Contacts of the helix formed by residues 81 - 92 (chain G) in PDB entry 2BZN
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 SER 81 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G HIS 4.4 0.2 + - - -
80G TYR* 1.3 77.1 - - - +
82G LEU* 1.3 58.3 + - - +
83G VAL* 3.0 15.7 + - - +
84G GLN* 2.7 41.1 + - - +
85G TRP* 2.9 29.4 + - - -
116G ILE* 5.5 0.2 - - - -
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Residues in contact with LEU 82 (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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80G TYR 4.0 0.6 + - - -
81G SER* 1.3 73.4 - - - +
83G VAL* 1.3 56.6 + - + +
85G TRP* 3.5 7.2 + - + +
86G GLN* 2.9 54.1 + - + +
115G GLN* 3.0 60.1 - - + +
116G ILE* 3.5 20.0 - - + +
119G ALA* 3.7 14.4 - - + -
120G ILE* 5.6 1.3 - - + -
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Residues in contact with VAL 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G SER* 3.0 11.1 + - - +
82G LEU* 1.3 74.5 - - + +
84G GLN* 1.3 70.4 + - + +
86G GLN* 2.7 32.1 + - - +
87G GLU* 2.8 39.5 + - + +
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Residues in contact with GLN 84 (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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61G PHE* 4.0 5.6 - - + -
79G HIS 4.3 2.6 - - - +
80G TYR* 3.4 30.2 - - + -
81G SER* 2.7 41.6 + - - +
83G VAL* 1.3 73.9 - - + +
85G TRP* 1.3 56.4 + - - +
87G GLU* 3.5 10.3 + - + +
88G PHE* 2.8 30.8 + - - +
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Residues in contact with TRP 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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61G PHE* 3.7 17.2 - + - -
76G VAL* 3.5 39.7 - - + +
77G HIS 4.8 4.3 + - - -
80G TYR* 3.6 26.9 + - + +
81G SER 2.9 22.3 + - - +
82G LEU* 3.6 11.2 - - + +
84G GLN* 1.3 76.4 - - - +
86G GLN* 1.3 54.5 + - - +
88G PHE* 3.0 5.9 + + - +
89G ALA* 2.8 36.0 + - + +
96G LEU* 5.8 0.7 - - + -
99G LEU* 3.8 17.7 - - + -
100G ALA 4.2 9.0 - - - -
101G ALA* 4.2 21.5 - - + -
102G SER 5.6 0.2 - - - -
116G ILE* 3.6 41.1 - - + +
120G ILE* 4.0 19.4 - - + +
123G VAL* 3.6 23.8 - - + -
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Residues in contact with GLN 86 (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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82G LEU* 2.9 42.6 + - + +
83G VAL* 2.7 36.6 + - - +
85G TRP* 1.3 72.2 - - - +
87G GLU* 1.3 52.4 + - + +
89G ALA* 3.3 3.0 + - - +
90G GLY* 2.8 32.4 + - - -
119G ALA* 4.6 13.0 - - + +
120G ILE* 4.4 10.1 - - + +
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Residues in contact with GLU 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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83G VAL* 2.8 47.2 + - + +
84G GLN* 3.6 9.0 - - + +
86G GLN* 1.3 72.8 - - + +
88G PHE* 1.3 63.6 + - - +
90G GLY* 3.0 2.6 + - - +
91G GLN* 2.9 31.9 + - + +
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Residues in contact with PHE 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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61G PHE* 3.4 70.9 - + + -
64G ALA* 4.6 7.6 - - + -
65G LYS* 4.2 9.2 - - + -
84G GLN 2.8 21.8 + - - +
85G TRP* 3.0 7.4 + + - +
87G GLU* 1.3 73.6 - - - +
89G ALA* 1.3 61.8 + - + +
91G GLN* 5.0 0.7 - - - -
92G ASN* 2.9 55.3 + - + +
95G CYS* 4.0 21.8 - - + -
96G LEU* 3.8 22.9 - - + -
99G LEU* 3.8 12.6 - - + -
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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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85G TRP 2.8 19.1 + - - +
86G GLN* 3.7 4.3 - - - +
88G PHE* 1.3 74.3 - - + +
90G GLY* 1.3 60.8 + - - +
92G ASN 4.6 0.4 - - - +
93G PRO* 3.5 23.4 - - - +
96G LEU* 4.1 33.7 - - + +
120G ILE* 3.9 23.6 - - + -
122G GLN* 5.1 1.8 - - - +
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Residues in contact with GLY 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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86G GLN 2.8 14.5 + - - -
87G GLU* 3.0 4.2 + - - -
89G ALA* 1.3 79.3 - - - +
91G GLN* 1.3 64.2 + - - +
93G PRO* 3.5 10.0 - - - +
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Residues in contact with GLN 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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87G GLU* 2.9 19.7 + - + +
88G PHE* 4.8 0.9 - - - -
90G GLY* 1.3 76.2 + - - +
92G ASN* 1.3 76.5 + - - +
93G PRO* 3.3 6.9 - - - +
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Residues in contact with ASN 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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65G LYS* 3.4 32.9 + - - +
88G PHE* 2.9 43.8 + - + +
89G ALA 3.8 4.0 - - - -
90G GLY 3.3 0.4 - - - -
91G GLN* 1.3 97.6 + - - +
93G PRO* 1.3 65.4 - - - +
94G ASP* 3.1 3.6 - - - -
95G CYS* 3.0 28.6 + - - +
96G LEU* 4.1 7.8 - - - +
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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