Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 6B0Z
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 THR 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY* 1.3 75.6 + - - -
107A VAL* 1.3 67.5 + - - +
108A PHE* 3.6 28.0 - - + -
132A HIS 3.5 24.0 - - - +
133A HIS* 5.3 0.4 + - - -
191A ASP 4.5 0.3 + - - -
192A PHE* 3.6 39.2 - - + +
195A SER* 3.7 14.2 + - - -
294A VAL 3.6 0.7 - - - +
295A LEU* 3.4 3.9 - - - +
296A VAL* 2.6 36.2 + - - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.9 23.8 - - - +
105A GLY 5.5 0.2 - - - +
106A THR* 1.3 73.7 - - - +
108A PHE* 1.3 64.3 + - - +
109A ARG* 4.4 24.4 + - - +
130A ILE 3.8 1.0 - - - +
131A GLY* 3.2 21.0 - - - -
132A HIS 3.7 8.9 + - - +
293A SER* 3.3 26.9 - - - +
294A VAL 3.4 5.6 - - - +
295A LEU* 3.8 22.7 - - + -
306A GLU* 5.6 3.4 - - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 3.6 28.7 - - + -
107A VAL* 1.3 73.0 - - - +
109A ARG* 1.3 62.1 + - - +
110A GLU* 4.4 0.3 + - - +
129A ILE* 3.8 17.7 - - + -
130A ILE 3.3 4.7 - - - -
131A GLY* 3.5 27.6 - - - -
195A SER 3.9 13.9 - - - -
196A SER* 3.7 33.0 - - - -
199A MET* 3.5 25.1 - - + -
266A ILE* 3.9 18.4 - - + -
267A TRP 5.1 1.1 - - - -
268A ALA* 5.2 3.1 - - - -
292A THR* 4.2 0.7 - - - +
293A SER* 3.4 1.4 - - - -
294A VAL* 2.7 39.2 + - + +
296A VAL* 3.6 25.1 - - + -
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 4.4 20.8 + - + +
108A PHE* 1.3 76.4 - - - +
110A GLU* 1.3 61.2 + - - +
129A ILE* 3.3 6.7 - - - +
130A ILE 2.9 34.3 + - - +
132A HIS* 4.9 6.9 + - - +
277A GLN* 3.6 27.5 - - - +
278A SER* 4.0 13.8 - - - +
279A ASP* 3.7 22.1 + - - +
291A MET* 3.9 21.1 - - - -
292A THR 3.4 10.8 - - - +
293A SER* 4.3 11.2 + - - +
308A ALA* 4.1 17.8 + - - +
502A C81 3.6 17.1 - - + +
503A FLC 5.2 7.3 + - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE 5.6 0.7 - - - +
109A ARG* 1.3 76.0 - - - +
111A ALA* 1.3 72.0 + - - +
112A ILE* 4.8 1.6 - - + +
127A PRO* 3.4 25.5 - - + +
128A ILE 3.9 5.4 - - - +
129A ILE* 3.5 34.4 - - + +
203A LYS* 3.4 21.1 + - - -
205A TRP* 4.1 2.3 - - - -
290A MET 4.0 0.2 - - - +
291A MET* 3.7 4.0 - - - -
292A THR* 3.0 42.2 + - + +
338A ARG* 3.2 28.5 + - - +
502A C81 4.1 1.1 - - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 1.3 78.7 - - - +
112A ILE* 1.3 66.4 + - - +
113A ILE* 4.3 1.5 - - + +
127A PRO* 3.3 25.6 - - - +
287A SER* 6.1 1.3 - - - +
290A MET* 3.6 7.2 - - + +
291A MET* 4.4 7.9 - - + +
502A C81 3.3 55.9 + - + +
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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