Contacts of the strand formed by residues 128 - 133 (chain J) in PDB entry 6O85
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 LEU 128 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121J PHE* 4.9 0.2 - - - -
126J ALA* 3.5 3.0 - - - +
127J SER* 1.3 81.4 - - - +
129J ALA* 1.3 63.7 + - - +
130J MET* 4.2 28.7 - - + -
205J TYR* 5.0 11.2 - - + -
206J CYS 3.3 10.5 - - - +
207J LEU* 4.2 24.0 - - + -
211J ILE* 5.6 5.2 - - + -
228J LEU* 4.1 32.5 - - + +
229J ILE* 5.3 6.3 - - + -
232J LEU* 5.8 4.0 - - + -
262J ASP 3.6 2.9 + - - +
263J ILE* 3.3 30.9 - - + +
264J TYR 2.9 23.9 + - - -
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Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J VAL* 3.6 32.7 - - + +
120J LEU* 4.8 1.6 - - + -
121J PHE* 4.1 24.0 - - + +
126J ALA* 4.8 1.1 - - + -
128J LEU* 1.3 76.4 - - - +
130J MET* 1.3 61.6 - - - +
205J TYR* 3.5 4.5 - - - -
206J CYS* 3.1 28.4 + - + +
264J TYR* 3.1 17.5 - - + +
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Residues in contact with MET 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J VAL* 3.9 7.4 - - - +
128J LEU* 4.2 15.5 - - + -
129J ALA* 1.3 75.6 - - - +
131J LEU* 1.3 61.3 - - - +
132J MET* 3.7 23.6 - - + -
167J LEU* 3.9 19.3 - - + -
170J MET* 4.8 17.3 - - + +
201J ASP* 3.4 30.3 - - - +
204J LEU 3.4 5.6 - - - -
205J TYR* 3.7 26.5 - - + -
229J ILE* 5.6 4.9 - - + -
264J TYR 2.9 14.4 + - - +
265J SER* 3.1 16.7 - - - +
266J PHE 2.9 24.4 + - - -
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Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J THR* 4.5 9.6 - - + +
112J VAL* 4.1 24.0 - - + -
114J LEU* 6.2 1.8 - - + -
117J VAL* 3.8 18.2 - - + -
130J MET* 1.3 76.9 - - - +
132J MET* 1.3 74.5 + - - +
133J ARG* 5.9 1.1 - - + -
201J ASP* 3.8 4.9 - - - +
202J ALA* 3.4 35.3 + - + +
203J HIS 4.5 0.9 + - - -
204J LEU* 3.6 33.7 + - + -
266J PHE* 3.4 38.6 - - + +
268J LYS* 4.1 9.6 - - + -
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Residues in contact with MET 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J MET* 3.7 33.9 - - + -
131J LEU* 1.3 84.9 - - - +
133J ARG* 1.3 62.2 + - - +
158J ILE* 3.7 46.4 - - + -
167J LEU* 5.2 4.0 - - + -
170J MET* 5.1 6.7 - - + -
199J LEU* 3.8 31.0 - - + -
200J VAL 3.5 19.1 - - - +
201J ASP* 4.6 3.1 - - + -
202J ALA* 4.7 2.0 - - - +
265J SER* 4.2 15.0 - - - +
266J PHE 2.9 10.2 + - - +
267J ILE* 4.4 1.8 - - - -
268J LYS 2.9 25.2 + - - -
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Residues in contact with ARG 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J VAL* 5.5 4.3 - - + -
131J LEU* 5.9 1.3 - - + -
132J MET* 1.3 77.8 - - - +
134J LYS* 1.3 63.9 + - - +
199J LEU* 3.5 4.7 - - - -
200J VAL* 3.4 32.5 + - + +
202J ALA* 5.3 6.6 - - + +
268J LYS* 3.9 14.6 - - + +
271J ASN 3.3 25.8 - - - +
272J THR* 4.1 11.0 - - - -
273J LEU 5.0 2.2 - - - +
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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