Contacts of the strand formed by residues 84 - 88 (chain B) in PDB entry 3RIE
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 LYS 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.7 32.5 - - + -
76B VAL* 5.2 0.7 - - + -
77B PHE 3.3 6.7 - - - +
78B GLU* 4.1 15.3 - - + +
83B GLY* 1.3 73.3 - - - -
85B VAL* 1.3 57.8 + - - +
95B THR* 3.3 3.1 - - - -
96B GLU* 2.7 58.3 + - - +
158B ILE 5.5 0.2 + - - -
159B TYR* 2.5 34.9 + - + +
160B PHE* 3.5 23.4 - - + +
161B LYS 5.3 1.2 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.0 7.4 - - + -
75B LEU 3.7 0.5 - - - +
76B VAL* 3.4 5.7 - - - -
77B PHE* 2.8 64.7 + - + +
79B SER* 3.7 20.6 - - - +
83B GLY 3.6 11.2 - - - +
84B LYS* 1.3 77.8 - - - +
86B LEU* 1.3 64.1 + - - +
87B VAL* 3.8 11.4 - - + -
92B ILE* 4.2 9.6 - - + -
94B LEU 3.5 11.7 - - - +
95B THR* 3.8 21.1 - - + -
160B PHE* 3.7 6.1 - - - -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.9 18.4 - - + -
75B LEU 3.3 15.7 - - - +
76B VAL* 3.7 17.7 - - + -
85B VAL* 1.3 75.7 - - - +
87B VAL* 1.3 76.8 + - - +
88B LEU* 4.6 4.0 - - + -
92B ILE* 3.7 1.7 - - - -
93B GLN* 3.0 39.6 + - + -
94B LEU* 3.1 24.2 + - + +
127B ASP* 4.9 7.6 - - + -
152B VAL* 4.4 22.9 - - + +
155B VAL* 4.4 7.2 - - + -
156B SER* 5.8 1.8 - - - -
160B PHE* 3.9 20.1 - - + -
401B MTA 4.6 5.4 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.8 23.1 - - + -
73B ASN 3.6 1.8 - - - +
75B LEU* 2.8 51.6 + - + +
77B PHE* 3.9 15.7 - - + -
85B VAL* 3.8 19.1 - - + -
86B LEU* 1.3 83.8 - - - +
88B LEU* 1.3 71.5 + - - +
90B GLY* 3.6 16.8 - - - +
91B VAL 3.4 26.2 - - - +
92B ILE* 4.4 4.3 - - - -
93B GLN 4.4 0.4 - - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 3.8 27.1 - - + +
73B ASN 3.3 2.5 - - - +
74B VAL* 3.6 35.7 - - + -
86B LEU* 4.6 5.8 - - + -
87B VAL* 1.3 77.0 - - - +
89B ASP* 1.3 72.8 + - - +
90B GLY 3.1 0.9 - - - -
91B VAL* 2.9 24.4 + - - +
93B GLN* 3.5 32.8 + - + +
152B VAL* 4.1 9.6 - - + -
198B SER* 4.7 3.8 - - - -
401B MTA 3.6 38.6 - - + +
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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
------------------------------------------------------------
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