Contacts of the strand formed by residues 129 - 139 (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 CYS 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A CYS 4.3 2.0 + - - -
6A VAL* 3.7 5.8 - - + +
9A PHE* 6.2 0.2 - - + -
118A TYR* 3.3 17.9 - - - +
120A CYS* 2.0 48.9 - - - -
122A LEU 4.0 0.2 - - - -
123A LEU* 4.3 0.2 - - - +
124A ASN* 3.6 8.9 + - - -
128A THR* 1.3 75.5 + - - +
130A ALA* 1.3 62.5 + - - +
131A ASP 3.0 31.6 - - - -
132A SER* 3.6 9.2 - - - +
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Residues in contact with ALA 130 (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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33A GLU* 5.3 3.8 - - - +
122A LEU* 2.4 45.8 + - + +
123A LEU 3.9 5.2 - - - +
124A ASN* 3.2 28.3 - - - +
128A THR 3.7 1.6 + - - -
129A CYS* 1.3 72.3 - - - +
131A ASP* 1.3 57.8 + - - +
132A SER 4.3 0.2 - - - -
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Residues in contact with ASP 131 (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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30A LYS* 5.7 0.2 + - - -
32A PRO* 3.7 5.2 - - - +
33A GLU* 3.0 47.4 + - - +
121A ARG* 2.6 54.0 + - - +
122A LEU* 2.8 25.2 + - + +
129A CYS* 3.0 7.6 - - - -
130A ALA* 1.3 81.8 - - + +
132A SER* 1.3 55.6 + - - +
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Residues in contact with SER 132 (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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30A LYS* 3.2 28.5 + - - +
32A PRO* 3.2 22.4 - - - +
118A TYR* 3.8 19.3 - - - -
119A SER 2.9 14.1 - - - -
121A ARG* 5.1 0.4 - - - -
129A CYS* 3.6 16.8 - - - +
130A ALA 4.3 0.2 - - - -
131A ASP* 1.3 74.7 + - - +
133A TYR* 1.3 65.5 + - - +
161A LEU* 4.0 8.6 - - - +
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Residues in contact with TYR 133 (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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30A LYS* 3.1 23.3 - - - +
32A PRO* 4.0 26.0 - - + -
36A PHE* 3.4 26.0 - + + -
88A MET* 3.7 11.8 - - - +
102A ASP* 2.4 44.5 + - - +
103A ASP 4.4 0.5 + - - -
104A HIS* 5.4 0.2 + - - -
117A GLN* 3.3 25.0 + - - -
118A TYR* 3.5 4.7 - - - -
119A SER* 2.7 49.9 + - - +
121A ARG* 3.4 18.8 - - + -
132A SER* 1.3 74.6 - - - +
134A SER* 1.3 61.4 + - - +
135A PHE* 3.9 13.0 - + - -
161A LEU* 5.3 0.2 - - - -
183A RTL 4.5 6.1 - - + +
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Residues in contact with SER 134 (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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29A LYS* 3.5 6.1 - - - +
30A LYS* 3.1 30.3 + - - +
116A VAL* 4.3 5.4 - - - +
117A GLN* 2.4 26.2 + - - -
118A TYR* 4.3 2.2 - - - -
133A TYR* 1.3 78.0 - - - +
135A PHE* 1.3 66.4 + - - +
159A LEU* 4.4 3.1 - - - +
161A LEU* 4.2 8.5 - - - -
165A TYR* 2.7 39.2 + - - -
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Residues in contact with PHE 135 (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* 4.2 14.6 - - + -
28A ALA 3.5 5.8 - - - -
29A LYS* 3.3 27.4 - - + -
36A PHE* 3.4 38.6 - + - -
37A LEU* 4.5 9.0 - - + -
41A ILE* 3.9 20.2 - - + -
116A VAL* 3.6 2.4 - - - -
117A GLN* 2.9 57.0 + - - +
133A TYR* 3.9 5.4 - + - -
134A SER* 1.3 76.4 + - - +
136A VAL* 1.3 63.4 + - - +
137A PHE* 3.6 23.5 + + + -
183A RTL 3.6 35.4 - - + -
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Residues in contact with VAL 136 (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* 3.7 3.8 - - - -
27A MET* 3.0 29.6 + - + -
28A ALA* 2.7 29.9 + - + +
114A TYR* 5.3 0.2 - - + -
115A ALA 3.6 9.2 - - - +
116A VAL* 4.7 7.0 - - + -
135A PHE* 1.3 75.1 - - - +
137A PHE* 1.3 66.1 + - - +
144A LEU* 4.6 11.2 - - + -
152A VAL* 3.8 33.2 - - + -
156A GLN* 3.8 23.8 - - + +
165A TYR* 4.0 15.5 - - + +
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Residues in contact with PHE 137 (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* 5.3 4.3 - + - -
24A TRP* 3.6 31.4 - + + -
25A TYR 3.2 18.4 - - - -
26A ALA* 3.7 21.8 - - + -
41A ILE* 4.8 3.1 - - + -
43A ALA* 4.4 19.1 - - + -
45A PHE* 5.1 8.7 - + - -
104A HIS* 5.4 1.1 - + - -
114A TYR* 3.1 10.9 - - - +
115A ALA* 2.6 48.5 + - + +
117A GLN* 4.3 15.5 - - + -
135A PHE* 3.6 38.8 + + + -
136A VAL* 1.3 76.6 - - - +
138A SER* 1.3 60.7 + - - +
144A LEU* 4.0 0.9 - - - +
183A RTL 4.3 20.0 - - + -
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Residues in contact with SER 138 (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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24A TRP* 3.7 4.5 - - - -
25A TYR* 2.6 39.3 + - - +
27A MET* 3.2 29.1 - - - +
113A THR* 3.3 5.5 + - - +
137A PHE* 1.3 73.5 - - - +
139A ARG* 1.3 65.5 + - - +
140A ASP* 2.9 23.1 + - - +
143A GLY 3.6 11.4 + - - -
144A LEU* 3.6 15.2 - - - +
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Residues in contact with ARG 139 (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 ARG 3.6 10.7 + - - -
20A PHE* 3.4 7.7 + - - +
21A SER 2.4 32.5 + - - -
22A GLY* 3.2 17.0 - - - -
23A THR* 3.4 20.5 + - - +
24A TRP* 3.2 35.2 - - - +
25A TYR* 3.6 15.3 - - - -
111A TYR 2.4 42.0 + - - -
112A ASP* 3.6 24.5 - - - +
113A THR* 2.8 11.2 + - - +
138A SER* 1.3 73.6 - - - +
140A ASP* 1.3 58.0 + - + +
141A PRO* 3.9 1.6 - - - +
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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