Contacts of the strand formed by residues 55 - 60 (chain S) in PDB entry 2DYS
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 55 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507N GLU* 3.9 2.8 - - - +
11Q TYR* 4.8 8.2 + - - -
12Q ALA* 3.5 22.7 - - + -
51S SER* 3.7 3.5 + - - -
53S THR* 3.4 18.9 + - - +
54S ASN* 1.3 94.7 - - - +
56S ARG* 1.3 63.8 + - - +
73S TRP* 3.5 37.1 - - + -
74S LEU 3.1 13.2 - - - +
75S HIS* 3.7 30.3 - - + +
91S LEU* 3.6 2.6 - - - +
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Residues in contact with ARG 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507N GLU* 3.7 26.1 - - + +
508N PRO* 2.9 28.7 + - - +
509N THR 3.2 14.8 + - - -
510N TYR* 3.6 29.5 - - - +
32S ASN* 2.9 33.6 + - - -
49S VAL* 3.9 8.5 - - + -
50S PRO* 3.0 36.6 + - - +
51S SER* 4.1 2.0 - - - +
55S LYS* 1.3 76.8 - - - +
57S ILE* 1.3 72.4 + - - +
58S VAL* 3.3 1.2 + - - +
73S TRP* 3.8 5.2 - - - -
74S LEU* 2.7 36.7 + - - +
91S LEU* 3.7 15.0 - - + -
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Residues in contact with ILE 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492N LEU* 4.2 1.6 - - + -
495N LEU* 3.9 33.2 - - + -
496N ASN* 4.2 11.2 - - - +
505N PHE* 4.0 22.9 - - + -
509N THR* 3.4 16.0 - - + +
510N TYR* 3.0 22.7 + - - +
56S ARG* 1.3 76.9 - - - +
58S VAL* 1.3 67.3 + - - +
71S TRP* 4.1 15.5 - - + -
72S PHE 3.5 7.0 - - - +
73S TRP* 3.6 44.1 - - + +
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Residues in contact with VAL 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510N TYR* 3.5 15.7 - - + +
49S VAL* 4.2 14.4 - - + -
56S ARG 3.9 0.9 - - - +
57S ILE* 1.3 76.1 - - - +
59S GLY* 1.3 71.4 + - - +
70S ILE 3.5 1.2 - - - +
71S TRP* 3.2 9.9 - - - -
72S PHE* 2.7 62.9 + - + +
74S LEU* 3.6 36.6 - - + -
89S TYR* 4.0 22.4 - - + -
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Residues in contact with GLY 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510N TYR* 2.7 22.9 + - - +
511N VAL* 3.5 19.2 - - - +
512N ASN* 4.2 3.5 + - - +
58S VAL* 1.3 77.8 - - - +
60S CYS* 1.3 61.3 + - - -
61S ILE 4.1 0.6 + - - -
69S VAL* 3.8 8.7 - - - -
70S ILE 3.3 4.9 - - - -
71S TRP* 3.5 22.9 - - - -
89S TYR* 4.6 1.6 + - - -
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Residues in contact with CYS 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514N LYS* 3.9 6.1 - - - +
59S GLY* 1.3 72.4 - - - -
61S ILE* 1.3 62.7 + - - +
62S CYS* 3.3 8.0 + - - -
68S THR 4.3 0.5 - - - +
69S VAL* 3.7 3.5 - - - +
70S ILE* 2.6 45.0 + - - +
72S PHE* 4.4 4.0 - - + -
82S CYS* 3.7 13.5 - - + -
85S CYS* 3.6 8.5 - - - -
87S THR* 3.9 2.0 - - - -
89S TYR* 3.1 29.6 - - + +
101S ZN 2.3 36.8 - - - -
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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