Contacts of the strand formed by residues 29 - 36 (chain A) in PDB entry 2J86
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 PHE 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.6 34.5 - + - -
23A ASP* 3.3 40.6 + - + +
27A GLN 3.6 0.4 - - - -
28A ARG* 1.3 84.7 - - + +
30A PHE* 1.3 72.4 + - - +
31A ILE* 4.1 11.4 - - + -
54A ARG* 3.9 21.3 - - + -
57A LEU* 3.5 34.8 - - + -
58A GLU* 3.8 34.8 - - + -
61A LEU* 6.3 2.5 - - + -
102A VAL* 4.8 1.1 - - + -
103A ILE 3.1 12.8 - - - +
104A LEU* 4.0 9.2 - - + -
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Residues in contact with PHE 30 (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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1A MET* 5.0 0.4 - - - -
3A VAL* 3.8 17.3 - - + -
21A TYR 3.7 4.9 - - - +
22A ILE* 3.2 38.1 - - + -
27A GLN* 3.5 38.1 - - + -
29A PHE* 1.3 82.1 - - - +
31A ILE* 1.3 64.5 + - - +
102A VAL* 3.2 11.4 - - - +
103A ILE* 3.1 36.3 + - + +
105A LEU* 3.9 22.4 - - + -
190A LEU* 3.9 17.9 - - + -
236A VAL* 4.4 7.0 - - + -
238A ILE* 3.3 36.8 - - + -
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Residues in contact with ILE 31 (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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20A PHE* 3.2 1.9 - - - +
21A TYR* 3.0 37.0 + - + +
29A PHE* 4.1 15.3 - - + -
30A PHE* 1.3 82.0 - - - +
32A VAL* 1.3 89.6 + - - +
33A ALA* 5.1 2.0 - - + -
49A ALA 5.6 0.2 - - - -
50A VAL* 3.8 36.3 - - + +
53A ILE* 3.7 29.2 - - + -
54A ARG* 3.8 24.0 - - + +
100A ALA* 5.2 1.8 - - + -
101A VAL 3.5 9.4 - - - +
102A VAL* 4.1 13.9 - - + -
190A LEU* 4.5 0.2 - - - -
236A VAL* 4.3 2.4 - - - +
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Residues in contact with VAL 32 (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 ALA 3.3 11.9 - - - +
20A PHE* 3.9 3.4 - - + -
31A ILE* 1.3 89.8 - - - +
33A ALA* 1.3 65.8 + - - +
34A ASP 5.2 0.2 - - - +
99A THR* 4.9 0.3 + - - -
100A ALA* 3.2 3.8 - - - +
101A VAL* 3.0 44.5 + - + +
120A SER* 5.3 1.1 - - - -
190A LEU* 3.7 28.9 - - + +
191A CYS 4.3 16.8 - - - +
192A SER* 4.5 6.5 - - - +
234A THR* 4.1 21.8 - - + +
236A VAL* 3.8 16.8 - - + -
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Residues in contact with ALA 33 (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 ASP* 3.4 4.4 - - - +
19A ALA 2.9 34.0 + - - -
31A ILE* 5.1 0.7 - - + -
32A VAL* 1.3 79.6 - - - +
34A ASP* 1.3 61.0 + - - +
35A GLY 3.6 1.3 + - - -
46A SER* 3.6 11.3 - - - +
49A ALA* 4.4 6.7 - - + -
50A VAL* 4.1 19.5 - - + -
98A THR* 3.3 9.6 - - - +
99A THR 2.9 19.5 - - - +
100A ALA* 4.4 2.7 - - + -
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Residues in contact with ASP 34 (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 ASP* 3.0 22.5 - - - +
33A ALA* 1.3 70.1 - - - +
35A GLY* 1.3 60.2 + - - +
36A MET* 5.0 2.6 - - - +
98A THR* 3.2 4.2 - - - -
99A THR* 2.7 47.8 + - + +
119A ASP* 5.1 1.1 - - - +
120A SER* 3.7 10.8 + - - +
192A SER* 3.7 7.6 - - - -
193A ASP* 2.4 15.4 - - - +
231A ASP* 3.1 2.3 - - - +
1242A MG 2.1 24.6 - - - -
1243A MG 2.4 26.0 - - - -
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Residues in contact with GLY 35 (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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17A GLN* 2.8 35.7 + - - +
33A ALA 3.6 1.6 + - - -
34A ASP* 1.3 74.4 + - - +
36A MET* 1.3 57.6 + - - -
42A GLY 3.7 9.6 - - - -
46A SER* 4.0 0.9 - - - -
97A GLY 3.4 10.1 - - - -
98A THR* 3.8 6.5 + - - -
1243A MG 2.4 31.1 - - - -
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Residues in contact with MET 36 (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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17A GLN* 3.5 7.2 - - - -
34A ASP* 5.0 3.1 - - - +
35A GLY* 1.3 74.1 - - - +
37A GLY* 1.3 59.6 + - - +
42A GLY* 3.3 14.1 + - - -
95A ASP 4.6 6.7 - - - +
96A MET* 3.4 0.7 - - - -
97A GLY* 2.9 45.0 + - - +
98A THR* 3.6 5.4 - - - +
163A LEU* 3.6 25.8 - - + -
166A CYS* 3.5 33.2 - - + -
1243A MG 4.7 3.1 - - - -
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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