Contacts of the strand formed by residues 109 - 116 (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 109 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N VAL* 5.6 0.2 - - - +
53N ALA* 4.0 0.3 - - - -
54N SER 3.2 35.4 + - - +
107N TRP 4.0 2.8 + - - -
108N ASN* 1.3 75.7 + - - +
110N MET* 1.4 59.9 + - - +
124N TYR* 3.3 42.2 - - + +
125N VAL 3.4 7.6 - - - +
126N ASP* 4.2 2.9 + - - -
127N MET* 3.7 19.2 + - - +
139N THR* 3.8 19.4 - - + +
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Residues in contact with MET 110 (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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43N MET* 4.3 4.9 - - - -
51N LEU* 3.8 24.5 - - + -
52N GLY 3.2 12.1 - - - +
53N ALA* 3.6 28.3 - - + -
60N PHE* 4.3 10.8 - - - -
63N LEU* 3.6 35.9 - - + -
92N LEU* 3.8 24.2 - - + -
96N MET* 4.0 11.2 - - + -
108N ASN* 4.2 15.9 - - + +
109N THR* 1.4 76.7 - - - +
111N VAL* 1.4 61.1 + - - +
112N ILE* 4.1 3.5 - - - +
124N TYR* 3.5 2.4 - - - -
125N VAL* 3.0 33.2 + - - +
139N THR* 4.8 1.1 - - - -
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Residues in contact with VAL 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N VAL* 4.6 15.7 - - + +
12N LEU 5.1 0.2 - - - +
13N GLY* 4.4 7.2 - - - +
22N ILE* 4.4 15.4 - - + +
50N MET 4.0 0.5 - - - +
51N LEU* 3.3 3.1 - - - -
52N GLY 3.1 27.2 + - - -
110N MET* 1.4 71.7 - - - +
112N ILE* 1.4 64.3 + - - +
113N GLY 4.0 0.8 + - - +
122N LEU* 4.2 19.1 - - + -
123N GLY 3.4 10.3 - - - +
124N TYR* 4.7 2.5 - - + -
137N LEU* 3.8 36.8 - - + +
139N THR* 3.7 26.8 - - + +
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Residues in contact with ILE 112 (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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49N THR* 5.3 2.7 - - - +
50N MET 3.4 18.4 - - - +
51N LEU* 3.5 36.6 - - + -
85N PRO* 4.5 15.3 - - + +
88N ILE* 4.1 13.0 - - + -
89N HIS* 3.3 45.1 - - + +
92N LEU* 4.0 6.3 - - + -
110N MET 4.1 2.9 - - - +
111N VAL* 1.4 71.7 - - - +
113N GLY* 1.3 57.6 + - - +
114N GLY 3.7 0.3 + - - -
121N PHE* 3.3 10.7 - - - +
122N LEU* 4.3 0.9 - - - -
123N GLY 3.0 33.9 + - - +
125N VAL* 3.7 15.5 - - + -
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Residues in contact with GLY 113 (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* 4.2 4.9 - - - -
22N ILE* 3.7 21.3 - - - +
49N THR* 3.4 1.5 - - - -
50N MET* 3.0 38.4 + - - +
111N VAL* 4.4 0.2 - - - +
112N ILE* 1.3 70.8 - - - +
114N GLY* 1.3 57.2 + - - -
121N PHE 3.5 6.1 - - - -
122N LEU* 4.0 11.7 - - - -
192N VAL* 3.7 7.4 - - - +
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Residues in contact with GLY 114 (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* 4.5 4.0 - - - +
49N THR* 3.7 24.7 - - - -
85N PRO* 3.5 13.5 - - - +
112N ILE 3.7 1.4 + - - -
113N GLY* 1.3 74.0 - - - -
115N TYR* 1.3 62.5 + - - -
116N ALA 3.4 1.9 + - - -
120N SER* 4.5 1.6 - - - -
121N PHE 3.0 32.3 + - - +
192N VAL* 4.6 2.0 - - - -
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Residues in contact with TYR 115 (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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18N GLY* 4.1 20.0 - - - -
19N GLY 4.6 5.4 - - - +
20N VAL* 4.8 0.4 - - + +
48N SER* 3.5 18.2 + - - +
49N THR* 4.9 1.8 - - - +
85N PRO* 5.2 0.7 - - - -
114N GLY* 1.3 69.7 - - - -
116N ALA* 1.3 57.1 - - - +
117N ASP 4.2 2.0 + - - -
118N GLY* 2.8 48.3 + - - -
119N GLU 3.3 14.6 - - - -
120N SER* 3.6 16.4 - - - +
192N VAL* 3.5 28.0 - - + +
193N THR 5.1 0.2 - - - +
194N GLU* 3.7 44.9 - - + -
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Residues in contact with ALA 116 (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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84N SER* 5.0 6.5 - - - -
85N PRO* 3.6 31.4 - - + -
86N ARG* 5.3 4.5 - - - +
114N GLY 3.4 0.8 + - - -
115N TYR* 1.3 73.7 - - - +
117N ASP* 1.4 73.9 + - + +
118N GLY 3.4 1.3 - - - -
119N GLU* 2.7 32.0 + - - +
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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