Contacts of the strand formed by residues 119 - 126 (chain R) in PDB entry 5FYW
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 GLU 119 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105R THR* 3.8 10.8 - - + +
106R LEU 2.8 12.6 - - - +
107R LEU* 3.3 35.5 - - + +
117R PRO 4.2 4.5 - - - +
118R HIS* 1.3 81.3 - - - +
120R TYR* 1.3 67.0 + - - +
226R PRO 3.6 12.8 - - - +
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Residues in contact with TYR 120 (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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74R PRO* 5.5 7.4 - - + -
76R PHE* 5.2 11.3 - + - -
77R LEU* 5.3 12.9 - - + +
105R THR* 2.2 42.5 + - - -
106R LEU* 2.8 32.8 + - + -
108R LEU* 3.4 29.1 - - + +
118R HIS* 3.1 38.7 + + + -
119R GLU* 1.3 77.9 - - - +
121R ASP* 1.3 56.4 + - - +
122R LEU* 5.4 0.3 - - - +
224R VAL* 4.1 19.1 - - + -
225R MET 3.2 7.6 - - - +
226R PRO* 3.2 41.3 - - + -
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Residues in contact with ASP 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R LYS* 5.8 4.1 - - - +
104R ILE 3.1 12.1 + - - +
105R THR* 3.2 21.5 + - - -
120R TYR* 1.3 75.7 - - - +
122R LEU* 1.3 56.0 + - - +
224R VAL* 5.0 0.2 - - - -
225R MET* 2.7 52.5 + - + +
226R PRO* 4.9 2.9 + - - +
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Residues in contact with LEU 122 (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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376Q LEU* 4.8 6.3 - - + -
69R TRP* 5.1 5.6 - - + -
71R VAL* 3.9 13.7 - - + -
95R ILE* 6.2 2.9 - - + -
104R ILE* 3.0 48.8 + - + +
105R THR* 5.7 0.2 - - - -
120R TYR 3.9 1.0 + - - +
121R ASP* 1.3 74.7 - - - +
123R GLU* 1.3 65.8 + - - +
124R LEU* 3.7 6.3 + - + +
222R CYS* 3.4 41.7 - - + -
223R GLN 3.5 13.9 - - - +
224R VAL* 3.8 26.9 - - + +
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Residues in contact with GLU 123 (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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121R ASP 4.1 1.6 + - - -
122R LEU* 1.3 85.7 - - - +
124R LEU* 1.3 60.9 + - - +
125R THR* 3.0 28.4 + - - +
222R CYS* 3.6 5.4 - - - -
223R GLN* 3.0 39.2 + - - +
225R MET* 4.0 25.2 - - + +
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Residues in contact with LEU 124 (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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69R TRP* 5.2 9.6 - - + -
102R SER* 5.0 27.1 - - - +
104R ILE* 5.4 9.9 - - + -
122R LEU* 3.7 10.9 + - + +
123R GLU* 1.3 72.3 - - - +
125R THR* 1.3 65.9 + - - +
126R LYS 3.6 1.7 - - - -
127R LYS* 3.4 33.7 + - + +
220R HIS* 3.1 34.3 - - + +
222R CYS* 5.1 0.2 - - - -
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Residues in contact with THR 125 (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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123R GLU* 3.0 21.1 + - - +
124R LEU* 1.3 75.5 - - - +
126R LYS* 1.3 61.9 + - + +
127R LYS 4.2 0.2 - - - -
221R GLU* 2.8 27.5 + - + -
222R CYS 4.0 0.9 - - - -
223R GLN* 2.8 33.0 + - + +
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Residues in contact with LYS 126 (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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570B VAL* 5.7 2.2 - - - +
573B GLN* 3.6 31.3 + - - +
125R THR* 1.3 81.8 + - + +
127R LYS* 1.3 61.1 + - - +
128R VAL* 3.1 29.1 + - + +
129R VAL* 3.5 21.7 - - + +
132R GLU* 5.2 6.7 - - - +
220R HIS* 2.7 25.7 + - - -
221R GLU* 3.5 19.8 + - + -
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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