Contacts of the strand formed by residues 106 - 112 (chain C) in PDB entry 2X06
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 VAL 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C ALA* 3.8 7.5 - - - +
100C LYS 4.1 1.0 - - - +
101C ALA* 3.9 5.6 - - - -
104C VAL* 3.4 19.2 - - - +
105C GLY* 1.3 78.5 - - - +
107C GLY* 1.3 66.8 + - - +
108C VAL* 4.3 13.0 - - + -
265C ILE* 4.5 2.2 - - + -
266C ALA 3.4 13.7 - - - +
267C ILE* 3.8 17.7 - - + -
75D ALA* 3.5 26.9 - - + +
76D THR* 3.8 10.1 - - + -
106D VAL* 4.1 11.2 - - + -
108D VAL* 3.9 26.0 - - + -
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Residues in contact with GLY 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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75C ALA 3.3 8.3 - - - -
97C ALA* 3.5 23.6 - - - +
100C LYS* 4.0 7.2 - - - -
101C ALA* 3.8 3.4 - - - +
106C VAL* 1.3 75.1 - - - +
108C VAL* 1.3 65.3 + - - +
265C ILE* 3.4 4.2 - - - +
266C ALA 2.9 33.0 + - - +
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Residues in contact with VAL 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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75C ALA 2.9 9.0 + - - +
76C THR* 3.1 26.6 - - + -
77C ALA 3.2 3.6 + - - +
106C VAL* 4.3 3.8 - - + -
107C GLY* 1.3 78.6 - - - +
109C VAL* 1.3 65.7 + - - +
110C ALA 4.3 0.2 - - - -
263C LEU* 3.5 28.9 - - + -
264C PHE 3.4 3.4 - - - -
265C ILE* 4.0 27.4 - - + -
106D VAL* 4.0 28.9 - - + -
267D ILE* 5.0 10.1 - - + -
272D PHE* 3.7 19.7 - - + -
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Residues in contact with VAL 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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77C ALA* 3.3 19.1 - - + +
79C ILE* 4.0 14.6 - - + -
93C ALA* 3.7 42.4 - - + +
96C LEU* 4.1 14.1 - - + -
97C ALA* 3.8 18.6 - - + +
100C LYS* 4.9 3.1 - - + -
108C VAL* 1.3 82.0 - - - +
110C ALA* 1.3 68.6 + - - +
263C LEU* 3.4 4.4 - - - +
264C PHE* 2.8 43.6 + - + +
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Residues in contact with ALA 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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77C ALA 3.1 6.8 + - - +
78C VAL* 3.3 5.5 - - + -
79C ILE 2.9 24.6 + - - -
109C VAL* 1.3 77.5 - - - +
111C THR* 1.3 63.2 + - - +
237C SER 5.3 0.2 - - - +
239C ILE* 3.9 3.1 - - + +
240C GLY* 3.4 32.3 - - - +
262C ASP 3.4 7.6 - - - +
263C LEU* 3.8 15.2 - - + +
272D PHE* 3.8 16.0 - - + -
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Residues in contact with THR 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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78C VAL* 5.4 0.2 - - - -
79C ILE* 3.2 11.9 - - + -
89C VAL* 4.4 15.4 - - + +
90C GLY* 5.6 0.4 - - - -
93C ALA* 3.9 13.9 - - + -
109C VAL* 4.8 0.4 - - + -
110C ALA* 1.3 80.0 - - - +
112C ARG* 1.3 66.5 + - - +
114C ALA* 4.4 5.9 - - - +
237C SER 4.6 1.4 - - - +
240C GLY* 4.5 7.9 - - - -
242C ALA* 4.5 1.6 - - - +
260C LYS* 4.4 5.4 + - - -
261C GLY* 3.7 5.4 - - - -
262C ASP* 2.2 53.1 + - - +
264C PHE* 3.3 28.3 - - + -
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Residues in contact with ARG 112 (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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70C VAL* 3.9 27.6 - - - +
71C LYS* 6.0 1.8 - - - +
78C VAL* 4.2 3.4 - - + +
79C ILE 3.0 12.3 + - - +
80C ASP* 3.4 27.2 + - - +
81C GLY* 2.7 31.2 + - - -
111C THR* 1.3 79.0 + - - +
113C ASN* 1.3 76.4 + - - +
114C ALA* 3.2 5.5 + - - +
240C GLY 2.9 29.0 + - - +
241C GLY* 4.2 13.7 + - - +
242C ALA* 4.2 14.4 - - + +
260C LYS 4.4 8.3 - - - -
272D PHE 5.9 0.6 + - - -
273D MSE 5.6 5.5 - - - +
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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