Contacts of the strand formed by residues 84 - 90 (chain G) in PDB entry 2BX5
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 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G GLN* 4.9 7.0 - - + +
38G GLN 3.4 18.8 - - - +
39G LYS* 3.8 15.5 - - + -
40G PRO* 4.1 4.7 - - + -
82G ASP 2.8 11.6 + - - +
83G PHE* 1.3 79.7 - - - +
85G THR* 1.3 68.3 + - - +
86G TYR* 4.0 2.7 - - - -
102G THR 2.9 2.6 - - - +
103G LYS* 4.1 3.4 - - - +
104G VAL* 2.6 41.1 + - - +
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Residues in contact with THR 85 (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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36G TYR 3.1 3.6 - - - +
37G GLN* 3.4 2.8 - - - -
38G GLN* 3.0 41.0 + - - +
84G ALA* 1.3 80.1 - - - +
86G TYR* 1.3 64.2 + - - +
87G TYR* 3.2 36.8 - - + +
101G GLY* 4.0 3.6 - - - -
102G THR 3.1 22.0 - - - +
103G LYS* 3.4 29.7 - - + +
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Residues in contact with TYR 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.3 4.8 + - - +
21G ILE* 4.1 15.0 - - + -
35G TRP* 4.3 6.7 - - + -
36G TYR 2.8 16.8 - - - +
37G GLN* 3.7 16.2 + - + -
47G LEU* 3.7 13.2 - - + -
62G PHE* 3.4 24.9 - + - -
73G LEU* 4.1 20.2 - - + -
75G ILE* 3.7 16.6 - - + +
82G ASP* 2.8 46.7 + - - +
84G ALA 4.0 5.2 - - - -
85G THR* 1.3 75.7 - - - +
87G TYR* 1.3 57.1 + - - +
101G GLY* 2.8 10.6 - - - -
102G THR 2.4 42.3 + - - +
104G VAL* 3.8 21.0 - - + +
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Residues in contact with TYR 87 (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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6G GLN* 4.3 0.4 - - - -
34G ASN 3.4 0.2 - - - +
35G TRP* 3.2 15.0 - - - -
36G TYR* 3.1 46.0 + - + -
38G GLN* 3.6 30.3 + - + -
44G PRO* 5.6 1.3 - - + -
85G THR* 3.2 31.4 - - + +
86G TYR* 1.3 80.7 - - - +
88G CYS* 1.3 60.7 + - - +
98G PHE* 3.8 28.0 - + + -
99G GLY 3.9 17.9 - - - -
100G GLN* 4.6 2.8 - - - -
101G GLY* 4.1 16.6 - - - -
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Residues in contact with CYS 88 (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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4G MET* 4.1 3.2 - - - +
6G GLN* 3.3 18.2 - - - -
23G CYS* 2.0 53.8 - - + -
33G LEU* 4.5 5.8 - - + -
34G ASN 3.1 8.3 - - - +
35G TRP* 3.6 14.4 - - + -
87G TYR* 1.3 76.1 - - - +
89G GLN* 1.3 62.8 + - - +
97G THR 4.2 0.2 - - - +
98G PHE 3.1 1.0 - - - -
99G GLY* 2.5 43.2 + - - -
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Residues in contact with GLN 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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4G MET* 5.2 1.8 - - - -
33G LEU* 4.1 4.5 - - - +
34G ASN* 2.7 50.1 + - - +
36G TYR* 3.2 33.1 + - + -
88G CYS* 1.3 76.6 - - - +
90G GLN* 1.3 70.0 + - - +
96G ASN* 3.5 27.8 + - - +
97G THR 3.0 22.2 - - - +
98G PHE* 3.0 41.2 - - + -
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Residues in contact with GLN 90 (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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2G ILE* 3.2 33.7 - - - +
4G MET* 4.8 4.2 - - - +
29G ILE* 3.8 14.5 - - + +
32G TYR 2.8 17.3 - - - +
33G LEU* 4.2 2.6 - - - +
34G ASN* 3.2 12.9 + - - -
89G GLN* 1.3 87.9 - - - +
91G SER* 1.3 58.6 + - - +
92G TYR* 2.9 17.7 - - - +
93G SER* 3.3 25.2 + - - +
95G PRO 3.5 3.2 + - - -
96G ASN* 3.5 5.7 + - - +
97G THR* 2.7 49.3 + - - +
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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