A ARG* 5.8 1.1 + - - +
168A ILE* 3.7 9.4 - - + -
169A VAL* 3.7 28.7 - - + +
171A ASN* 5.0 2.8 + - - -
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Residues in contact with ASN 40 (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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39A ASP* 1.3 84.2 + - - +
41A ILE* 1.3 60.2 + - - +
42A VAL* 3.6 5.4 + - - +
58A LYS* 3.1 12.3 - - - +
59A GLY* 3.3 4.3 - - - -
60A ARG 4.3 6.1 - - - +
168A ILE* 3.4 0.6 - - - +
169A VAL* 2.4 25.7 + - - +
170A HIS* 3.3 16.5 + - - +
171A ASN* 2.6 45.5 + - - +
172A GLY 3.4 10.4 + - - -
173A TYR* 3.2 23.6 + - + +
174A CYS* 4.2 12.6 + - + +
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Residues in contact with ILE 41 (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 ALA* 3.0 42.2 + - + -
29A LYS* 4.0 9.4 - - - -
37A LEU* 3.6 50.7 - - + +
39A ASP* 3.5 20.4 - - - +
40A ASN* 1.3 76.6 - - - +
42A VAL* 1.3 67.3 + - - +
57A ALA* 5.6 0.4 - - + -
58A LYS 3.2 6.5 - - - +
59A GLY* 4.2 5.6 - - - -
135A PHE* 3.9 24.7 - - + -
137A PHE* 4.8 2.7 - - + -
168A ILE* 4.1 6.7 - - + +
170A HIS* 3.1 11.5 - - - -
183A RTL 4.6 8.5 - - + -
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Residues in contact with VAL 42 (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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23A THR* 3.6 17.9 - - + -
24A TRP 3.2 12.8 - - - +
25A TYR* 3.6 25.4 - - + -
40A ASN 4.4 4.7 - - - +
41A ILE* 1.3 80.3 - - - +
43A ALA* 1.3 73.1 + - - +
44A GLU* 5.9 1.1 - - + -
56A THR 4.0 0.2 - - - +
57A ALA* 3.2 3.6 - - - -
58A LYS* 3.0 44.0 + - + +
170A HIS* 4.3 8.5 - - - +
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Residues in contact with ALA 43 (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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22A GLY 4.5 0.2 - - - -
23A THR* 3.5 2.4 - - - -
24A TRP* 2.8 35.2 + - + +
41A ILE* 4.3 0.4 - - + -
42A VAL* 1.3 81.8 - - - +
44A GLU* 1.3 62.4 + - - +
45A PHE* 3.7 25.8 - - + -
56A THR 3.4 7.6 - - - +
57A ALA* 4.2 4.0 - - + +
137A PHE* 4.4 17.6 - - + -
183A RTL 4.5 14.1 - - + -
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Residues in contact with GLU 44 (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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22A GLY* 3.2 17.7 - - - -
23A THR* 2.9 22.6 + - + -
42A VAL* 5.9 1.1 - - + -
43A ALA* 1.3 74.8 - - - +
45A PHE* 1.3 70.8 + - - +
46A SER* 4.5 8.6 + - - +
55A ALA* 3.2 5.0 - - - -
56A THR* 2.8 45.4 + - + +
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.7 36.1 - + + +
21A SER* 3.6 17.1 - - - -
22A GLY* 2.8 29.7 + - - +
24A TRP* 3.8 19.1 - + - -
43A ALA* 3.7 25.6 - - + -
44A GLU* 1.3 78.8 - - - +
46A SER* 1.3 65.0 + - - +
53A MET* 4.0 16.8 - - + -
54A SER 3.5 13.0 - - - -
55A ALA* 4.2 1.3 - - + -
77A PHE* 3.6 23.1 - + - -
104A HIS* 4.1 13.5 - + - -
106A ILE* 5.7 0.2 - - + -
137A PHE* 5.1 8.3 - + - -
183A RTL 3.8 24.0 - - + -
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Residues in contact with SER 46 (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 SER* 4.6 8.7 - - - -
44A GLU* 4.5 11.6 + - - +
45A PHE* 1.3 76.9 + - - +
47A VAL* 1.3 59.3 + - - +
53A MET* 3.1 6.8 - - - +
54A SER* 2.5 51.9 + - - +
55A ALA* 5.4 0.4 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 4.2 16.6 - - + +
18A ALA* 4.1 32.5 - - + +
21A SER* 4.2 7.4 + - - +
46A SER* 1.3 77.3 - - - +
48A ASP* 1.3 65.0 + - - +
51A GLY* 3.5 13.0 - - - +
52A GLN 3.2 31.0 - - - +
53A MET* 3.7 6.7 - - + +
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Residues in contact with ASP 48 (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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47A VAL* 1.3 75.4 - - - +
49A GLU* 1.4 55.9 + - - +
50A THR* 2.4 46.7 + - - -
51A GLY* 2.7 30.8 + - - -
52A GLN* 3.0 35.8 + - - +
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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