Contacts of the strand formed by residues 162 - 168 (chain C) in PDB entry 1Y8Q
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 HIS 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C VAL* 3.6 2.1 - - - -
159C PHE* 2.7 57.0 + - + +
161C TYR* 1.3 84.0 - - + +
163C GLY* 1.3 55.0 + - - +
239C ASP* 3.2 35.6 + - - +
242C LEU* 3.6 17.2 - - + +
291C PHE* 5.7 5.8 - - + -
294C TYR* 3.4 33.1 + + + -
295C CYS* 4.8 1.0 - - + +
302C VAL* 3.6 8.8 - - - +
331C PHE 3.4 8.1 - - - +
332C ASP* 3.4 30.8 + - - -
334C MET* 5.5 1.8 - - + -
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ASP 3.4 12.8 - - - -
158C VAL* 4.1 1.1 - - - -
159C PHE* 4.1 6.3 - - - -
162C HIS* 1.3 77.9 - - - +
164C TYR* 1.3 60.8 + - - +
239C ASP* 5.0 0.7 - - - +
302C VAL* 4.4 0.2 - - - +
306C VAL* 3.7 20.2 - - - -
329C PHE* 5.8 0.2 - - - -
330C PHE* 3.6 2.3 - - - +
331C PHE* 2.7 38.4 + - - +
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ILE* 3.8 12.6 - - - +
155C THR* 3.2 39.6 + - + +
156C GLY* 3.4 9.1 + - - -
157C ASP* 3.1 54.4 + - + +
159C PHE* 3.8 20.2 - + + -
163C GLY* 1.3 75.9 - - - +
165C THR* 1.3 83.0 + - - +
166C PHE* 4.1 8.5 - - + -
243C LEU* 3.6 38.5 - - + +
247C LEU* 5.2 1.4 - - + +
306C VAL* 3.6 9.9 - - - +
328C PHE* 4.2 7.2 - + - -
329C PHE* 3.1 13.5 - - - +
330C PHE* 3.7 19.1 - - + -
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Residues in contact with THR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR 3.6 4.5 - - - -
164C TYR* 1.3 79.5 - - - +
166C PHE* 1.3 62.3 + - - +
167C ALA* 5.5 0.9 - - + +
306C VAL* 4.9 3.4 - - - -
309C ILE* 4.7 8.1 - - + -
310C LEU* 3.0 47.6 - - + +
313C GLU* 5.3 7.6 - - + -
325C HIS* 6.3 1.6 - - + -
327C ASN 5.3 0.7 - - - +
328C PHE* 3.3 7.5 - - - -
329C PHE* 2.9 62.0 + - + +
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE* 4.2 5.6 - + - -
154C PHE* 3.1 9.9 - - - +
155C THR* 2.9 54.7 + - + +
164C TYR* 4.1 7.6 - - + -
165C THR* 1.3 78.3 + - - +
167C ALA* 1.3 80.7 + - - +
168C ASN* 3.7 6.7 - - + -
214C CYS 3.8 14.4 - - - -
215C PRO 4.2 0.2 - - - -
216C VAL* 3.3 46.2 - - + -
219C ALA* 3.7 12.8 - - + -
327C ASN* 3.2 39.3 - - - -
328C PHE* 3.7 22.7 - + + -
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE 3.4 4.9 - - - -
154C PHE* 3.6 25.8 - - + -
165C THR* 6.3 0.9 - - + -
166C PHE* 1.3 90.9 - - - +
168C ASN* 1.3 60.3 + - - +
169C LEU* 4.2 9.4 - - + -
213C PHE* 3.5 25.2 - - + +
313C GLU* 5.6 4.5 - - + +
324C PRO* 6.0 0.9 - - + -
325C HIS 4.4 9.0 - - - +
327C ASN* 3.0 13.4 + - - +
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Residues in contact with ASN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ASP* 2.7 38.4 + - - +
147C HIS* 4.5 19.0 - - - +
151C ILE 4.5 2.1 - - - +
152C LYS* 4.1 1.4 - - - -
153C PHE* 2.9 31.5 + - + +
166C PHE* 3.7 11.9 - - + -
167C ALA* 1.3 74.7 - - - +
169C LEU* 1.3 60.2 + - - +
170C GLY* 3.1 18.4 + - - -
213C PHE* 3.7 9.9 - - - +
214C CYS 3.5 14.8 - - - +
215C PRO* 3.5 13.9 - - - +
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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