Contacts of the strand formed by residues 70 - 75 (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 ILE 70 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265N LYS* 4.9 9.9 - - + -
489N THR* 3.5 17.7 - - + +
490N THR* 4.2 18.6 - - + -
58S VAL 3.5 1.6 - - - +
59S GLY* 3.3 2.1 - - - -
60S CYS* 2.6 40.1 + - + +
62S CYS* 3.7 14.4 - - - -
68S THR* 4.6 9.6 - - + +
69S VAL* 1.3 74.8 - - - +
71S TRP* 1.3 61.7 + - - +
72S PHE* 4.1 4.8 - - + -
82S CYS* 3.8 21.3 - - - -
83S PRO* 3.9 17.9 - - + -
84S SER* 3.6 29.6 - - - +
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Residues in contact with TRP 71 (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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86N MET 4.9 2.2 + - - -
87N ILE 5.6 0.4 - - - -
173N PRO* 4.7 2.5 - - + -
176N MET* 3.6 33.7 - - + -
182N PRO* 6.3 0.6 - - - +
488N THR* 4.2 3.3 + - - +
489N THR* 2.9 41.6 + - - +
490N THR* 4.6 3.6 - - - -
492N LEU* 3.8 49.1 - - + +
495N LEU* 3.6 22.2 - - + +
509N THR* 3.5 33.2 - - + -
511N VAL* 4.1 7.4 - - + -
57S ILE* 4.1 4.5 - - + -
58S VAL 3.2 9.4 - - - -
59S GLY* 3.5 23.1 - - - -
69S VAL* 3.3 44.9 + - + +
70S ILE* 1.3 72.7 - - - +
72S PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 72 (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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489N THR* 4.8 5.2 - - + -
495N LEU* 3.8 9.0 - - - +
57S ILE* 4.2 4.3 - - - -
58S VAL* 2.7 66.2 + - + +
60S CYS* 4.4 3.6 - - + -
70S ILE* 4.1 12.3 - - + -
71S TRP* 1.3 79.6 - - - +
73S TRP* 1.3 71.8 + - - +
74S LEU* 4.5 13.7 - - + -
80S GLN* 5.0 8.5 - - + -
81S ARG 4.8 5.8 - - - -
82S CYS* 3.9 16.4 - - + -
83S PRO* 3.7 31.4 - - + -
89S TYR* 3.6 28.9 - + - -
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Residues in contact with TRP 73 (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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495N LEU* 3.0 44.6 + - + +
496N ASN* 3.9 13.5 - - - -
11Q TYR* 4.1 13.9 - + - -
12Q ALA* 3.4 46.2 - - + +
55S LYS* 3.5 50.7 - - + -
56S ARG* 3.7 4.3 - - - -
57S ILE* 3.6 42.6 - - + +
72S PHE* 1.3 81.4 - - - +
74S LEU* 1.3 58.1 + - - +
75S HIS* 3.7 10.5 + - + +
80S GLN* 3.5 16.1 + - - -
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Residues in contact with LEU 74 (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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49S VAL* 3.5 36.3 - - + -
55S LYS* 3.1 4.0 - - - -
56S ARG 2.7 41.9 + - - +
58S VAL* 3.6 11.4 - - + -
72S PHE* 3.5 5.7 + - + -
73S TRP* 1.3 71.5 - - - +
75S HIS* 1.3 63.3 + - - +
78S GLU 5.4 0.2 - - - +
80S GLN* 3.4 30.7 - - + +
89S TYR* 3.4 28.0 - - + +
90S LYS* 3.6 4.9 - - - +
91S LEU* 3.4 32.8 - - + +
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Residues in contact with HIS 75 (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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12Q ALA* 3.0 28.2 + - + -
13Q LEU* 3.4 33.5 - - + +
14Q PRO* 5.0 5.8 - - + -
54S ASN* 3.6 6.4 + - - -
55S LYS* 3.7 31.8 - - + +
73S TRP* 4.0 12.4 - - + +
74S LEU* 1.3 78.9 - - - +
76S LYS* 1.3 70.4 + - - +
77S GLY* 3.4 2.8 + - - -
78S GLU 4.5 2.4 - - - +
80S GLN* 2.9 31.2 + - - +
91S LEU* 3.9 10.1 + - - +
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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