Contacts of the strand formed by residues 146 - 152 (chain G) 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 ALA 146 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40G ARG* 3.5 31.0 + - + +
41G CYS 3.7 9.4 - - - +
43G ASP* 4.6 0.7 - - - -
44G GLY 3.4 34.3 - - - +
45G VAL* 4.0 0.7 - - + -
139G SER 3.7 5.8 - - - -
140G TYR* 3.4 11.8 - - - +
144G ASP 4.0 0.3 - - - +
145G GLY* 1.3 72.5 - - - -
147G GLN* 1.3 75.3 + - - +
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Residues in contact with GLN 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ARG* 4.1 17.6 + - - +
45G VAL* 3.4 4.7 - - - +
108G LEU* 3.6 25.6 - - + -
109G LYS* 5.5 4.7 - - + +
138G GLY* 3.1 3.6 - - - -
139G SER 2.9 34.4 + - - +
144G ASP* 3.1 48.6 + - + +
145G GLY 4.1 0.4 - - - +
146G ALA* 1.3 79.3 + - - +
148G LEU* 1.3 60.5 + - - +
149G TYR* 3.7 24.6 + - + -
159G GLY* 5.6 0.5 - - - -
160G TYR 5.5 0.3 - - - +
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Residues in contact with LEU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G GLY* 3.7 10.8 - - - -
39G ILE 3.8 0.4 - - - +
40G ARG* 3.3 37.5 - - + +
45G VAL* 3.8 23.6 - - + -
47G PHE* 5.4 0.4 - - + -
136G MET* 3.6 35.0 - - + -
137G LEU 3.8 7.0 - - - +
138G GLY* 4.2 0.4 - - - -
147G GLN* 1.3 75.4 + - - +
149G TYR* 1.3 60.7 + - - +
159G GLY* 3.6 0.7 - - - -
160G TYR* 2.9 35.1 + - + +
162G GLY* 3.8 6.3 - - - +
163G CYS* 3.7 29.6 - - + +
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Residues in contact with TYR 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G LEU* 3.8 21.1 - - + +
109G LYS* 4.4 25.6 - - + +
112G ALA* 3.6 33.9 - - + -
113G ASP* 4.9 4.7 - - - -
135G PHE 4.1 0.2 - - - +
136G MET* 3.4 3.3 - - - -
137G LEU* 2.8 32.5 + - + +
147G GLN* 3.7 28.3 + - + -
148G LEU* 1.3 79.5 - - - +
150G MET* 1.4 61.4 + - - +
151G ILE* 4.2 2.8 + - + +
157G SER* 4.7 3.6 - - - -
158G TYR* 3.3 20.0 - - - +
159G GLY* 3.6 23.9 + - - -
160G TYR* 4.3 0.2 - - - -
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Residues in contact with MET 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G SER* 3.3 25.8 - - - +
135G PHE 3.5 15.0 - - - +
136G MET* 3.9 3.1 - - + +
149G TYR* 1.4 72.5 - - - +
151G ILE* 1.4 62.3 + - - +
152G ASP* 3.3 33.0 - - - +
156G VAL 3.8 0.6 - - - +
157G SER* 3.3 20.7 - - - -
158G TYR 3.2 10.3 + - - -
160G TYR* 3.4 30.0 + - + +
163G CYS* 3.6 21.3 - - - -
165G ILE* 3.4 30.3 - - + -
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Residues in contact with ILE 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G ALA* 3.4 36.3 - - + +
115G VAL* 4.0 6.7 - - + -
116G ALA* 3.8 29.8 - - + +
119G VAL* 4.3 5.6 - - + -
134G SER* 3.0 19.3 + - - -
135G PHE* 2.9 60.2 + - + +
137G LEU* 5.1 7.0 - - + +
149G TYR 4.9 3.8 - - - +
150G MET* 1.4 73.9 - - - +
152G ASP* 1.4 70.5 + - - +
155G GLY* 4.6 1.6 - - - -
156G VAL 3.9 3.8 - - - +
157G SER* 4.1 10.8 - - - +
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Residues in contact with ASP 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G MET* 3.9 9.9 - - + +
119G VAL* 3.4 8.7 - - - +
133G CYS 4.2 0.9 - - - -
134G SER* 3.7 6.5 + - - -
135G PHE* 5.9 0.2 - - - -
150G MET* 3.3 24.4 - - - +
151G ILE* 1.4 78.0 - - - +
153G PRO* 1.3 69.2 - - + +
154G SER* 3.0 20.9 - - - +
155G GLY 3.1 14.6 + - - -
156G VAL* 3.1 28.0 + - - +
158G TYR* 5.7 2.4 - - - -
160G TYR* 5.1 1.6 + - - -
165G ILE* 5.8 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