Contacts of the strand formed by residues 28 - 36 (chain A) in PDB entry 2D9Y
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 TRP 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.4 54.2 - - + -
19A LYS 4.5 1.1 - - - -
20A GLN* 3.3 46.5 - - + +
26A LYS* 4.1 10.6 + - - +
27A GLN* 1.3 83.2 + - - +
29A ASN* 1.3 64.7 + - - +
71A ILE* 3.9 16.4 - - + -
72A SER 6.1 0.8 - - - +
73A ARG* 4.2 32.4 - - + +
76A THR* 4.0 15.7 - - + -
88A PHE* 3.8 25.1 - - + -
90A SER* 3.9 17.7 - - - -
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Residues in contact with ASN 29 (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 PHE* 3.2 4.4 - - - -
19A LYS* 3.0 33.7 + - - +
21A ALA* 4.2 14.8 - - - +
27A GLN* 3.9 36.1 + - - +
28A TRP* 1.3 78.7 - - - +
30A LYS* 1.3 67.1 + - - +
31A ARG* 4.7 5.6 - - - +
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Residues in contact with LYS 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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16A TRP* 3.2 50.4 - - + -
17A LEU 3.8 4.7 - - - +
18A PHE* 3.2 51.6 - - + -
29A ASN* 1.3 76.3 - - - +
31A ARG* 1.3 75.6 + - - +
44A LYS 5.1 1.2 - - - +
92A GLU* 4.1 11.9 + - - -
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Residues in contact with ARG 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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16A TRP* 3.7 8.1 - - - -
17A LEU 2.9 20.6 + - - +
19A LYS* 3.8 23.8 - - + +
29A ASN* 4.7 7.2 - - - +
30A LYS* 1.3 85.5 + - - +
32A TRP* 1.3 58.4 + - - +
33A PHE* 3.0 35.1 - - + -
42A TYR* 3.6 31.2 + - + -
43A TYR 3.3 16.8 - - - +
44A LYS* 3.9 27.4 - - - +
52A LEU* 3.5 30.9 - - - +
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Residues in contact with TRP 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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14A ALA* 3.8 22.7 - - + -
15A GLY* 3.3 38.1 - - - -
16A TRP* 3.3 46.4 - + + -
31A ARG* 1.3 70.9 - - - +
33A PHE* 1.3 60.0 + - - +
34A VAL* 3.4 30.0 - - + +
42A TYR* 2.9 6.8 - - - +
43A TYR* 2.7 48.9 + + - +
45A ASP* 3.3 33.9 - - - +
46A GLU* 3.5 26.8 + - + +
48A GLU* 4.0 11.1 - - + +
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Residues in contact with PHE 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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14A ALA* 3.1 3.3 - - - +
15A GLY 3.0 37.2 + - - +
17A LEU* 3.2 42.6 - - + -
19A LYS* 3.9 28.7 - - + -
31A ARG* 3.0 36.1 - - + -
32A TRP* 1.3 73.6 - - - +
34A VAL* 1.3 65.6 + - - +
35A LEU 4.1 0.7 - - - -
40A LEU* 4.0 22.4 - - + -
41A PHE 3.4 7.0 - - - +
42A TYR* 3.6 20.2 - + + -
55A ILE* 4.0 13.0 - - + -
89A PHE* 3.8 22.0 - + - -
100A TRP* 4.1 11.7 - - + -
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Residues in contact with VAL 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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11A VAL* 3.8 35.7 - - + -
13A LYS 3.3 3.1 - - - -
14A ALA* 3.8 7.0 - - + -
32A TRP* 3.4 29.2 - - + +
33A PHE* 1.3 78.7 - - - +
35A LEU* 1.3 66.3 + - - +
36A VAL* 3.3 7.4 + - + +
40A LEU* 3.7 2.5 - - - -
41A PHE* 2.8 28.0 + - + +
43A TYR* 3.8 17.5 - - + +
48A GLU* 3.5 20.0 - - - +
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Residues in contact with LEU 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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11A VAL* 4.1 4.2 - - - +
12A THR* 3.3 42.9 + - + -
13A LYS* 2.5 23.0 + - + +
33A PHE 4.1 0.6 - - - -
34A VAL* 1.3 72.9 - - - +
36A VAL* 1.3 68.3 + - - +
39A CYS 3.2 20.4 - - - +
40A LEU* 3.6 11.3 - - + +
57A LEU* 3.7 20.2 - - + -
100A TRP* 3.8 15.2 - - + -
103A ALA* 3.4 46.0 - - + +
104A MET* 3.6 9.9 - - + +
107A ALA* 5.0 4.5 - - + -
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Residues in contact with VAL 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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9A ALA* 5.5 7.2 - - + +
10A PRO 5.2 7.4 - - - +
11A VAL* 5.8 3.6 - - + -
12A THR* 3.9 9.8 + - - +
34A VAL* 3.3 5.5 + - + +
35A LEU* 1.3 84.4 - - - +
37A ASP* 1.3 75.4 - - + +
38A ARG 3.1 3.3 + - - -
39A CYS* 2.7 53.4 + - + +
41A PHE* 3.7 27.4 - - + -
107A ALA* 4.9 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