Contacts of the strand formed by residues 91 - 96 (chain H) in PDB entry 5OA3
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 HIS 91 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H ARG* 3.3 48.0 + - + +
58H LYS 3.3 10.5 + - - +
59H ALA* 3.4 5.6 - - + +
60H ILE 2.8 29.2 + - - +
84H GLU* 3.9 15.5 - - - -
90H LYS* 1.3 72.9 - - - +
92H VAL* 1.3 59.3 + - - +
93H VAL* 3.8 7.1 + - + +
168H HIS* 4.0 29.6 + + - -
169H LYS* 3.8 26.5 - - + -
172H THR* 4.0 26.4 - - + +
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H ILE* 3.5 23.3 - - + +
62H ILE* 4.2 12.8 - - + -
80H VAL* 3.7 31.7 - - + +
83H LEU* 4.0 29.2 - - + +
84H GLU* 4.3 23.2 + - + +
87H PHE* 5.6 3.4 - - + -
90H LYS* 4.2 4.2 + - + -
91H HIS* 1.3 73.4 - - - +
93H VAL* 1.3 65.2 + - - +
94H PHE* 3.5 27.8 - - + -
169H LYS* 6.1 0.5 - - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ALA* 6.0 0.2 - - + -
60H ILE 3.1 8.9 + - - +
61H ILE* 3.7 17.9 - - + +
62H ILE* 3.2 23.7 + - - +
76H GLN* 5.5 0.4 - - - +
91H HIS* 4.4 11.2 - - + +
92H VAL* 1.3 79.7 - - - +
94H PHE* 1.3 68.4 + - - +
95H ILE* 4.1 0.8 + - + -
133H LEU* 3.4 53.4 - - + +
169H LYS* 6.2 2.5 - - + -
172H THR* 4.8 13.7 - - + +
173H PHE* 4.6 16.4 - - + -
176H VAL* 5.0 3.8 - - + -
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Residues in contact with PHE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H LEU* 6.2 2.9 - - + -
45H ILE* 5.4 1.1 - - + -
62H ILE* 3.7 22.7 - - + -
64H VAL* 3.7 22.2 - - + -
69H LEU* 5.4 4.9 - - + -
72H PHE* 3.9 28.3 - + + -
76H GLN* 3.2 39.2 + - - +
79H LEU* 4.9 11.7 - - + -
80H VAL* 4.2 16.2 - - + -
83H LEU* 4.4 15.0 - - + -
92H VAL* 3.5 26.0 - - + -
93H VAL* 1.3 80.9 - - - +
95H ILE* 1.3 62.3 + - - +
132H ASP* 2.7 36.4 - - - +
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Residues in contact with ILE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ILE* 3.8 26.0 - - + -
62H ILE 3.1 6.2 + - - +
63H PHE* 3.1 23.8 - - + -
64H VAL* 3.0 24.7 + - - -
93H VAL* 4.7 2.5 - - + -
94H PHE* 1.3 79.5 - - - +
96H ALA* 1.3 71.8 + - - +
129H ILE* 3.8 32.1 - - + +
132H ASP* 3.4 4.9 - - + +
133H LEU* 3.6 29.8 - - + -
176H VAL* 4.0 5.6 - - + -
180H LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H PHE* 4.1 3.7 - - - -
64H VAL* 3.3 15.0 - - + +
66H VAL* 4.1 22.9 - - + -
69H LEU* 3.9 25.6 - - + -
95H ILE* 1.3 87.9 - - - +
97H GLN* 1.3 62.8 + - - +
98H ARG* 3.4 25.8 + - - +
129H ILE* 5.7 0.2 - - - +
132H ASP* 3.6 7.2 + - + +
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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