Contacts of the strand formed by residues 261 - 267 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196G SER* 5.8 3.4 - - - -
197G TYR* 4.7 13.0 - + + -
159H SER* 3.3 15.3 - - - +
160H SER 2.9 30.1 - - - -
161H GLY 3.1 16.4 - - - -
162H SER* 4.2 12.6 - - - -
200H PHE* 3.3 51.8 - + + -
201H PRO* 3.4 4.6 + - + +
202H PHE* 3.0 26.0 - + + -
203H TRP* 2.8 21.8 + - - +
260H ALA* 1.3 79.2 - - - +
262H SER* 1.3 59.9 + - - +
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Residues in contact with SER 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H SER* 2.5 44.3 + - - -
168H SER* 3.6 31.7 + - - -
171H LYS* 5.4 1.9 - - - +
172H CYS* 4.4 4.9 - - - -
179H LEU* 3.5 21.0 - - - +
202H PHE* 3.7 3.6 - - - -
203H TRP* 3.8 11.2 - - - +
260H ALA 3.9 0.2 + - - -
261H PHE* 1.3 74.7 - - - +
263H ILE* 1.3 71.0 + - - +
264H CYS* 4.3 0.9 - - - -
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Residues in contact with ILE 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H TYR* 4.7 5.4 - - + -
157H LEU 3.4 13.5 - - - +
158H PHE* 4.1 26.7 - - + -
172H CYS* 4.2 0.9 - - - -
179H LEU* 3.5 3.7 - - - +
180H LEU* 2.6 64.7 + - + +
191H ILE* 4.2 18.2 - - + -
195H ILE* 4.4 6.1 - - + -
202H PHE* 3.5 35.4 - - + -
203H TRP 3.5 6.2 + - - +
246H ILE* 4.5 4.3 - - + -
262H SER* 1.3 84.7 - - - +
264H CYS* 1.3 64.1 + - - +
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Residues in contact with CYS 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H TRP* 4.2 20.0 - - + -
155H CYS 3.6 0.4 - - - +
156H TYR* 3.2 7.1 - - - +
157H LEU* 2.8 47.4 + - + +
159H SER* 5.6 5.2 - - - -
171H LYS* 4.7 2.9 - - - -
172H CYS* 2.0 56.5 - - + -
175H LEU* 5.3 2.7 - - - -
177H ALA* 4.4 1.8 - - + -
178H LYS 3.2 6.3 - - - +
262H SER* 4.5 6.5 - - - -
263H ILE* 1.3 73.2 - - - +
265H GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 265 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148H TRP* 4.5 0.2 - - - -
154H ASN* 3.2 30.4 + - + +
155H CYS 3.1 6.5 - - - -
156H TYR* 3.7 29.4 + - + -
177H ALA* 4.0 1.3 - - - -
178H LYS* 2.7 60.2 + - + +
179H LEU 4.0 0.7 - - - +
180H LEU* 3.5 6.3 - - - +
181H LYS* 2.5 49.2 + - - +
187H ASP* 6.3 0.4 - - - -
263H ILE 4.1 0.2 + - - -
264H CYS* 1.3 75.8 - - - +
266H LYS* 1.3 66.7 + - - +
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Residues in contact with LYS 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H PRO* 3.9 29.0 - - - +
148H TRP* 3.6 29.5 - - + -
154H ASN* 2.9 11.5 - - - +
155H CYS* 2.7 43.0 + - + -
175H LEU 3.2 18.8 + - - -
176H ASP* 3.3 24.5 + - - +
177H ALA* 3.6 14.1 - - + -
178H LYS* 5.4 4.0 - - - +
265H GLN* 1.3 80.2 - - - +
267H LYS* 1.3 70.4 + - - +
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Residues in contact with LYS 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H PRO 4.6 0.9 - - - +
153H GLU 3.8 0.9 - - - +
154H ASN* 3.5 11.9 - - - +
155H CYS* 4.0 6.8 - - - -
266H LYS* 1.3 86.5 - - - +
268H ALA* 1.3 68.1 + - - +
269H ASN* 5.4 0.2 - - - +
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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