Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 2BYE
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 GLU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY* 3.7 20.4 - - - +
32A THR 3.8 4.2 - - - +
33A LYS* 3.5 31.8 - - + +
34A ALA 4.3 6.5 - - - +
83A GLU 3.1 11.2 + - - +
84A GLU* 1.3 71.7 - - - +
86A ILE* 1.3 60.2 + - - +
87A MET* 4.3 7.4 - - + +
88A GLN* 3.0 51.9 + - + +
89A ILE* 3.3 9.8 - - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.8 28.3 - - + -
28A ILE* 4.5 8.1 - - + -
32A THR 4.6 9.6 - - - +
34A ALA* 3.7 19.5 - - + +
37A LEU* 3.4 33.0 - - + -
57A LEU* 3.4 29.8 - - + -
80A ILE* 3.8 12.1 - - + -
85A GLU* 1.3 70.2 - - - +
87A MET* 1.3 70.0 + - + +
89A ILE* 2.9 23.8 + - + +
90A LEU* 2.9 27.0 + - + +
103A ILE* 5.2 2.9 - - + -
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Residues in contact with MET 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 4.5 16.8 - - - +
10A HIS* 3.9 33.2 - - + +
12A VAL* 6.3 2.2 - - + -
28A ILE* 3.7 28.9 - - + -
32A THR 5.2 5.8 - - - +
85A GLU* 3.2 7.5 - - + +
86A ILE* 1.3 88.0 - - + +
88A GLN* 1.3 58.9 + - + +
90A LEU* 3.9 18.8 - - + +
91A SER* 3.0 26.7 + - - -
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU 4.5 3.0 + - - -
84A GLU* 4.4 6.7 - - - +
85A GLU* 3.0 48.3 + - + +
87A MET* 1.3 76.6 - - + +
89A ILE* 1.3 61.0 + - + +
91A SER* 3.4 7.8 - - - -
92A SER* 2.7 37.0 + - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.3 47.0 - - + +
61A LYS* 5.8 1.4 + - - +
78A ARG* 5.3 7.2 - - + -
80A ILE* 4.0 21.3 - - + -
84A GLU* 4.8 13.7 - - + +
85A GLU 3.3 17.7 - - - +
86A ILE* 3.0 18.2 - - - +
88A GLN* 1.3 81.5 - - + +
90A LEU* 1.3 60.8 + - + +
92A SER* 3.2 7.8 + - - -
93A TRP* 2.9 34.0 + - + +
103A ILE* 4.9 4.7 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.9 11.0 - - + -
86A ILE* 2.9 41.0 + - + +
87A MET* 4.1 22.0 - - + +
89A ILE* 1.3 81.0 - - + +
91A SER* 1.3 57.7 + - - +
93A TRP* 3.2 47.0 - - + +
103A ILE* 4.8 16.2 - - + -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 3.0 20.3 + - - -
88A GLN* 3.4 9.4 - - - -
89A ILE 3.1 0.2 - - - -
90A LEU* 1.3 76.7 - - - +
92A SER* 1.3 58.5 + - - +
93A TRP 3.1 9.9 + - - +
94A PHE* 5.7 1.2 - - - -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 5.7 2.9 - - - -
61A LYS* 5.4 1.8 + - - -
88A GLN 2.7 20.7 + - - -
89A ILE* 3.6 7.6 - - - -
91A SER* 1.3 70.9 - - - +
93A TRP* 1.3 58.8 + - - +
94A PHE* 3.0 42.7 + - - -
97A GLU* 3.6 1.6 - - - +
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Residues in contact with TRP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 5.9 3.1 - - + -
61A LYS* 4.3 15.0 - - - +
89A ILE* 2.9 17.9 + - + +
90A LEU* 3.2 42.5 - - + +
91A SER 3.1 6.3 - - - +
92A SER* 1.3 73.1 - - - +
94A PHE* 1.3 76.1 + - - +
95A PRO* 3.7 4.5 - - + +
97A GLU* 3.4 10.3 - - + +
98A GLY* 3.0 36.3 + - - +
99A TYR 4.5 1.3 - - - -
100A MET 3.3 28.5 - - - -
101A GLY* 3.5 30.1 - - - -
102A ARG* 4.3 6.1 - - - -
103A ILE* 6.2 4.0 - - + -
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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