Contacts of the strand formed by residues 145 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B THR* 3.2 3.1 - - - -
142B ALA* 2.9 39.4 + - + +
144B TYR* 1.3 85.5 - - + +
146B GLY* 1.3 59.4 + - - +
390B THR* 3.5 8.6 - - - +
418B LEU 3.4 14.6 - - - +
419B ASN* 3.8 8.3 - - + +
420B LYS* 3.6 28.5 - - + +
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Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLY 3.1 14.4 - - - -
141B THR* 4.1 0.9 - - - -
145B LEU* 1.3 77.1 - - - +
147B GLN* 1.3 67.8 + - - +
390B THR* 4.8 0.2 - - - -
394B ILE* 3.7 20.4 - - - -
417B PHE* 3.7 2.4 - - - +
418B LEU* 2.8 31.6 + - - +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ARG* 6.2 0.7 - - - +
138B GLU 4.6 0.4 - - - +
139B SER* 3.3 4.4 - - - -
140B GLY* 3.0 38.3 + - - +
146B GLY* 1.3 78.2 - - - +
148B VAL* 1.3 71.2 + - - +
394B ILE* 3.8 3.1 - - - +
415B THR* 5.2 3.3 - - + +
416B ILE 3.1 11.9 - - - +
417B PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.7 25.1 - - + -
138B GLU 3.5 4.0 - - - -
139B SER* 3.8 4.9 - - - +
147B GLN* 1.3 82.9 - - - +
149B THR* 1.3 66.1 + - - +
394B ILE* 3.5 37.7 - - + +
397B LEU* 4.1 16.2 - - + -
398B ILE* 4.1 6.7 - - + -
401B GLU* 4.2 20.9 - - + -
414B ARG 3.7 1.5 - - - +
415B THR* 3.1 6.7 - - - +
416B ILE* 2.8 36.6 + - + +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ILE* 3.3 6.7 - - - +
138B GLU* 2.8 51.9 + - + +
148B VAL* 1.3 79.9 - - - +
150B THR* 1.3 69.6 + - - +
151B ILE* 4.7 8.5 - - + -
159B TYR* 6.2 1.6 - - + -
414B ARG 4.1 5.4 - - - -
415B THR* 2.7 27.3 + - - -
434B LEU* 3.6 9.2 - - - +
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PRO* 5.3 0.7 - - + -
136B LEU 3.5 5.8 - - - +
137B ILE* 4.2 3.1 - - - +
149B THR* 1.3 82.0 + - - +
151B ILE* 1.3 71.2 + - - +
152B LYS 4.7 0.2 - - - +
156B THR* 3.5 12.4 + - + +
157B GLU 4.5 0.7 - - - +
401B GLU* 4.2 13.0 + - - +
405B ILE* 3.7 32.4 - - + +
410B ILE* 4.0 26.9 - - + -
413B CYS* 3.9 13.5 - - - +
414B ARG 4.6 0.6 + - - -
434B LEU* 3.9 26.3 - - + +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASN* 3.8 11.0 - - - +
129B CYS* 6.1 1.1 - - + -
130B LEU* 4.6 11.4 - - + -
134B VAL 4.2 1.9 - - - +
135B PRO* 3.7 2.6 - - - +
136B LEU* 2.6 61.1 + - + +
138B GLU* 4.2 15.3 - - + -
149B THR* 4.7 10.1 - - + -
150B THR* 1.3 80.0 - - - +
152B LYS* 1.3 63.8 + - - +
153B LYS 5.1 0.2 - - - +
156B THR* 3.4 2.7 - - - -
157B GLU 3.8 16.8 - - - +
158B CYS* 3.8 12.1 - - + -
159B TYR* 3.3 37.7 - - + +
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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