Contacts of the strand formed by residues 133 - 138 (chain A) in PDB entry 2CUA
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 SER 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE 3.4 4.5 - - - +
106A LYS* 3.5 0.9 - - - -
107A ILE* 2.7 51.3 + - - +
125A VAL* 4.2 19.5 - - - -
126A GLU 2.6 30.1 + - - -
127A VAL* 3.8 5.1 - - - -
128A LEU* 4.5 4.2 + - - +
131A GLU* 4.0 1.2 + - - +
132A VAL* 1.3 73.5 - - - +
134A THR* 1.3 59.5 + - - +
135A VAL* 4.1 0.7 - - - -
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Residues in contact with THR 134 (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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48A GLY 6.1 2.9 - - - +
49A LYS* 3.8 6.5 - - - +
50A LEU 4.1 6.1 + - - -
104A VAL* 4.1 11.4 - - + -
105A PHE 3.3 3.4 - - - +
106A LYS* 2.5 39.9 + - - +
125A VAL* 5.4 0.5 - - - +
132A VAL* 3.8 3.6 + - - +
133A SER* 1.3 71.9 - - - +
135A VAL* 1.3 64.2 - - - +
136A ARG* 3.3 30.7 + - - +
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Residues in contact with VAL 135 (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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104A VAL* 3.7 0.7 - - - -
105A PHE* 2.7 56.6 + - + -
107A ILE* 4.2 9.2 - - + -
116A PHE* 4.9 0.7 - - + -
123A ILE* 3.7 27.8 - - + -
125A VAL* 3.3 46.9 - - + -
134A THR* 1.3 80.0 - - - +
136A ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 136 (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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47A ALA 6.0 0.6 - - - +
48A GLY* 5.1 7.1 - - - +
49A LYS* 2.7 38.1 - - - +
78A GLN* 5.1 3.6 - - - +
102A GLU* 3.4 26.9 - - - +
103A ILE 3.2 4.3 - - - +
104A VAL* 4.0 22.6 - - + +
123A ILE* 5.6 0.2 - - - +
134A THR* 3.3 21.1 + - - +
135A VAL* 1.3 76.1 - - - +
137A TYR* 1.3 69.1 + - - +
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Residues in contact with TYR 137 (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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102A GLU* 4.7 2.3 - - - +
103A ILE* 2.8 43.5 + - - +
105A PHE* 4.5 5.4 - - + -
120A GLY 5.0 0.7 + - - -
121A THR* 3.6 23.8 - - + +
122A ASN* 3.1 31.2 + - - -
123A ILE* 3.6 25.4 - - + -
136A ARG* 1.3 77.5 - - - +
138A THR* 1.3 90.2 + - - +
139A PHE* 3.7 41.9 + + + -
145A TYR* 6.0 0.2 - + - -
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Residues in contact with THR 138 (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 GLY* 3.6 33.7 - - - +
101A ALA 3.8 3.6 - - - +
102A GLU* 3.7 18.2 - - - +
137A TYR* 1.3 91.0 - - - +
139A PHE* 1.3 61.9 + - - +
140A LYS* 3.5 39.1 + - + +
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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