Contacts of the strand formed by residues 127 - 136 (chain D) in PDB entry 1L9X
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 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D LEU* 1.3 75.5 + - - +
128D ALA* 1.3 72.3 + - - +
129D THR* 3.4 2.5 + - - +
173D TRP* 3.3 5.8 - - - -
174D SER 2.8 34.6 + - - -
176D SER* 3.6 17.4 + - - -
179D ASN* 3.5 19.9 + - - -
201D ILE* 4.0 34.1 - - + -
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Residues in contact with ALA 128 (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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127D THR* 1.3 79.7 - - - +
129D THR* 1.3 65.0 + - - +
172D LYS 3.4 9.9 - - - +
173D TRP* 3.4 28.5 - - + -
198D ASP* 4.4 0.7 - - - +
201D ILE* 4.2 8.3 - - - +
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Residues in contact with THR 129 (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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127D THR 3.4 6.3 + - - +
128D ALA* 1.3 80.6 - - - +
130D ASP* 1.3 58.4 + - - +
131D THR* 2.7 40.1 + - - -
132D VAL* 4.8 1.6 + - - +
171D HIS* 3.9 1.2 + - - +
172D LYS* 2.9 21.9 + - - +
174D SER* 2.7 30.9 + - - +
198D ASP* 3.3 13.0 - - - +
201D ILE* 4.0 23.1 - - + -
203D PHE* 4.1 7.6 - - + -
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Residues in contact with ASP 130 (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 THR* 1.3 67.4 - - - +
131D THR* 1.3 63.0 + - - +
132D VAL* 3.7 4.1 + - - +
134D VAL* 4.4 6.4 - - - +
198D ASP* 2.9 29.2 + - + +
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Residues in contact with THR 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 THR* 2.7 26.8 + - - +
130D ASP* 1.3 78.8 - - - +
132D VAL* 1.3 59.4 + - - +
134D VAL* 3.8 10.1 - - + -
136D MET* 4.2 13.0 - - + -
169D ASN* 3.3 16.5 - - - +
171D HIS* 2.6 53.6 + - - -
198D ASP* 4.2 6.7 - - + -
203D PHE* 3.7 33.9 - - + -
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Residues in contact with VAL 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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129D THR 5.1 1.1 - - - +
130D ASP* 3.7 5.2 + - - +
131D THR* 1.3 76.4 - - - +
133D ASP* 1.3 78.6 + - + +
134D VAL* 4.4 2.1 - - - +
169D ASN 4.1 0.2 - - - -
170D PHE* 4.9 8.5 - - + -
171D HIS 3.7 17.5 - - - +
172D LYS* 3.3 42.2 - - + -
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Residues in contact with ASP 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 VAL* 1.3 85.0 - - + +
134D VAL* 1.3 59.6 + - - +
169D ASN 3.0 8.5 + - - -
170D PHE* 3.3 31.7 - - + -
231D LEU* 3.3 20.9 - - - +
232D ASP* 3.5 16.8 + - - +
233D GLY* 2.8 29.9 + - - -
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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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130D ASP 4.4 5.2 - - - +
131D THR* 3.8 32.5 - - - -
132D VAL 4.4 2.0 - - - +
133D ASP* 1.3 77.8 - - - +
135D ALA* 1.3 72.1 + - - +
136D MET* 4.1 16.4 - - + -
169D ASN* 3.0 34.3 + - + +
232D ASP 4.9 0.7 - - - -
233D GLY* 3.3 7.4 - - - -
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Residues in contact with ALA 135 (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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134D VAL* 1.3 79.6 - - - +
136D MET* 1.3 61.7 + - - +
137D PRO* 4.7 0.2 - - - +
165D PRO* 3.4 38.8 - - + +
167D THR 3.3 8.1 - - - +
232D ASP 4.1 8.1 + - - +
233D GLY* 3.6 22.4 - - - +
235D SER* 4.3 11.4 - - - -
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Residues in contact with MET 136 (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 THR* 4.2 16.8 - - + -
134D VAL* 3.9 17.7 - - + +
135D ALA* 1.3 79.3 - - - +
137D PRO* 1.3 76.5 - - + +
165D PRO* 3.8 5.2 - - - -
166D LEU 3.2 1.4 + - - -
167D THR* 2.6 45.5 + - - +
169D ASN* 3.5 36.1 - - - +
196D ASN* 3.9 20.6 - - + +
197D THR 3.3 28.7 - - - +
198D ASP* 4.9 2.2 - - - +
203D PHE* 4.3 5.8 - - + -
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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