Contacts of the strand formed by residues 261 - 267 (chain G) in PDB entry 1YPO
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159G SER* 3.8 16.6 - - - -
160G SER 3.4 22.4 - - - -
161G GLY* 3.4 20.2 - - - -
162G SER* 3.3 25.1 - - - -
200G PHE* 3.2 52.5 - + + -
201G PRO 3.1 10.2 + - - +
202G PHE* 3.9 16.4 - + + -
203G TRP* 2.6 32.0 + - - +
260G ALA* 1.3 79.9 - - - +
262G SER* 1.3 60.1 + - - +
196H SER* 5.3 2.2 - - - -
197H TYR* 4.2 20.6 - + + -
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Residues in contact with SER 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G PHE* 3.6 0.5 - - - -
159G SER* 2.8 36.1 + - - -
168G SER* 3.6 19.6 + - - -
172G CYS* 4.9 4.7 - - - -
179G LEU* 4.1 12.6 - - - +
202G PHE* 3.5 9.3 - - - -
203G TRP* 3.5 28.7 - - - +
261G PHE* 1.3 80.4 - - - +
263G ILE* 1.3 71.2 + - - +
264G CYS* 5.3 1.3 - - - -
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Residues in contact with ILE 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G TYR* 4.0 21.3 - - + -
157G LEU 3.2 12.3 - - - +
158G PHE* 4.0 28.5 - - + -
159G SER 4.7 0.2 - - - +
172G CYS* 4.1 0.2 - - - -
179G LEU* 3.7 9.4 - - - +
180G LEU* 3.2 40.1 + - + +
191G ILE* 3.4 34.1 - - + -
195G ILE* 4.1 2.9 - - + -
202G PHE* 3.5 22.9 - - + -
203G TRP 3.7 4.1 + - - +
246G ILE* 5.0 0.2 - - + -
262G SER* 1.3 81.4 - - - +
264G CYS* 1.3 73.9 + - - +
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Residues in contact with CYS 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G TRP* 3.9 17.7 - - + -
156G TYR* 3.3 6.1 - - - -
157G LEU* 2.9 35.4 + - + +
159G SER* 5.9 4.3 - - - -
171G LYS* 4.7 3.1 - - - -
172G CYS* 2.0 53.8 - - + -
175G LEU* 4.9 10.1 - - - -
177G ALA* 4.4 2.9 - - + -
178G LYS 3.1 7.2 - - - +
179G LEU 4.9 0.2 - - - -
262G SER* 5.3 2.5 - - - -
263G ILE* 1.3 80.1 - - - +
265G GLN* 1.3 62.8 + - - +
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Residues in contact with GLN 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G TRP* 4.6 0.7 - - - -
154G ASN* 3.8 25.3 - - + +
155G CYS 3.2 11.4 - - - +
156G TYR* 3.9 17.6 + - + -
177G ALA* 3.4 1.6 - - - +
178G LYS* 2.7 56.4 + - - +
179G LEU 3.5 11.4 - - - +
180G LEU* 3.1 16.2 - - - +
181G LYS* 2.6 46.3 + - - +
183G ASN* 5.8 1.8 + - - -
264G CYS* 1.3 76.0 - - - +
266G LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G PRO* 4.9 15.9 - - + +
148G TRP* 3.7 38.1 - - + -
154G ASN* 3.2 8.0 - - - -
155G CYS* 2.8 37.7 + - + -
175G LEU 3.5 10.7 + - - -
176G ASP* 3.2 40.7 + - - +
177G ALA* 3.7 8.5 - - + -
178G LYS* 5.4 4.5 - - - +
265G GLN* 1.3 76.1 - - - +
267G LYS* 1.3 73.4 + - - +
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Residues in contact with LYS 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G PRO 4.7 0.3 - - - +
153G GLU 3.7 2.2 - - - +
154G ASN* 3.7 11.9 + - - +
155G CYS* 4.0 6.4 - - - -
266G LYS* 1.3 88.2 - - - +
268G ALA* 1.3 62.8 + - - +
269G ASN* 4.1 6.9 + - - +
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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