Contacts of the strand formed by residues 202 - 208 (chain A) 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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PHE* 4.3 18.8 - + + -
159A SER 5.7 0.7 - - - -
195A ILE* 4.1 22.4 - - + -
198A SER* 3.7 30.3 - - - -
200A PHE* 3.3 29.2 - - + -
201A PRO* 1.3 73.6 - - - +
203A TRP* 1.3 62.7 + - - +
245A TYR* 3.7 4.2 - - - +
246A ILE* 2.7 53.2 + - + +
261A PHE* 2.8 32.8 - + + +
262A SER 4.4 2.7 - - - -
263A ILE* 4.0 27.1 - - + -
197B TYR* 4.3 18.4 - + + -
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Residues in contact with TRP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE 3.4 6.3 + - - -
165A TRP* 3.6 29.5 - + + +
168A SER* 3.6 17.7 - - - -
179A LEU* 4.5 5.1 - - + +
180A LEU* 4.5 0.2 - - - +
201A PRO 4.3 0.2 - - - -
202A PHE* 1.3 75.9 - - - +
204A MET* 1.3 58.9 + - - +
243A CYS* 3.4 37.0 - - + -
244A ALA 3.5 21.1 - - - -
245A TYR* 3.6 15.3 - + + -
254A GLU* 4.2 11.0 - - + -
255A ASN 3.8 16.8 - - - -
256A CYS* 4.0 10.3 - - - -
258A LEU* 3.2 30.9 + - + -
260A ALA* 3.4 36.7 - - + +
261A PHE 2.6 11.2 + - - +
262A SER* 4.0 9.9 - - - -
263A ILE* 3.5 28.2 + - - +
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 2.8 22.3 + - - -
179A LEU* 3.8 5.8 - - - -
180A LEU* 3.6 28.3 - - + +
182A ILE* 4.1 16.8 - - + -
203A TRP* 1.3 73.7 - - - +
205A GLY* 1.3 59.1 + - - +
206A LEU* 3.0 17.4 + - + +
217A TRP* 3.9 20.9 - - + -
228A PHE* 4.3 11.2 - - - -
244A ALA* 3.0 24.4 + - - +
245A TYR 4.1 0.4 - - - -
246A ILE* 3.6 38.4 - - + +
251A VAL* 3.9 25.1 - - + -
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 3.9 13.2 - - - -
179A LEU* 3.4 20.2 - - - +
180A LEU 2.9 18.3 + - - -
204A MET* 1.3 69.6 - - - +
206A LEU* 1.3 56.2 + - - +
207A SER* 4.7 0.3 + - - -
216A LEU 3.3 1.7 - - - +
217A TRP* 3.1 13.5 - - - -
218A GLU* 3.0 33.8 + - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 3.9 5.9 + - - -
204A MET* 3.0 6.3 + - + +
205A GLY* 1.3 78.8 - - - +
207A SER* 1.3 66.6 + - - +
215A TRP* 3.5 46.2 - - + -
216A LEU* 3.4 19.3 - - - +
217A TRP* 3.8 28.7 - - + +
223A LEU* 4.1 21.1 - - + -
228A PHE* 4.2 15.7 - - + -
230A VAL* 4.3 4.9 - - + -
243A CYS* 3.7 1.6 - - - -
244A ALA* 3.2 38.6 + - + -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 3.7 20.9 - - - -
205A GLY 4.7 0.2 + - - -
206A LEU* 1.3 80.7 - - - +
208A ARG* 1.3 67.7 + - - +
214A PRO 3.9 1.0 - - - +
215A TRP* 3.7 5.6 - - - -
216A LEU* 3.2 31.2 + - - +
242A THR 3.1 15.3 - - - -
243A CYS* 3.7 17.7 - - - -
256A CYS* 4.8 0.7 - - - -
231D ARG* 5.9 1.4 + - - -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 1.3 81.0 - - - +
209A ARG* 1.3 57.9 + - - +
210A ASN 3.9 6.5 - - - +
211A PRO* 3.5 31.2 + - - +
213A TYR* 3.4 25.5 + - + +
214A PRO* 3.8 14.1 - - - +
215A TRP* 3.4 49.4 - - + +
234A VAL* 3.1 44.9 + - - +
236A GLN 5.2 1.0 + - - -
241A GLY* 4.6 1.3 - - - -
242A THR* 2.6 51.5 + - - +
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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