Contacts of the strand formed by residues 46 - 51 (chain S) in PDB entry 5A0Q
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 VAL 46 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40S ILE 4.2 3.8 - - - +
41S GLN* 5.3 2.7 - - + -
42S THR 5.0 0.2 - - - +
45S GLY* 1.3 73.8 - - - -
47S CYS* 1.3 65.8 + - - +
48S LEU* 3.9 28.9 - - + +
144S GLY* 4.0 13.9 - - - -
145S GLY 4.3 5.4 - - - +
146S VAL* 3.8 19.1 - - + -
151S PRO* 4.6 3.6 - - + -
152S GLN 3.8 28.0 - - - +
153S LEU* 4.6 7.0 - - + -
191S LEU* 5.2 2.4 - - - +
218S ALA 5.3 0.4 - - - +
219S THR* 3.4 4.2 - - - -
220S VAL* 3.0 45.5 + - + +
226S PHE* 6.3 0.4 - - + -
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Residues in contact with CYS 47 (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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40S ILE* 3.3 45.1 + - + +
42S THR* 5.4 1.3 - - + +
45S GLY 4.3 1.1 + - - +
46S VAL* 1.3 77.1 - - - +
48S LEU* 1.3 63.9 + - - +
49S ALA* 3.5 2.6 + - - +
191S LEU* 6.5 0.2 - - + -
194S ALA* 5.3 1.6 - - + -
195S ILE* 3.4 36.8 - - + +
198S SER* 3.5 22.4 - - - -
217S LEU* 3.8 15.0 - - - -
218S ALA 3.7 5.4 - - - -
219S THR* 4.1 4.7 - - + +
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Residues in contact with LEU 48 (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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38S ILE 4.0 2.2 - - - -
39S GLY* 4.2 6.5 - - - -
46S VAL* 3.9 10.7 - - + +
47S CYS* 1.3 72.8 - - - +
49S ALA* 1.3 58.6 + - - +
67S ILE* 3.4 33.9 - - + -
75S GLY* 3.8 21.3 - - - -
76S CYS 3.9 0.4 - - - +
77S ALA* 4.0 4.9 - - + +
142S LEU* 3.4 43.5 - - + +
144S GLY* 3.8 11.2 - - - +
153S LEU* 3.7 27.6 - - + -
216S GLU 5.4 0.2 - - - -
217S LEU* 3.8 2.3 - - - +
218S ALA 2.8 33.1 + - - +
220S VAL* 6.4 0.2 - - + -
226S PHE* 5.4 2.2 - - + -
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Residues in contact with ALA 49 (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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37S ALA* 3.4 5.0 - - - +
38S ILE* 2.9 35.4 + - + +
47S CYS 4.2 1.8 - - - +
48S LEU* 1.3 74.9 - - - +
50S VAL* 1.3 66.3 + - - +
77S ALA* 5.2 2.5 - - - +
198S SER* 3.8 22.7 - - - +
202S LEU* 3.9 11.9 - - + -
216S GLU 4.3 3.8 - - - -
217S LEU* 3.4 25.4 - - + -
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Residues in contact with VAL 50 (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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35S SER* 3.6 5.2 - - - +
36S THR 3.6 15.7 - - - +
37S ALA* 4.2 9.0 - - + +
48S LEU 5.7 0.2 - - - -
49S ALA* 1.3 78.8 - - - +
51S GLU* 1.4 65.2 + - - +
66S LYS* 3.2 50.5 - - + -
67S ILE* 4.5 13.0 - - + -
77S ALA* 5.1 6.3 - - + -
78S MET 4.5 7.4 - - - +
202S LEU* 4.3 5.0 - - - +
215S ILE* 3.5 7.3 - - - +
216S GLU* 3.2 39.6 + - + +
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Residues in contact with GLU 51 (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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35S SER* 2.9 18.7 + - - +
36S THR* 3.4 31.2 + - + +
50S VAL* 1.4 72.5 - - - +
52S LYS* 1.4 64.2 + - - +
53S ARG* 3.0 45.1 + - - -
54S ILE 4.1 4.9 - - - +
66S LYS* 3.0 11.6 - - - +
202S LEU* 4.0 9.2 - - + +
206S MET* 3.4 41.2 - - + +
210S LEU* 4.8 3.1 - - + -
214S ASN* 2.9 31.0 - - - +
215S ILE* 4.6 0.9 - - - +
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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