Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 2DK6
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 GLN 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 6.1 0.2 - - - +
78A LYS* 4.0 28.9 + - + +
79A GLN 4.3 4.5 - - - -
80A MET* 6.0 0.2 - - - +
85A GLY 3.8 3.3 + - - +
86A LYS* 1.3 71.5 - - - +
88A ARG* 1.3 71.9 + - - +
89A LEU* 3.6 25.6 - - + +
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Residues in contact with ARG 88 (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 TYR* 4.0 26.7 + - + -
25A LEU* 3.4 29.5 + - - +
26A ALA* 5.0 5.1 - - - +
27A GLU* 3.8 36.5 + - - +
70A TYR* 6.0 3.4 - - - -
78A LYS* 3.5 1.6 - - - +
79A GLN* 2.8 57.7 + - + +
81A ASN* 5.9 4.2 - - - +
86A LYS* 4.2 28.9 - - + +
87A GLN* 1.3 85.3 - - - +
89A LEU* 1.3 64.2 + - - +
90A ILE* 4.2 0.2 - - - +
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Residues in contact with LEU 89 (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 TYR* 3.7 0.7 - - - -
25A LEU* 2.8 41.0 + - + +
31A TRP* 2.8 21.4 - - + -
76A GLU 4.7 3.8 - - - +
77A MET* 3.3 20.9 - - + +
78A LYS* 3.6 15.0 - - + +
87A GLN* 3.6 30.5 - - + +
88A ARG* 1.3 76.3 - - - +
90A ILE* 1.3 58.7 + - - +
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Residues in contact with ILE 90 (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 TRP* 3.6 25.6 - - + -
23A PHE 3.5 13.5 - - - +
24A TYR* 3.9 14.8 - - + -
31A TRP* 3.3 13.7 - - - -
34A PHE* 4.5 8.5 - - + -
72A ILE* 4.1 15.9 - - + -
73A ASP 4.3 2.9 - - - +
74A PHE* 4.4 3.1 - - + -
77A MET* 3.3 34.3 + - + +
78A LYS* 3.3 23.1 - - - +
79A GLN* 3.9 21.5 - - + +
88A ARG 3.8 0.4 + - - +
89A LEU* 1.3 77.6 - - - +
91A LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 91 (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 TRP* 4.0 6.6 - - - -
23A PHE* 3.1 49.9 + - + +
31A TRP* 3.0 60.7 - - + +
77A MET* 4.9 8.1 - - - -
90A ILE* 1.3 83.4 - - - +
92A ARG* 1.3 62.0 + - - +
93A ALA* 4.1 12.2 + - + -
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Residues in contact with ARG 92 (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 TRP* 3.3 55.9 - - + +
21A GLY 3.8 10.3 - - - +
22A TRP* 3.4 41.5 - - + +
50A GLU* 3.8 13.2 + - - -
53A PHE* 3.8 33.2 - - + -
77A MET* 5.1 6.1 - - + +
91A LYS* 1.3 73.8 - - - +
93A ALA* 1.3 66.4 - - - +
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Residues in contact with ALA 93 (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 TRP* 4.4 4.9 - - - -
21A GLY* 2.6 37.2 + - - +
23A PHE* 3.6 14.4 - - + -
91A LYS* 4.1 12.9 + - + -
92A ARG* 1.3 77.7 - - - +
94A PRO* 1.3 79.4 - - + +
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Residues in contact with PRO 94 (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 THR* 4.5 16.2 - - + -
19A GLN 3.6 15.7 - - - +
20A TRP* 3.9 24.4 - - + -
21A GLY 4.0 1.1 - - - +
23A PHE* 5.0 3.9 - - - -
93A ALA* 1.3 96.4 - - + +
95A PHE* 1.3 66.3 + - - +
96A SER* 3.9 18.9 - - - +
97A SER* 5.2 8.7 - - - +
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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