Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 1YA8
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 3.9 17.7 - - + -
125B ALA* 3.8 26.0 - - + +
131B ASN* 4.5 11.0 - - + +
132B ARG* 1.3 79.6 - - - +
134B PRO* 1.3 79.2 - - + +
135B VAL* 3.3 0.3 + - - +
162B ASN* 3.0 41.7 - - - +
164B VAL* 4.1 6.1 - - + -
209B GLY 2.8 19.7 + - - +
210B GLY* 3.5 4.2 - - - -
211B ASN* 2.9 20.0 + - - -
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Residues in contact with PRO 134 (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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132B ARG 3.9 3.1 - - - +
133B LEU* 1.3 88.5 - - + +
135B VAL* 1.3 60.2 + - - +
136B MET* 5.4 0.2 - - - -
162B ASN 4.2 6.1 - - - +
163B VAL* 3.5 25.6 - - + +
164B VAL 3.0 22.5 + - - -
211B ASN* 5.7 0.2 - - - -
214B SER* 3.7 28.0 - - - +
504B ALA* 4.3 16.2 - - + +
505B ARG* 3.7 28.3 - - + +
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Residues in contact with VAL 135 (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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133B LEU 3.6 13.7 - - - +
134B PRO* 1.3 74.9 - - - +
136B MET* 1.3 66.0 + - - +
137B VAL* 4.1 12.6 - - + -
164B VAL* 3.5 15.9 - - + +
166B VAL* 3.9 15.3 - - + -
201B VAL* 4.6 3.8 - - + -
205B ILE* 3.8 33.7 - - + -
210B GLY* 3.9 2.5 - - - -
211B ASN 3.6 25.4 - - - +
214B SER 3.0 8.8 + - - +
215B VAL* 4.3 9.0 - - + -
216B THR* 2.8 27.9 + - - -
504B ALA* 5.2 0.2 - - - +
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Residues in contact with MET 136 (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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134B PRO 4.2 0.2 + - - -
135B VAL* 1.3 78.2 - - - +
137B VAL* 1.3 60.9 + - - +
157B LEU* 4.6 9.9 - - + -
163B VAL* 4.3 23.8 - - + -
164B VAL 2.9 13.2 + - - +
165B VAL* 3.6 8.4 - - + +
166B VAL 3.0 23.8 + - - +
216B THR* 3.3 10.8 - - + -
218B PHE* 3.6 44.6 - - + -
244B ILE* 4.6 5.6 - - + -
500B TRP* 4.1 28.7 - - + +
501B ALA* 4.3 10.3 - - - -
504B ALA* 3.8 27.1 - - + -
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Residues in contact with VAL 137 (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 VAL* 4.3 5.2 - - + -
136B MET* 1.3 72.2 - - - +
138B TRP* 1.3 61.2 + - - +
139B ILE* 4.1 3.0 + - + +
166B VAL* 3.3 13.0 - - + +
168B ILE* 3.6 38.4 - - + -
198B LEU* 4.1 23.1 - - + -
201B VAL* 4.2 16.6 - - + -
215B VAL* 3.7 26.2 - - + -
216B THR 2.8 11.2 + - - +
217B ILE* 3.4 8.0 - - + +
218B PHE* 2.9 26.4 + - - +
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Residues in contact with TRP 138 (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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136B MET 5.1 0.2 - - - +
137B VAL* 1.3 73.0 - - - +
139B ILE* 1.3 66.3 + - - +
140B HIS* 3.6 20.5 - - + +
149B ALA* 5.9 1.1 - - - -
152B TYR* 3.6 37.2 - + - -
165B VAL* 5.4 1.3 - - + -
166B VAL 2.8 14.3 + - - +
167B THR* 4.2 16.4 - - + -
168B ILE* 3.3 29.7 + - - +
218B PHE* 3.0 60.9 - + + -
219B GLY* 3.6 11.4 - - - -
220B GLU* 3.5 33.7 - - + -
246B GLU* 3.8 11.7 - - - -
472B LEU* 3.5 16.2 - - + -
475B VAL* 5.3 0.2 - - + -
476B PHE* 3.3 29.8 - + + -
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Residues in contact with ILE 139 (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 VAL* 4.8 5.2 - - + +
138B TRP* 1.3 79.1 - - - +
140B HIS* 1.3 63.4 + - - +
168B ILE* 3.9 19.1 - - + -
170B TYR* 3.5 28.3 - - + -
194B GLN* 3.9 20.2 - - + +
198B LEU* 6.2 0.9 - - + -
217B ILE* 5.1 6.7 - - + -
218B PHE 3.1 9.5 + - - +
219B GLY* 3.3 12.2 - - - -
220B GLU 3.7 1.4 + - - -
223B GLY* 3.2 30.1 - - - +
226B SER* 4.0 8.5 - - - +
227B VAL* 4.1 17.5 - - + -
230B LEU* 4.0 27.1 - - + -
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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