Contacts of the strand formed by residues 145 - 151 (chain D) in PDB entry 1Y8Q
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 LEU 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D THR* 3.3 2.9 - - - -
142D ALA* 2.8 41.5 + - + +
144D TYR* 1.3 83.7 - - + +
146D GLY* 1.3 60.3 + - - +
390D THR* 3.5 9.0 - - - +
418D LEU* 3.3 15.9 - - - +
419D ASN* 3.7 5.6 - - + +
420D LYS* 3.6 29.4 - - + +
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Residues in contact with GLY 146 (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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140D GLY 3.1 13.5 - - - -
141D THR* 4.1 0.9 - - - -
145D LEU* 1.3 77.3 - - - +
147D GLN* 1.3 67.9 + - - +
394D ILE* 4.0 14.8 - - - -
417D PHE* 3.7 3.1 - - - +
418D LEU* 2.9 34.0 + - - +
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Residues in contact with GLN 147 (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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138D GLU 4.6 0.2 - - - -
139D SER* 3.3 6.8 - - - -
140D GLY* 3.0 34.9 + - - +
146D GLY* 1.3 77.5 + - - +
148D VAL* 1.3 69.4 + - - +
149D THR* 5.8 4.9 - - + +
164D LYS* 3.7 30.1 + - - +
394D ILE* 4.0 4.3 - - - +
397D LEU* 6.3 0.4 - - - -
415D THR* 4.7 6.1 - - + +
416D ILE 3.2 13.7 - - - +
417D PHE* 3.6 35.0 - - + -
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Residues in contact with VAL 148 (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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137D ILE* 3.7 25.1 - - + -
138D GLU 3.5 4.7 - - - -
139D SER* 3.8 3.6 - - - +
147D GLN* 1.3 81.6 - - - +
149D THR* 1.3 67.3 + - - +
394D ILE* 3.7 36.3 - - + +
397D LEU* 4.0 17.5 - - + +
398D ILE* 4.0 6.3 - - + +
401D GLU* 4.1 22.9 - - + -
414D ARG 4.5 0.4 - - - -
415D THR* 3.2 7.7 - - - +
416D ILE* 3.0 36.2 + - + +
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Residues in contact with THR 149 (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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137D ILE* 3.3 8.7 - - - +
138D GLU* 2.9 55.4 + - + +
147D GLN* 5.8 3.8 - - - +
148D VAL* 1.3 79.6 - - - +
150D THR* 1.3 72.0 + - - +
151D ILE* 4.8 7.6 - - + -
159D TYR* 6.2 0.4 - - + -
401D GLU* 6.2 0.2 - - - -
414D ARG 4.2 7.0 - - - -
415D THR* 2.8 25.9 + - - -
434D LEU* 3.7 6.6 - - - +
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Residues in contact with THR 150 (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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135D PRO* 5.2 0.7 - - + -
136D LEU 3.5 6.7 - - - +
137D ILE* 4.3 5.6 - - - +
149D THR* 1.3 83.2 + - - +
151D ILE* 1.3 77.3 + - - +
152D LYS* 4.8 4.0 - - + +
156D THR* 3.3 15.7 + - + -
157D GLU 4.4 1.0 - - - +
401D GLU* 4.0 19.6 + - - +
405D ILE* 3.6 35.4 - - + +
410D ILE* 4.8 11.2 - - + -
413D CYS* 4.0 2.5 - - - +
414D ARG 4.8 0.6 + - - -
434D LEU* 4.1 28.2 - - + +
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Residues in contact with ILE 151 (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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126D ASN* 3.9 11.4 - - - +
129D CYS* 6.1 1.1 - - + -
130D LEU* 4.4 12.3 - - + -
134D VAL 4.4 1.4 - - - +
135D PRO* 3.6 3.1 - - - +
136D LEU* 2.7 59.5 + - + +
138D GLU* 4.1 17.7 - - + -
149D THR* 4.8 6.5 - - + -
150D THR* 1.3 81.7 - - - +
152D LYS* 1.3 66.6 + - - +
156D THR* 3.4 2.9 - - - -
157D GLU 3.8 8.7 - - - +
158D CYS* 3.6 22.2 - - + -
159D TYR* 3.3 37.2 - - + +
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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