Contacts of the strand formed by residues 152 - 159 (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 LYS 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ASP 3.3 16.6 + - - +
128C ALA* 3.2 3.9 - - + +
129C VAL* 2.9 27.4 + - - +
150C SER 3.9 5.6 + - - +
151C ILE* 1.3 74.5 - - - +
153C PHE* 1.3 60.1 + - - +
154C PHE* 4.1 8.0 - - + -
168C ASN 4.1 5.6 - - - -
169C LEU* 4.0 25.5 + - + +
172C HIS* 3.7 19.1 + - - -
317C ALA* 3.1 40.8 - - + +
318C LEU* 4.3 13.7 - - + +
320C GLN* 4.8 9.4 + - - -
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Residues in contact with PHE 153 (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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129C VAL* 3.6 5.4 - - + -
131C LEU* 3.7 21.8 - - + -
139C ILE* 3.4 21.1 - - + -
142C VAL* 3.7 28.3 - - + -
143C ASP* 3.3 36.6 - - + +
146C CYS* 4.1 17.7 - - + -
151C ILE 3.3 1.0 + - - +
152C LYS* 1.3 73.0 - - - +
154C PHE* 1.3 93.4 + - - +
155C THR* 4.1 9.0 - - - -
166C PHE* 4.2 8.1 - + - -
167C ALA* 3.4 0.3 - - - -
168C ASN 2.9 38.6 + - - +
216C VAL* 3.6 22.0 - - + -
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Residues in contact with PHE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ALA* 4.5 7.4 - - + -
129C VAL 2.9 16.5 + - - +
130C CYS* 3.3 10.1 - - - -
131C LEU 2.9 20.9 + - - -
152C LYS* 4.1 14.4 - - + -
153C PHE* 1.3 87.9 - - - +
155C THR* 1.3 62.8 + - - +
166C PHE 3.1 8.5 - - - +
167C ALA* 3.6 27.4 - - + -
169C LEU* 3.5 26.2 - - + -
310C LEU* 3.8 26.7 - - + -
313C GLU* 4.1 10.1 - - + -
314C ILE* 3.6 47.3 - - + -
317C ALA* 3.9 8.5 - - + -
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Residues in contact with THR 155 (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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130C CYS* 5.1 0.2 - - - -
131C LEU* 3.3 16.5 + - - +
134C CYS* 5.7 0.2 - - - +
139C ILE* 3.3 28.5 - - + +
153C PHE* 4.1 12.8 - - - -
154C PHE* 1.3 75.8 - - - +
156C GLY* 1.3 61.8 + - - +
157C ASP* 5.1 1.2 + - - -
164C TYR* 3.2 22.8 + - + +
165C THR* 3.6 4.9 + - - -
166C PHE* 2.9 59.0 + - + +
216C VAL* 5.1 1.8 - - + -
310C LEU* 4.1 5.4 - - - +
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Residues in contact with GLY 156 (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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47C LEU* 3.6 7.2 - - - -
131C LEU 3.0 14.8 + - - +
132C THR* 3.6 7.8 + - - -
155C THR* 1.3 79.1 + - - +
157C ASP* 1.3 74.7 - - - +
164C TYR* 3.4 20.9 - - - -
310C LEU* 4.0 12.5 - - - +
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Residues in contact with ASP 157 (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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47C LEU* 3.5 10.6 - - - +
132C THR* 4.1 1.2 - - - +
133C CYS* 2.8 34.9 + - - -
134C CYS 4.2 2.4 + - - +
139C ILE* 5.1 1.7 - - - +
155C THR* 5.1 2.1 + - - -
156C GLY* 1.3 79.7 - - - +
158C VAL* 1.3 66.7 + - - +
159C PHE* 4.1 12.3 - - + -
163C GLY* 3.4 1.9 - - - -
164C TYR* 3.1 52.1 + - + +
247C LEU* 5.7 1.0 - - - +
250C ARG* 3.0 35.5 + - - +
306C VAL* 4.1 2.1 - - - +
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Residues in contact with VAL 158 (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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47C LEU* 4.4 8.4 - - + +
157C ASP* 1.3 83.0 + - - +
159C PHE* 1.3 69.4 + - - +
160C GLY 5.0 0.2 - - - +
162C HIS 3.6 3.4 - - - +
163C GLY* 4.1 0.2 - - - -
250C ARG* 5.5 0.2 + - - -
256C ASP* 4.7 7.3 - - - +
297C SER 4.5 1.7 - - - +
298C GLU* 4.1 38.4 - - + +
299C MET 4.5 2.9 - - - +
302C VAL* 3.3 46.9 - - + +
303C CYS* 4.0 18.6 - - - +
306C VAL* 4.2 11.0 - - + -
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Residues in contact with PHE 159 (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* 4.1 12.8 - - + -
158C VAL* 1.3 80.5 - - - +
160C GLY* 1.3 67.8 + - - +
161C TYR 3.3 0.2 + - - -
162C HIS* 2.7 50.7 + - + +
163C GLY* 3.9 6.5 - - - -
164C TYR* 3.8 34.3 - + + -
239C ASP 5.9 0.9 - - - -
242C LEU* 4.2 9.2 - - + -
243C LEU* 4.5 15.9 - - + -
246C LEU* 3.3 38.4 - - + -
250C ARG* 5.3 7.2 - - - -
256C ASP* 5.3 4.9 - - - +
257C PRO* 6.2 0.9 - - + -
295C CYS* 3.6 23.1 - - + +
297C SER 3.7 5.4 - - - +
330C PHE* 6.4 0.4 - + - -
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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