Contacts of the strand formed by residues 131 - 134 (chain A) in PDB entry 1UFU
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 PHE 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PRO* 4.6 0.9 - - + -
122A CYS* 3.2 38.1 - - + -
124A SER* 3.8 31.0 - - - -
128A PHE* 3.4 33.4 - + + -
129A ASP 5.2 0.2 - - - -
130A GLY* 1.3 77.8 - - - -
132A ILE* 1.3 66.8 + - - +
146A ASN* 3.7 1.3 + - - +
147A SER* 3.0 33.1 + - - -
154A SER 4.2 2.0 - - - -
155A SER* 3.9 12.6 - - - -
156A ARG* 4.1 15.7 - - - -
157A ALA* 3.6 30.1 - - + -
159A PHE* 3.5 6.9 - - + -
175A TYR 3.3 11.7 - - - +
176A ALA* 3.9 11.4 - - + -
177A TYR* 3.9 1.6 + - - -
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Residues in contact with ILE 132 (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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131A PHE* 1.3 73.2 - - - +
133A LEU* 1.3 62.3 + - - +
134A CYS* 4.0 6.3 - - - -
144A CYS* 3.5 27.6 - - + -
145A LEU* 3.6 1.8 - - - +
146A ASN* 3.2 52.3 - - - +
159A PHE* 4.3 1.1 - - - -
174A CYS* 2.9 8.4 - - - +
175A TYR* 2.7 43.4 + - + -
177A TYR* 3.6 20.2 - - + -
185A TRP* 3.8 33.0 - - + -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.3 14.1 - - + -
120A LEU* 3.6 21.8 - - + -
132A ILE* 1.3 74.7 - - - +
134A CYS* 1.3 57.9 + - - +
135A LYS* 3.9 0.4 + - + -
144A CYS* 3.0 21.4 - - - -
145A LEU* 3.0 26.8 + - + +
159A PHE* 3.2 52.7 - - + -
160A SER 5.2 1.8 - - - +
161A VAL* 5.7 0.9 - - + -
172A TYR* 3.5 39.9 - - + -
173A ARG 3.5 8.1 - - - +
174A CYS* 4.1 2.0 - - + +
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Residues in contact with CYS 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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15A VAL* 5.1 4.0 - - - -
132A ILE* 4.0 10.5 - - - -
133A LEU* 1.3 71.0 - - - +
135A LYS* 1.3 60.3 + - - +
136A GLU* 2.9 21.5 + - - +
144A CYS* 2.0 47.8 - - - -
172A TYR* 3.6 2.2 - - - -
173A ARG 2.6 34.1 + - - +
175A TYR* 4.0 20.0 - - + -
185A TRP* 4.1 7.2 - - - -
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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