Contacts of the strand formed by residues 83 - 90 (chain C) in PDB entry 3ORH
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 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C SER* 3.9 17.9 - - - -
61C GLY* 3.9 14.4 - - - -
62C GLY 3.5 9.6 - - - +
64C VAL* 3.8 23.3 - - + -
78C VAL* 3.8 26.9 - - + +
79C GLN* 4.3 3.6 - - - +
81C ALA* 2.8 20.6 + - + +
82C PRO* 1.3 74.8 - - - +
84C ASP* 1.3 63.3 + - - +
85C GLU 3.8 17.7 - - - +
86C HIS* 3.8 17.3 - - + -
108C HIS* 2.8 44.1 + - + -
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY* 2.8 32.9 + - - +
63C ARG* 4.9 3.1 - - + +
82C PRO 4.8 2.6 - - - +
83C ILE* 1.3 78.3 - - - +
85C GLU* 1.3 69.4 + - + +
108C HIS* 4.5 4.0 - - - +
109C LYS* 4.1 18.2 + - - +
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Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY 3.3 4.2 + - - +
63C ARG* 3.4 38.4 + - + +
64C VAL 3.0 25.7 + - - -
83C ILE* 3.8 8.4 - - - +
84C ASP* 1.3 86.9 - - + +
86C HIS* 1.4 60.9 + - - +
87C TRP* 2.9 41.0 + - + +
109C LYS* 3.6 17.3 - - + +
111C ILE* 4.7 8.7 - - + +
128C HIS* 4.6 0.9 + - - -
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Residues in contact with HIS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL* 3.6 7.4 - - + -
66C GLU* 2.9 32.5 + - + +
75C ALA* 3.5 23.8 - - + -
78C VAL* 3.7 23.3 - - + +
79C GLN* 3.1 33.1 + - - +
83C ILE* 3.8 4.9 - - + -
85C GLU* 1.4 72.9 - - - +
87C TRP* 1.4 66.7 + - - +
88C ILE* 3.5 29.2 - - + +
102C TRP* 3.9 2.7 - + - -
109C LYS 2.8 11.4 + - - +
110C VAL* 3.2 8.1 - - + +
111C ILE 2.8 27.7 + - - +
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ARG* 4.5 2.5 - - + +
64C VAL 2.9 12.8 + - - +
65C LEU* 3.8 15.7 - - + -
66C GLU* 2.7 32.2 + - - +
85C GLU* 2.9 38.6 + - + +
86C HIS* 1.4 72.5 - - - +
88C ILE* 1.3 57.8 + - - +
89C ILE* 6.1 0.2 - - + -
111C ILE* 3.4 35.4 - - + +
113C LEU* 4.2 14.4 - - + -
124C LEU* 4.0 29.2 - - + -
125C PRO* 4.2 18.4 - - + -
128C HIS* 3.9 19.7 - + - -
129C PHE* 3.5 28.9 - + + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.3 14.4 - - + +
68C GLY 4.9 0.2 - - - -
69C PHE* 4.0 30.1 - - + +
75C ALA* 4.4 1.8 - - + -
86C HIS* 3.5 40.6 - - + +
87C TRP* 1.3 79.8 - - - +
89C ILE* 1.4 69.2 + - - +
99C LEU* 3.8 29.9 - - + +
102C TRP* 3.6 25.6 - - + -
110C VAL* 4.0 4.9 - - + -
111C ILE 2.9 11.8 + - - +
112C PRO* 3.6 2.4 - - - +
113C LEU* 2.9 28.0 + - - +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LEU* 3.9 26.2 - - + -
66C GLU 2.9 9.8 + - - +
67C VAL* 4.4 13.9 - - + -
68C GLY* 2.8 30.7 + - - -
87C TRP 5.6 0.2 - - - -
88C ILE* 1.4 73.9 - - - +
90C GLU* 1.3 65.1 + - - +
113C LEU* 3.4 12.6 - - + +
115C GLY 3.5 18.6 - - - +
117C TRP* 4.1 17.5 - - + +
120C VAL* 3.8 37.0 - - + -
121C ALA* 4.4 9.0 - - + +
124C LEU* 3.9 14.4 - - + -
151C PHE* 5.8 0.4 - - + -
4002C SAH 4.4 5.0 + - + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLY* 3.7 0.2 - - - -
69C PHE* 2.8 31.6 + - + -
88C ILE 4.1 0.2 + - - -
89C ILE* 1.3 77.0 - - - +
91C CYS* 1.4 63.5 + - - +
92C ASN* 2.9 22.4 + - - +
95C VAL* 3.5 20.3 - - + +
96C PHE* 3.8 28.8 - - + +
99C LEU* 4.3 5.4 - - + -
113C LEU 3.1 6.9 + - - -
114C LYS* 3.3 11.3 - - - +
115C GLY 2.9 20.8 + - - -
4002C SAH 2.6 52.6 + - - -
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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