Contacts of the strand formed by residues 88 - 97 (chain G) in PDB entry 2N0A
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 ILE 88 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87F SER 3.2 2.3 + - - +
88F ILE* 3.4 33.9 - - + -
89F ALA 3.0 19.8 + - - +
90F ALA 4.9 0.4 - - - +
91F ALA* 4.0 19.7 - - + -
94F PHE* 4.1 7.4 - - + -
82G VAL* 5.4 1.5 - - - +
86G GLY 4.0 9.6 - - - +
87G SER* 1.3 84.8 + - - +
89G ALA* 1.3 60.3 + - - +
91G ALA* 4.2 9.2 - - + -
94G PHE* 4.0 30.1 - - + -
87H SER* 5.8 0.2 - - - -
88H ILE* 3.4 33.9 - - + +
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Residues in contact with ALA 89 (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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89F ALA* 3.4 11.2 - - - +
90F ALA* 2.8 32.1 + - - +
79G GLN* 3.4 10.1 + - - +
82G VAL* 4.2 23.5 - - + +
87G SER 4.3 0.2 - - - -
88G ILE* 1.3 72.1 - - - +
90G ALA* 1.3 61.6 + - - +
79H GLN* 3.1 28.0 - - - +
82H VAL* 5.7 0.7 - - + -
87H SER* 5.3 0.4 + - - -
88H ILE 3.0 7.1 + - - -
89H ALA* 3.4 11.2 - - - +
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ALA 3.3 4.7 - - - -
77G VAL* 4.0 18.2 - - + -
89G ALA* 1.3 77.0 - - + +
91G ALA* 1.3 61.8 + - - +
92G THR* 5.7 2.2 - - + -
77H VAL* 3.8 30.7 - - + -
79H GLN* 4.7 1.8 - - - +
88H ILE* 4.9 1.4 - - - +
89H ALA 2.8 20.6 + - - +
90H ALA* 3.3 2.0 - - - -
91H ALA 3.1 22.3 + - - -
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Residues in contact with ALA 91 (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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90F ALA 3.1 7.9 + - - +
91F ALA* 3.3 5.2 - - + +
92F THR* 3.1 23.4 + - - +
88G ILE* 4.2 19.3 - - + -
90G ALA* 1.3 74.6 - - - +
92G THR* 1.3 63.4 + - - +
93G GLY 3.5 1.8 + - - -
94G PHE* 4.3 11.8 + - + -
88H ILE* 4.0 23.6 - - + -
91H ALA* 3.3 9.9 - - + +
94H PHE* 5.0 3.8 - - + -
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Residues in contact with THR 92 (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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92F THR* 3.2 14.1 - - + +
69G ALA 5.9 0.2 - - - -
71G VAL* 3.6 15.5 - - + -
75G THR* 4.7 16.2 - - + +
90G ALA* 5.7 1.1 - - + -
91G ALA* 1.3 72.3 - - - +
93G GLY* 1.3 60.7 + - - +
71H VAL* 3.0 25.9 - - + +
75H THR* 4.1 31.9 - - + +
91H ALA 3.1 8.8 + - - +
92H THR* 3.2 5.4 - - + -
93H GLY* 2.7 27.9 + - - -
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Residues in contact with GLY 93 (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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69F ALA 5.2 0.7 - - - -
92F THR* 2.7 23.9 + - - -
93F GLY* 3.8 1.3 - - - -
69G ALA* 3.6 26.2 - - - +
71G VAL* 3.4 8.0 - - - +
91G ALA 3.5 2.7 + - - -
92G THR* 1.3 69.8 - - - +
94G PHE* 1.3 57.4 + - - +
93H GLY* 3.7 0.9 - - - -
94H PHE* 2.8 35.2 + - - +
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Residues in contact with PHE 94 (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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91F ALA* 5.0 3.8 - - + -
92F THR 4.0 0.2 + - - -
93F GLY 2.8 21.5 + - - +
94F PHE* 3.3 44.6 - + + -
95F VAL* 3.1 18.5 + - - +
69G ALA* 4.2 0.8 - - - +
88G ILE* 4.0 25.4 - - + -
91G ALA* 4.3 10.7 + - + -
93G GLY* 1.3 73.2 - - - +
95G VAL* 1.3 65.1 + - - +
96G LYS* 4.2 26.9 - - + -
88H ILE* 4.1 12.1 - - + -
94H PHE* 3.3 47.8 - + + -
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Residues in contact with VAL 95 (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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68F GLY* 3.9 13.9 - - - -
95F VAL* 3.3 28.0 - - + +
97F LYS* 6.0 4.9 - - + -
67G GLY 5.4 0.7 - - - +
68G GLY* 3.6 24.5 - - - +
69G ALA* 3.9 6.1 - - + +
94G PHE* 1.3 81.0 - - - +
96G LYS* 1.3 66.1 + - - +
97G LYS* 5.0 6.1 - - + +
94H PHE* 3.1 6.1 + - - +
95H VAL* 3.3 27.8 - - + +
96H LYS 3.1 22.3 + - - +
97H LYS* 5.9 3.4 - - + -
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Residues in contact with LYS 96 (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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95F VAL 3.1 8.3 + - - +
96F LYS* 3.4 35.5 - - + +
97F LYS* 3.0 26.0 + - - +
98F ASP 6.1 0.2 - - - +
99F GLN* 6.5 0.4 - - - +
100F LEU* 6.2 3.6 - - - +
94G PHE* 4.2 21.4 - - + -
95G VAL* 1.3 76.0 - - - +
97G LYS* 1.3 66.5 + - - +
98G ASP* 5.1 12.3 - - + +
96H LYS* 3.4 40.7 - - + +
98H ASP* 5.7 2.9 - - - -
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Residues in contact with LYS 97 (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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97F LYS* 3.8 42.0 - - + +
95G VAL* 4.3 5.8 - - + -
96G LYS* 1.3 76.4 - - - +
98G ASP* 1.3 64.4 + - - +
99G GLN* 4.3 29.2 + - + +
96H LYS 3.0 9.9 + - - +
97H LYS* 3.5 21.6 - - + +
98H ASP* 3.1 26.1 + - - +
99H GLN* 5.9 2.9 - - - -
99I GLN* 5.2 10.3 - - - +
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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