Contacts of the strand formed by residues 79 - 82 (chain H) in PDB entry 1RFU
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 TYR 79 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H CYS* 4.5 4.7 - - - -
6H ARG 3.1 3.2 + - - -
7H VAL* 3.7 29.4 - - + -
8H LEU 3.2 18.3 + - - -
33H PHE* 4.5 4.7 - + - -
77H TYR* 3.5 7.1 - - - +
78H ASP* 1.3 95.5 - - + +
80H VAL* 1.3 71.6 + - - +
108H LEU* 4.5 0.7 - - - -
109H VAL* 3.0 50.1 - - + +
111H VAL* 4.5 2.7 - - + -
146H ILE* 6.1 0.2 - - + -
242H LEU* 3.7 33.0 - - + -
245H THR* 5.5 3.1 - - - -
246H HIS* 2.8 50.4 + + + +
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Residues in contact with VAL 80 (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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7H VAL* 4.6 0.7 - - - -
8H LEU* 3.6 22.9 - - + +
10H ILE* 5.3 2.2 - - + -
77H TYR* 4.9 0.4 - - + -
79H TYR* 1.3 82.5 - - - +
81H LEU* 1.3 61.2 + - - +
82H THR* 3.8 15.0 - - + -
98H VAL* 4.4 16.4 - - + -
101H LEU* 4.1 17.5 - - + -
108H LEU* 3.6 25.4 - - + -
109H VAL 2.9 5.3 + - - -
110H TYR* 3.8 23.8 - - + -
111H VAL* 2.7 33.6 + - - +
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Residues in contact with LEU 81 (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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7H VAL* 4.2 8.5 - - + +
8H LEU 3.1 7.9 + - - +
9H SER* 3.1 12.9 + - - +
10H ILE 2.6 32.7 + - - -
11H GLN* 4.0 21.8 - - - +
24H ALA* 4.6 0.9 - - + -
28H LEU* 4.1 16.6 - - + -
80H VAL* 1.3 74.3 - - - +
82H THR* 1.3 61.8 + - - +
111H VAL* 3.4 37.7 - - + +
113H ASP* 5.3 2.0 - - + +
235H ASP 5.6 0.2 - - - +
238H ALA* 4.2 13.9 - - + -
239H ALA* 3.8 29.2 - - + +
242H LEU* 4.2 7.2 - - + -
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Residues in contact with THR 82 (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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10H ILE* 3.3 16.8 - - + -
11H GLN* 4.1 4.0 - - - -
80H VAL* 3.8 10.3 - - + -
81H LEU* 1.3 82.4 - - - +
83H GLY* 1.3 61.0 + - - +
91H LEU* 5.7 5.2 - - - +
94H VAL* 3.8 25.6 - - + -
110H TYR* 2.6 40.2 + - + +
111H VAL 3.3 5.3 + - - -
112H CYS* 4.1 5.9 - - - -
113H ASP* 3.2 26.9 + - - +
136H TYR* 5.7 3.1 - - - -
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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