Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 2ZUC
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 MET 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A THR* 1.3 76.7 + - - +
110A THR* 1.3 64.0 + - - +
237A LEU* 4.0 40.6 - - + +
240A LEU* 4.7 8.3 - - - -
241A THR* 4.1 32.9 - - + +
244A ALA* 5.0 0.2 - - - +
251A VAL* 3.2 20.2 - - + +
253A ILE* 4.2 26.0 - - + -
280A VAL* 4.2 3.6 - - + -
281A PRO* 3.2 38.4 - - + -
282A GLY* 3.5 7.6 + - - +
283A ILE 3.2 21.5 + - - +
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Residues in contact with THR 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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100A LEU* 4.9 6.7 - - + -
104A ILE* 4.3 17.1 - - + +
105A GLU 5.1 1.4 + - - -
108A THR* 4.2 12.0 + - - +
109A MET* 1.3 76.4 - - - +
111A GLU* 1.3 66.7 + - - +
112A PHE* 4.2 24.0 - - + -
251A VAL 2.8 10.2 + - - -
252A ILE* 3.4 12.5 - - - +
253A ILE* 2.9 28.0 + - - +
283A ILE* 3.5 27.9 - - + +
285A ILE* 4.5 4.3 - - + -
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Residues in contact with GLU 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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109A MET* 5.0 0.2 - - - +
110A THR* 1.3 76.0 - - - +
112A PHE* 1.3 68.5 + - - +
113A PHE* 3.3 21.4 - - - +
253A ILE* 3.2 29.8 - - + +
255A ASN* 3.1 33.2 - - + +
281A PRO* 3.7 18.1 - - + +
283A ILE 2.7 16.9 + - - +
284A ARG* 3.2 26.8 + - - -
285A ILE* 2.7 35.3 + - - +
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Residues in contact with PHE 112 (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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96A LEU* 5.3 4.9 - - + -
100A LEU* 4.7 10.1 - - + -
104A ILE* 4.5 17.0 - - + -
110A THR* 4.2 17.7 - - + -
111A GLU* 1.3 73.9 - - - +
113A PHE* 1.3 61.1 + - - +
120A LYS* 4.3 3.3 - - + +
123A LEU* 3.4 37.9 - - + -
124A CYS* 6.0 0.4 - - - -
127A LEU* 4.6 6.1 - - + -
252A ILE* 4.1 27.1 - - + -
253A ILE 3.0 6.5 + - - -
254A THR* 3.1 21.0 - - + -
255A ASN 3.1 20.3 + - - +
285A ILE* 3.2 42.6 - - + +
287A LEU* 4.2 21.5 - - + -
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Residues in contact with PHE 113 (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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111A GLU* 3.3 33.0 - - + +
112A PHE* 1.3 73.9 - - - +
114A GLY* 1.3 58.6 + - - +
120A LYS* 4.7 2.5 - - - -
255A ASN* 3.0 20.6 - - + +
257A VAL* 3.6 22.4 - - + -
284A ARG* 4.0 31.4 - - + -
285A ILE 3.1 21.6 + - - -
286A GLN* 3.4 24.9 - - + +
287A LEU* 2.8 27.0 + - - +
300A VAL* 3.3 33.4 - - + -
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Residues in contact with GLY 114 (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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113A PHE* 1.3 78.8 - - - +
115A GLU* 1.3 72.5 + - - +
118A SER* 3.5 4.3 - - - -
120A LYS* 3.1 15.8 + - - +
255A ASN 3.3 4.0 + - - -
256A GLN* 3.8 0.7 - - - -
257A VAL* 3.5 25.4 + - - +
286A GLN* 5.0 3.4 - - - -
287A LEU 3.5 14.4 - - - -
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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