Contacts of the strand formed by residues 106 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C GLY* 1.3 74.4 - - - -
107C VAL* 1.3 65.0 + - - +
108C PHE* 3.7 22.3 - - + -
132C HIS 3.3 21.8 - - - +
133C HIS* 3.7 4.5 + - - -
134C ALA 4.3 0.9 - - - +
191C ASP 4.2 0.3 - - - -
192C PHE* 3.3 50.6 + - + -
195C SER* 3.7 18.9 + - - -
295C LEU* 3.9 0.4 - - - -
296C VAL* 2.8 35.7 + - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 4.3 17.5 - - - +
106C THR* 1.3 72.1 - - - +
108C PHE* 1.3 62.3 + - - +
109C ARG* 4.2 6.5 - - + +
131C GLY* 3.7 0.3 - - - -
132C HIS* 3.2 56.0 + - + +
134C ALA* 3.6 28.9 - - + -
293C SER* 3.1 27.1 - - - +
294C VAL 3.6 8.1 - - - +
295C LEU* 3.7 15.7 - - + +
306C GLU* 6.1 0.7 - - - +
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Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR* 3.7 31.4 - - + -
107C VAL* 1.3 72.3 - - - +
109C ARG* 1.3 62.4 + - - +
110C GLU* 5.5 0.2 - - - +
129C ILE* 3.7 24.0 - - + -
130C ILE 3.2 4.3 - - - -
131C GLY* 3.6 25.8 - - - -
195C SER* 3.6 27.4 - - - -
196C SER* 3.7 16.8 - - - -
199C MET* 3.8 20.2 - - + -
266C ILE* 4.0 16.4 - - + -
268C ALA* 6.0 0.2 - - + -
292C THR 4.1 0.2 - - - +
293C SER* 3.4 4.5 + - - -
294C VAL* 3.0 37.7 + - + +
296C VAL* 3.6 28.7 - - + -
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 4.9 4.3 - - + +
108C PHE* 1.3 76.6 - - - +
110C GLU* 1.3 61.1 + - - +
129C ILE* 3.2 9.2 - - - +
130C ILE* 2.9 34.1 + - + +
132C HIS* 2.9 39.4 + - - +
272C TYR* 4.5 5.4 - - - -
274C GLY* 3.7 19.9 - - - -
275C ASP* 4.4 1.4 - - - +
278C SER* 3.5 22.7 - - - +
279C ASP* 2.9 38.0 + - - -
291C MET* 4.6 4.7 - - + -
292C THR 3.4 8.1 - - - +
293C SER* 4.5 13.1 - - - +
308C ALA* 4.9 7.4 + - - +
502C C81 3.5 17.7 - - + +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE 4.3 0.6 + - - +
109C ARG* 1.3 77.3 - - - +
111C ALA* 1.3 72.3 + - - +
112C ILE* 4.0 0.3 + - - +
127C PRO* 3.8 22.0 - - + +
128C ILE 4.0 4.3 - - - +
129C ILE* 3.3 36.3 - - + +
203C LYS* 3.2 23.3 + - - +
205C TRP* 4.2 0.3 - - - -
291C MET* 4.0 3.8 - - - -
292C THR* 2.9 45.1 + - + +
338C ARG* 3.4 28.3 + - - +
502C C81 3.9 0.6 - - - +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU* 1.3 78.4 - - - +
112C ILE* 1.3 65.9 + - - +
113C ILE* 4.5 1.7 - - + +
127C PRO* 3.4 25.5 - - - +
128C ILE 4.4 0.2 + - - -
287C SER* 6.6 0.4 - - - -
290C MET* 3.2 10.8 - - + +
291C MET* 3.8 15.2 - - + -
502C C81 3.4 48.0 + - + +
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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