Contacts of the strand formed by residues 89 - 93 (chain R) in PDB entry 1E50
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 PHE 89 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72R CYS* 3.6 22.4 - - + -
73R SER* 2.9 33.4 - - - -
75R LEU* 3.6 32.8 - - + -
85R LEU* 4.5 5.4 - - + +
87R ILE* 3.7 2.5 + - - -
88R ALA* 1.3 74.2 - - - +
90R LYS* 1.3 61.6 + - - +
91R VAL* 3.9 20.6 - - + -
105R VAL* 4.2 6.5 - - + -
130R ARG* 3.6 0.7 - - - +
131R PHE* 2.9 59.9 + + + +
134R LEU* 3.9 28.9 - - + +
148R LEU* 3.6 22.7 - - + -
150R ILE* 4.8 2.9 - - + -
162R TYR* 6.2 0.9 - + - -
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Residues in contact with LYS 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q LEU* 3.4 44.9 + - + +
62R LEU* 4.6 10.2 - - + +
72R CYS* 3.2 6.2 - - - +
73R SER* 2.8 40.5 + - - +
88R ALA* 4.4 10.5 - - - +
89R PHE* 1.3 81.6 - - - +
91R VAL* 1.3 64.2 + - - +
92R VAL* 4.1 1.3 - - + -
128R VAL* 3.8 20.2 - - + +
129R ALA 3.7 5.4 - - - +
130R ARG* 3.6 52.1 - - + +
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Residues in contact with VAL 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R PHE* 5.3 5.2 - - + -
71R LEU 3.3 5.4 - - - +
72R CYS* 4.4 0.4 - - + -
89R PHE* 3.9 13.9 - - + -
90R LYS* 1.3 77.4 - - - +
92R VAL* 1.3 62.9 + - - +
103R VAL* 3.9 11.9 - - + -
124R MET* 3.5 14.2 - - + +
128R VAL* 3.5 4.7 - - - -
129R ALA* 3.2 48.5 + - + +
131R PHE* 3.9 6.5 - - + -
150R ILE* 3.4 44.0 - - + -
152R VAL* 5.7 0.2 - - + -
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Residues in contact with VAL 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q LEU* 4.9 4.9 - - + -
92Q VAL* 4.1 23.1 - - + -
127Q GLN* 5.7 2.2 - - + -
128Q VAL* 5.1 0.4 - - + -
62R LEU* 3.8 36.1 - - + -
70R PHE* 3.3 7.9 - - - -
71R LEU* 2.6 60.4 + - + +
90R LYS* 5.2 1.3 - - + -
91R VAL* 1.3 75.0 - - - +
93R ALA* 1.3 69.6 + - - +
94R LEU* 3.7 3.5 + - + +
127R GLN* 3.4 7.4 - - + +
128R VAL* 4.2 18.8 - - + -
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Residues in contact with ALA 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Q LEU* 5.1 1.0 - - - +
69R ASN 3.7 4.9 - - - +
70R PHE* 3.4 24.7 - - + -
91R VAL 3.9 0.8 + - - -
92R VAL* 1.3 74.1 - - - +
94R LEU* 1.3 60.0 + - - +
95R GLY 4.0 1.1 - - - +
97R VAL* 3.7 15.9 - - + -
124R MET* 3.6 23.1 - - - -
127R GLN* 2.6 45.2 + - - +
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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