Contacts of the strand formed by residues 261 - 267 (chain B) in PDB entry 1YXJ
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 PHE 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B SER* 3.5 20.6 - - - +
160B SER* 3.5 22.0 - - - -
161B GLY 3.5 20.9 - - - -
162B SER* 4.0 14.1 - - - -
200B PHE* 3.4 59.9 - + + -
201B PRO* 3.0 16.8 + - + +
202B PHE* 3.6 19.5 - + + -
203B TRP* 2.8 21.8 + - - -
260B ALA* 1.3 78.4 - - - +
262B SER* 1.3 63.7 + - - +
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 3.6 0.2 - - - +
158B PHE* 3.7 1.0 - - - -
159B SER* 2.9 44.2 + - - -
161B GLY 4.9 0.9 + - - -
168B SER* 3.8 26.0 + - - -
171B LYS* 5.9 1.0 - - - +
179B LEU* 3.8 21.7 - - - +
202B PHE* 4.0 3.1 - - - -
203B TRP* 3.7 12.1 - - - +
261B PHE* 1.3 77.2 - - - +
263B ILE* 1.3 67.4 + - - +
264B CYS* 4.2 5.9 - - - -
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Residues in contact with ILE 263 (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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156B TYR* 4.2 16.2 - - + -
157B LEU 3.1 9.6 - - - +
158B PHE* 3.6 37.0 - - + -
172B CYS* 4.4 0.2 - - - -
179B LEU* 3.5 8.5 - - - +
180B LEU* 2.8 59.3 + - + +
191B ILE* 3.9 16.4 - - + -
195B ILE* 4.5 0.7 - - + -
202B PHE* 3.9 23.1 - - + -
203B TRP 3.3 7.3 + - - +
246B ILE* 4.4 4.0 - - + -
262B SER* 1.3 80.8 - - - +
264B CYS* 1.3 71.3 + - - +
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Residues in contact with CYS 264 (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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148B TRP* 4.1 11.4 - - + -
156B TYR* 3.3 5.0 - - - -
157B LEU* 2.8 47.0 + - + -
159B SER* 5.6 2.9 - - - -
168B SER 4.9 0.2 - - - -
171B LYS* 4.8 2.7 - - - -
172B CYS* 2.0 53.6 - - + -
175B LEU* 4.9 2.0 - - - -
177B ALA* 4.1 10.3 - - + -
178B LYS 3.1 6.5 - - - +
262B SER* 4.7 7.4 - - - -
263B ILE* 1.3 78.8 - - - +
265B GLN* 1.3 62.4 + - - +
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Residues in contact with GLN 265 (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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148B TRP* 4.2 0.9 - - - -
154B ASN* 3.7 24.5 + - + +
155B CYS 3.1 11.7 - - - +
156B TYR* 3.6 19.8 + - + -
177B ALA* 3.3 3.2 - - - +
178B LYS* 2.8 67.2 + - + +
179B LEU 4.3 2.7 - - - +
180B LEU* 3.5 12.4 - - - +
181B LYS* 2.9 39.8 + - - +
183B ASN* 5.7 1.6 + - - -
264B CYS* 1.3 77.7 - - - +
266B LYS* 1.3 65.0 + - - +
267B LYS* 5.4 1.8 - - - +
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Residues in contact with LYS 266 (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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145B PRO* 4.0 28.6 - - - +
148B TRP* 3.7 35.8 - - + +
154B ASN* 3.4 9.2 - - - +
155B CYS* 2.8 32.8 + - + +
175B LEU* 3.1 21.2 + - - +
176B ASP* 3.6 28.1 - - + +
177B ALA* 3.9 1.1 - - + -
178B LYS* 6.2 1.1 - - - +
265B GLN* 1.3 77.2 - - - +
267B LYS* 1.3 65.5 + - - +
269B ASN* 6.3 0.4 - - - +
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Residues in contact with LYS 267 (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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153B GLU* 3.6 33.7 + - + +
154B ASN* 3.1 26.8 + - - +
155B CYS* 4.1 5.1 - - - -
178B LYS* 5.6 4.8 - - - +
265B GLN* 5.4 2.8 - - - +
266B LYS* 1.3 83.3 - - - +
268B ALA* 1.3 65.4 - - - +
269B ASN* 3.9 6.8 + - - +
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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