Contacts of the strand formed by residues 47 - 54 (chain N) in PDB entry 2A3W
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 TYR 47 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41N SER* 4.1 16.7 + - - -
43N LEU* 3.7 37.0 + - + -
45N ARG* 3.3 24.5 - - - +
46N ALA* 1.3 75.9 - - - +
48N SER* 1.3 61.2 + - - +
49N LEU* 3.5 27.5 - - + +
64N TYR* 3.6 7.7 - - - -
65N LYS* 2.9 69.8 + - + +
148N GLN* 3.4 7.0 - - - +
149N SER 3.4 24.2 - - - +
150N PHE* 3.5 22.4 - + - -
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Residues in contact with SER 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N TYR* 1.3 74.6 - - - +
49N LEU* 1.3 60.5 + - - +
50N PHE 3.5 6.4 + - - -
51N SER* 3.8 3.5 - - - -
62N LEU* 3.3 20.5 - - - +
63N VAL 3.9 3.6 - - - -
64N TYR* 3.9 5.3 - - - -
134N GLY* 4.9 4.5 + - - -
135N GLN 3.7 11.5 + - - -
136N GLU* 3.6 37.2 - - - -
148N GLN 2.9 11.3 + - - -
150N PHE* 3.3 26.0 + - - +
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Residues in contact with LEU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N PHE* 3.6 33.6 - - + -
39N ALA* 4.3 9.0 - - + -
47N TYR* 3.5 25.4 + - + -
48N SER* 1.3 75.9 - - - +
50N PHE* 1.3 61.1 + - - +
63N VAL* 3.0 25.3 + - + +
65N LYS* 3.9 33.9 - - + +
71N TYR* 4.6 3.1 - - + -
94N ILE* 4.3 13.5 - - + -
132N VAL 5.2 0.7 - - - -
133N LEU* 3.7 20.1 - - - +
134N GLY 5.0 0.8 + - - -
150N PHE* 3.7 20.2 - - + -
154N ILE* 4.1 15.2 - - + +
157N LEU* 5.9 0.3 - - - +
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Residues in contact with PHE 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N LEU* 4.1 6.5 - - + -
35N LEU* 3.5 45.8 - - + -
37N PHE* 4.6 2.5 - - + -
48N SER* 3.5 1.7 + - - -
49N LEU* 1.3 81.8 - - + +
51N SER* 1.3 59.6 + - - +
52N TYR* 4.0 20.4 - + + -
61N LEU* 4.4 17.9 - - + -
62N LEU* 3.2 8.5 - - - +
63N VAL* 3.0 33.6 + - + -
131N ILE* 3.4 32.1 - - + -
132N VAL 4.2 2.9 - - - -
133N LEU* 3.8 15.7 - - + -
157N LEU* 4.0 9.6 - - + -
159N MET* 4.2 9.2 - - + -
183N LEU* 3.9 20.9 - - + -
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Residues in contact with SER 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N SER* 3.8 6.9 + - - -
50N PHE* 1.3 74.6 - - - +
52N TYR* 1.3 60.1 + - - +
53N ASN* 4.4 2.6 + - - -
62N LEU* 3.9 8.0 - - - +
131N ILE* 3.2 4.3 - - - +
132N VAL* 2.9 40.9 + - - -
135N GLN 3.6 23.3 - - - -
136N GLU* 4.2 4.3 + - - -
137N GLN* 3.0 39.5 + - - +
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Residues in contact with TYR 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N THR* 5.8 0.4 - - + -
26N LEU* 4.2 8.8 - - + +
30N LEU* 4.1 14.6 - - + +
50N PHE* 4.0 11.4 - + + -
51N SER* 1.3 73.7 + - - +
53N ASN* 1.3 68.6 + - - +
54N THR* 3.9 7.4 - - + -
59N ASN* 4.3 0.3 - - - -
60N GLU* 3.4 6.9 + - + +
61N LEU* 2.9 69.2 + - + +
62N LEU* 5.1 0.6 - - - +
125N VAL* 3.6 19.9 + - + +
126N GLU 2.7 28.5 + - - -
127N ALA* 4.3 0.2 - - - -
129N PRO* 3.4 33.6 - - + +
130N LYS 3.7 4.0 - - - -
131N ILE* 3.8 22.4 - - + -
159N MET* 4.7 5.4 - - + -
182N ILE* 6.1 1.1 - - + -
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Residues in contact with ASN 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N SER* 4.4 2.6 + - - -
52N TYR* 1.3 81.6 + - - +
54N THR* 1.3 64.5 + - - +
57N ARG 3.6 10.0 + - - +
58N ASP* 2.9 28.9 + - - +
59N ASN* 3.0 22.0 + - - +
60N GLU* 4.5 0.4 - - - -
129N PRO* 3.4 3.3 - - - +
130N LYS 2.9 32.8 + - - -
136N GLU* 5.1 0.3 - - - +
137N GLN* 3.4 34.5 + - - +
138N ASP 4.1 0.4 - - - -
139N SER* 3.1 26.3 + - - +
140N TYR* 3.7 4.2 - - - -
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Residues in contact with THR 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N TYR* 3.9 13.7 - - + -
53N ASN* 1.3 79.7 - - - +
55N GLN* 1.3 56.9 + - - +
56N GLY 3.1 1.2 + - - -
57N ARG* 2.8 51.4 + - - +
60N GLU* 3.9 7.1 - - + +
126N GLU* 3.5 34.5 - - + +
127N ALA 3.3 26.7 - - - +
128N GLN 4.4 0.7 - - - -
129N PRO* 4.0 5.2 - - + -
139N SER 5.7 0.3 - - - -
140N TYR* 3.4 14.4 + - - +
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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