Contacts of the strand formed by residues 13 - 20 (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 LYS 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.6 4.3 - - - +
12A THR* 1.3 82.9 - - - +
14A ALA* 1.3 64.0 + - - +
34A VAL* 3.2 2.3 - - - -
35A LEU* 2.5 51.1 + - + +
96A GLU* 5.4 6.1 - - - +
99A ALA* 3.6 27.4 - - - +
100A TRP* 3.2 58.9 - - + +
103A ALA* 3.8 17.5 - - + -
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Residues in contact with ALA 14 (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* 4.4 7.2 - - + +
13A LYS* 1.3 82.1 - - - +
15A GLY* 1.3 59.6 + - - +
32A TRP* 3.8 22.2 - - + -
33A PHE 3.1 11.0 - - - +
34A VAL* 3.8 16.6 - - + -
100A TRP* 4.3 2.9 - - - -
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Residues in contact with GLY 15 (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* 1.3 74.8 - - - +
16A TRP* 1.3 64.5 + - - -
17A LEU* 3.4 3.3 + - - +
32A TRP* 3.3 16.6 - - - -
33A PHE* 3.0 30.1 + - - +
96A GLU* 6.0 1.8 - - - -
100A TRP* 3.8 14.8 - - - -
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Residues in contact with TRP 16 (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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15A GLY* 1.3 70.6 - - - -
17A LEU* 1.3 67.9 + - - +
18A PHE* 5.2 1.8 - - + -
30A LYS* 3.2 54.1 - - + -
31A ARG* 3.7 13.2 - - - -
32A TRP* 3.3 41.1 - + + -
44A LYS 4.2 5.4 - - - -
45A ASP* 3.6 29.6 - - + -
46A GLU* 3.6 26.5 - - + +
90A SER 4.9 0.3 - - - +
92A GLU* 4.5 22.3 + - - +
96A GLU* 4.5 11.0 + - - +
100A TRP* 5.7 0.3 + - - -
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Residues in contact with LEU 17 (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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15A GLY 3.4 1.7 + - - +
16A TRP* 1.3 80.7 - - - +
18A PHE* 1.3 64.7 + - - +
19A LYS 3.8 0.2 + - - -
31A ARG 2.9 31.1 + - - +
33A PHE* 3.2 32.4 - - + -
40A LEU* 6.0 0.2 - - + -
77A PHE* 3.9 21.8 - - + -
89A PHE* 4.4 11.7 - - + -
90A SER 3.7 20.4 - - - +
91A ALA* 3.9 16.8 - - + -
96A GLU* 5.5 0.7 - - - +
100A TRP* 3.4 52.3 - - + +
104A MET* 4.8 2.0 - - + -
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Residues in contact with PHE 18 (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 5.4 0.4 - - - -
17A LEU* 1.3 80.7 - - - +
19A LYS* 1.3 59.6 + - - +
28A TRP* 3.4 39.7 - - + -
29A ASN 3.2 9.0 - - - +
30A LYS* 3.2 59.7 - - + -
73A ARG* 5.8 8.5 - - - +
89A PHE* 3.2 10.5 - - - -
90A SER* 3.2 40.6 + - - +
92A GLU* 4.0 23.1 - - + -
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Residues in contact with LYS 19 (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 LEU 3.8 1.0 + - - -
18A PHE* 1.3 71.9 - - - +
20A GLN* 1.3 79.7 + - + +
21A ALA* 3.4 1.9 + - - -
22A SER* 6.0 5.2 - - - -
28A TRP* 4.1 2.0 - - - -
29A ASN* 3.0 25.1 + - - +
31A ARG* 3.8 24.7 - - + +
33A PHE* 3.9 23.8 - - + -
42A TYR* 4.9 16.9 + - - -
55A ILE* 4.7 3.4 - - + -
87A TYR* 4.5 17.5 - - + -
88A PHE 3.5 15.3 - - - +
89A PHE* 3.6 19.5 - - + -
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Residues in contact with GLN 20 (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 LYS* 1.3 89.7 + - + +
21A ALA* 1.3 66.3 + - - +
22A SER* 2.9 12.3 + - - -
26A LYS* 4.3 30.3 - - + +
27A GLN 3.7 10.8 - - - +
28A TRP* 3.3 43.9 - - + +
69A ASP 5.1 1.2 + - - -
70A ASN 5.0 0.4 + - - -
71A ILE* 3.6 15.2 - - - +
88A PHE* 3.5 37.9 + - + +
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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