Contacts of the strand formed by residues 129 - 134 (chain X) in PDB entry 2AW2
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 129 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ILE* 4.6 8.7 - - + +
44X SER* 2.8 29.7 + - - -
46X HIS* 3.2 20.1 - - - +
56X LEU* 3.6 36.6 - - + -
71X TRP* 4.2 13.0 - - + -
112X SER* 3.4 1.0 - - - -
113X TYR* 2.8 41.1 + - + +
127X HIS 3.9 1.4 + - - -
128X SER* 1.3 73.2 - - - +
130X THR* 1.3 62.1 + - - +
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Residues in contact with THR 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X SER 3.1 13.7 + - - -
45X GLU* 3.4 4.0 - - - +
46X HIS 3.0 26.6 + - - +
110X ASN* 5.9 0.2 - - - +
111X GLY* 3.5 11.0 - - - +
112X SER* 3.0 24.3 + - - +
128X SER* 4.6 4.5 + - - -
129X THR* 1.3 73.9 + - - +
131X LEU* 1.3 65.8 + - - +
132X TYR* 3.5 41.2 + - + +
5Y LYS* 5.4 5.2 - - - -
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Residues in contact with LEU 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X HIS* 3.5 15.0 - - + -
48X ILE* 4.1 13.9 - - + -
54X PHE* 3.6 29.4 - - + -
56X LEU* 3.8 15.5 - - + -
102X PHE* 3.5 32.1 - - + -
109X ASP* 3.9 10.8 - - + +
110X ASN* 3.2 8.3 - - - +
111X GLY* 2.8 32.0 + - - +
113X TYR* 3.4 30.1 - - + -
129X THR 5.4 0.2 - - - +
130X THR* 1.3 72.1 - - - +
132X TYR* 1.3 62.2 + - - +
133X VAL* 3.8 8.5 - - + -
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Residues in contact with TYR 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 6.1 1.1 - - - -
45X GLU* 3.9 33.0 + - + -
46X HIS 2.9 15.4 + - - +
47X SER* 3.4 14.6 - - - +
48X ILE 3.0 25.3 + - - +
110X ASN* 3.6 11.4 - - - -
130X THR* 3.5 35.9 + - + +
131X LEU* 1.3 69.8 - - - +
133X VAL* 1.3 61.0 + - - +
134X THR* 4.2 1.2 + - - +
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Residues in contact with VAL 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X ILE* 3.5 23.1 - - + +
50X ALA* 4.0 13.5 - - + +
105X VAL* 3.8 15.0 - - + -
106X LEU 3.9 16.4 - - - +
107X PRO* 3.9 22.1 - - + +
109X ASP* 4.2 2.0 - - + -
110X ASN* 3.6 36.0 + - + +
131X LEU* 4.4 4.5 - - + +
132X TYR* 1.3 75.9 - - - +
134X THR* 1.3 74.2 + - - +
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Residues in contact with THR 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X SER* 6.4 0.9 - - - -
48X ILE 3.1 17.3 + - - +
49X LEU* 3.4 22.9 - - + +
50X ALA* 3.0 24.1 + - - +
132X TYR 5.2 1.3 - - - +
133X VAL* 1.3 78.1 - - - +
135X ASP* 1.3 65.2 + - - +
136X VAL* 4.0 9.7 + - + +
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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