Contacts of the strand formed by residues 3 - 9 (chain C) in PDB entry 2Y05
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 MET 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 1.3 85.3 + - - +
4C THR* 1.3 60.4 + - - +
26C THR* 3.4 31.2 - - + -
27C SER* 3.4 16.4 - - - +
28C GLU* 4.2 12.3 - - + +
29C LEU* 5.0 2.7 - - - +
94C HIS* 3.4 27.4 + - - +
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Residues in contact with THR 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C MET* 1.3 75.4 - - - +
5C LYS* 1.3 64.3 + - - +
6C THR* 4.0 11.7 - - - +
25C LYS 3.8 0.5 - - - +
26C THR* 3.3 6.0 - - - +
27C SER* 3.0 55.6 + - - +
29C LEU* 4.1 18.8 - - + +
92C THR* 3.1 8.1 + - - +
93C THR* 3.3 4.2 + - - -
94C HIS* 2.9 42.7 + - - +
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Residues in contact with LYS 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR* 1.3 72.9 - - - +
6C THR* 1.3 61.9 + - - +
24C LEU* 4.2 19.0 - - + +
25C LYS 3.3 5.6 - - - +
26C THR* 4.1 20.9 - - + +
92C THR* 3.3 4.2 + - - -
93C THR* 2.9 41.6 + - + +
306C PHE* 3.4 29.0 - - + +
307C GLU* 4.2 18.6 + - - +
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Residues in contact with THR 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR* 4.0 11.3 - - - +
5C LYS* 1.3 73.4 - - - +
7C TRP* 1.3 65.7 + - - +
8C THR* 3.7 8.5 + - + +
23C GLU 3.6 1.6 - - - +
24C LEU* 3.5 3.9 - - - +
25C LYS* 2.8 42.0 + - - +
27C SER* 4.7 3.3 + - - -
62C THR* 3.3 42.2 - - + +
91C TRP 3.3 6.1 - - - +
92C THR* 3.0 18.4 + - - +
306C PHE* 4.2 0.9 - - - -
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Residues in contact with TRP 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C THR* 1.3 69.7 - - - +
8C THR* 1.3 60.3 + - - +
19C ASN 5.5 0.9 - - - -
22C PHE* 3.7 28.5 - - + -
23C GLU* 3.6 8.7 - - - -
24C LEU* 3.4 48.7 - - + +
62C THR* 3.6 7.4 - - - +
63C MET* 3.0 24.8 + - + +
91C TRP* 2.9 33.4 + + + +
306C PHE* 2.9 50.5 + + - -
307C GLU* 3.1 27.4 - - + -
309C MET* 4.0 8.1 - - + -
310C PRO* 3.4 23.6 - - + +
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Residues in contact with THR 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C THR* 4.3 15.3 - - + +
7C TRP* 1.3 78.4 - - - +
9C LEU* 1.3 61.7 + - - +
10C LYS* 5.2 0.2 - - - -
22C PHE* 3.5 10.4 - - - +
23C GLU* 2.7 54.1 + - - +
25C LYS* 4.3 24.1 + - + -
60C GLY* 3.5 24.1 - - - +
61C ASP 3.2 11.0 - - - +
62C THR* 4.1 8.3 - - - +
63C MET* 4.4 4.3 - - - -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C THR* 1.3 70.1 - - - +
10C LYS* 1.3 60.8 + - - +
11C LYS 3.4 24.0 - - - +
12C HIS* 3.6 35.4 - - + +
13C PHE* 3.4 36.3 - - + -
21C ASP 3.8 3.8 - - - +
22C PHE* 5.2 1.1 - - + -
54C ALA* 3.7 15.9 - - + +
57C LEU* 3.9 16.2 - - + +
58C LYS 4.8 4.9 - - - +
59C GLU* 3.4 4.3 - - - -
60C GLY* 2.7 31.9 + - - -
61C ASP 2.8 14.7 + - - +
63C MET* 4.1 15.9 - - - +
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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