Contacts of the strand formed by residues 49 - 54 (chain N) 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 THR 49 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44N ARG 3.9 0.7 - - - -
45N VAL* 3.0 35.4 + - - +
46N ASN* 3.1 20.7 + - + +
48N SER* 1.3 87.1 - - - +
50N MET* 1.3 65.1 + - - +
84N SER* 5.0 3.8 - - - +
85N PRO* 4.2 28.3 - - + +
88N ILE* 5.2 4.2 - - - +
112N ILE* 5.3 4.0 - - - +
113N GLY 3.4 8.3 - - - -
114N GLY* 3.7 20.4 - - - -
115N TYR 4.6 1.8 - - - +
197N VAL* 4.0 0.9 - - - +
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Residues in contact with MET 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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20N VAL* 3.2 13.0 - - + +
22N ILE* 3.8 25.5 - - + +
42N ILE* 4.3 4.5 - - + -
43N MET 3.1 17.0 - - - +
44N ARG* 4.1 7.4 - - + -
45N VAL* 3.8 6.9 - - - +
48N SER 3.9 2.7 - - - +
49N THR* 1.3 80.4 + - - +
51N LEU* 1.4 65.6 + - - +
112N ILE* 3.4 5.8 - - - +
113N GLY 3.0 33.4 + - - +
190N ALA* 3.7 24.2 - - - -
191N THR 4.1 3.4 - - - +
192N VAL* 2.7 52.3 - - + +
197N VAL* 5.5 3.8 - - + -
198N GLU 5.0 2.2 - - - +
199N ILE* 6.1 0.2 - - - -
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Residues in contact with LEU 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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22N ILE* 5.5 0.7 - - - -
41N ARG 3.7 0.3 - - - +
42N ILE* 3.5 5.0 - - - -
43N MET* 2.8 48.3 + - + +
45N VAL* 3.4 25.1 - - + -
50N MET* 1.4 71.8 - - - +
52N GLY* 1.3 62.1 + - - +
67N LEU* 3.5 24.7 - - + -
88N ILE* 4.0 3.6 - - + -
92N LEU* 3.3 33.9 - - + -
110N MET* 3.8 18.8 - - + -
111N VAL 3.3 6.5 - - - +
112N ILE* 3.5 30.1 - - + -
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Residues in contact with GLY 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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11N VAL* 4.2 19.4 - - - +
22N ILE* 5.1 4.9 - - - +
41N ARG 3.2 9.9 - - - -
42N ILE* 4.1 11.1 - - - +
51N LEU* 1.3 74.6 - - - +
53N ALA* 1.4 59.6 + - - -
60N PHE* 4.7 0.2 - - - -
110N MET* 3.2 25.7 - - - +
111N VAL 3.1 11.8 + - - -
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Residues in contact with ALA 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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11N VAL* 3.4 3.5 - - - +
41N ARG* 3.1 36.9 + - + +
52N GLY* 1.4 73.1 - - - -
54N SER* 1.3 63.8 + - - +
55N GLY 4.1 2.7 - - - +
57N TYR* 5.9 0.4 - - + -
60N PHE* 3.2 42.4 - - + -
108N ASN* 4.9 5.4 - - + +
109N THR 4.0 0.9 - - - -
110N MET* 3.6 19.3 - - + -
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Residues in contact with SER 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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7N THR* 5.1 0.2 - - - -
8N GLY 3.6 7.9 - - - -
9N THR* 3.9 18.4 - - - +
10N SER 3.8 2.7 + - - -
11N VAL* 2.7 44.1 + - - +
53N ALA* 1.3 70.7 + - - +
55N GLY* 1.3 57.7 + - - +
107N TRP 4.2 0.9 - - - +
109N THR* 3.2 34.7 + - - +
139N THR* 3.6 16.8 - - - -
140N GLY 4.8 1.1 - - - -
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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