Contacts of the strand formed by residues 202 - 209 (chain B) in PDB entry 1YH3
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 ASP 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASN* 3.6 28.0 - - + +
201B CYS* 1.3 85.3 - - - +
203B VAL* 1.3 67.7 + - - +
234B LYS 2.9 15.3 + - - -
235B VAL* 3.7 2.2 - - - +
236B GLN* 2.8 38.4 + - - +
237B THR 3.1 8.5 + - - +
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Residues in contact with VAL 203 (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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120B ASN 3.7 19.3 + - - +
122B ILE 4.6 1.7 + - - +
201B CYS 3.7 4.2 - - - +
202B ASP* 1.3 86.9 - - - +
204B VAL* 1.3 70.9 + - - +
205B HIS* 3.6 35.5 + - + +
236B GLN* 6.2 0.7 - - + -
237B THR* 3.4 31.4 - - + +
239B GLU* 4.1 5.8 - - + +
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Residues in contact with VAL 204 (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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119B CYS 4.9 1.3 - - - +
122B ILE* 3.8 13.5 - - + +
124B LEU* 3.9 26.2 - - + -
200B ALA* 3.4 28.3 - - + -
201B CYS 3.9 12.3 - - - +
203B VAL* 1.3 81.1 - - - +
205B HIS* 1.3 70.9 + - - +
230B LEU* 4.1 8.7 - - + -
235B VAL* 4.4 15.9 - - + -
237B THR 2.9 9.8 + - - +
238B LEU* 3.3 14.7 - - + +
239B GLU 2.8 24.8 + - - -
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Residues in contact with HIS 205 (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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120B ASN 5.5 3.8 + - - -
122B ILE 3.2 13.1 + - - +
123B LEU* 3.3 17.4 - - + -
124B LEU* 2.7 31.0 + - - +
142B MET* 4.1 27.7 - - + +
203B VAL* 3.6 27.7 + - + +
204B VAL* 1.3 76.9 - - - +
206B VAL* 1.3 56.9 + - - +
239B GLU* 3.1 38.2 + - + +
241B TRP* 3.7 29.3 - + + -
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Residues in contact with VAL 206 (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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123B LEU* 4.0 1.8 - - - -
124B LEU* 2.9 22.4 - - + +
125B TRP* 4.0 2.9 - - - +
205B HIS* 1.3 76.5 - - - +
207B MET* 1.3 64.5 + - - +
208B LEU* 3.7 26.0 + - + -
222B PHE* 3.8 32.3 - - + -
238B LEU* 3.8 20.4 - - + -
239B GLU 2.9 15.4 + - - +
240B ALA* 3.5 16.4 - - + +
241B TRP* 3.0 23.9 + - - -
262B LEU* 5.3 0.7 - - + -
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Residues in contact with MET 207 (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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123B LEU* 3.6 15.5 - - + +
124B LEU 2.7 13.9 + - - +
125B TRP* 3.4 5.6 - - + -
126B SER 3.0 26.0 + - - -
128B ILE* 3.5 13.4 - - + +
131B LEU* 3.7 41.1 - - + +
132B ALA* 3.8 25.1 - - - -
135B PHE* 4.3 8.1 - - + -
206B VAL* 1.3 73.2 - - - +
208B LEU* 1.3 62.5 + - - +
241B TRP* 3.5 34.3 - - + +
243B ILE* 4.3 9.2 - - + -
284B PHE* 3.8 19.1 - - + -
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Residues in contact with LEU 208 (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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126B SER* 3.7 21.3 - - - -
128B ILE* 4.1 4.5 - - - -
206B VAL* 3.7 24.5 - - + +
207B MET* 1.3 83.3 - - - +
209B ASP* 1.3 61.7 + - - +
210B GLY 3.2 0.2 + - - -
215B ILE* 3.8 25.1 - - + +
216B PHE* 4.6 6.5 - - + -
222B PHE* 4.3 9.6 - - + -
240B ALA* 4.2 18.4 - - + -
241B TRP 3.0 12.7 + - - +
242B VAL* 3.7 3.5 - - + -
243B ILE* 2.9 32.6 + - - +
259B ILE* 4.1 25.4 - - + -
262B LEU* 4.3 12.6 - - + -
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Residues in contact with ASP 209 (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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126B SER 3.7 5.7 + - - -
127B ARG* 3.4 35.4 - - + +
128B ILE* 3.5 23.0 - - + +
208B LEU* 1.3 71.6 - - - +
210B GLY* 1.3 59.9 + - - +
211B SER* 3.1 26.3 + - - -
212B ARG* 3.5 29.1 + - + +
215B ILE* 3.6 22.2 + - - +
243B ILE 4.2 3.3 - - - +
245B GLY* 5.6 0.3 - - - -
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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