Contacts of the strand formed by residues 130 - 134 (chain D) in PDB entry 1THF
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 ASP 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D ASN* 3.3 20.0 + - - +
128D ALA* 4.0 5.6 - - - +
129D ILE* 1.3 75.2 + - - +
131D ALA* 1.3 59.9 + - - +
140D VAL* 3.6 6.1 - - - +
141D PHE 2.9 38.1 + - - +
142D THR* 5.9 0.3 - - - -
144D SER* 4.9 6.1 + - - -
145D GLY 4.6 8.1 + - - -
171D THR* 3.4 28.4 + - - +
173D ILE* 3.6 26.4 - - + +
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 4.8 1.6 - - + -
130D ASP* 1.3 76.1 - - - +
132D LYS* 1.3 70.3 + - - +
138D PHE* 5.1 0.4 - - + -
139D MET 3.2 15.0 - - - +
141D PHE* 4.6 0.9 - - - -
153D LEU* 4.1 28.0 - - + -
170D LEU* 5.1 0.7 - - + -
171D THR 3.1 6.9 + - - -
172D SER* 4.2 0.7 + - - -
173D ILE* 3.5 17.2 + - - +
174D ASP 4.9 0.2 + - - -
186D MET* 3.5 34.1 - - + +
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA* 1.3 80.7 - - - +
133D ARG* 1.3 67.2 + - - +
134D VAL* 3.5 4.1 + - + +
138D PHE* 3.5 6.7 - - - -
139D MET 2.9 28.5 + - - +
141D PHE* 3.7 32.3 - - + -
145D GLY 4.2 14.7 + - - -
172D SER* 5.9 0.2 - - - -
173D ILE* 3.6 32.0 - - + +
174D ASP* 2.9 39.9 + - - +
186D MET* 4.6 2.9 - - - -
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 1.3 74.4 - - - +
134D VAL* 1.3 60.0 + - - +
135D ASP 4.0 2.2 + - - -
136D GLY* 3.8 34.9 - - - +
137D GLU 3.6 5.6 - - - +
138D PHE* 3.9 23.1 - - + -
174D ASP* 4.6 5.0 + - - +
185D GLU* 2.5 50.0 + - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 3.8 4.5 - - + +
133D ARG* 1.3 75.0 - - - +
135D ASP* 1.3 80.6 + - + +
137D GLU* 2.8 23.3 + - - +
139D MET* 3.5 38.8 - - + +
141D PHE* 3.7 31.2 - - + -
148D ASN* 4.1 12.8 - - - +
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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