Contacts of the strand formed by residues 155 - 160 (chain C) in PDB entry 4HYY
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 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C GLY* 1.3 74.8 - - - -
156C ILE* 1.3 65.6 + - - +
186C ASP 5.1 3.9 + - - +
187C ASN* 3.2 43.5 - - - +
216C ILE* 2.9 31.2 + - + +
217C PHE* 3.4 31.6 - - + -
218C LYS* 2.7 29.8 + - - +
219C LEU 3.4 3.8 + - - -
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Residues in contact with ILE 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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140C CYS* 3.5 28.5 - - - +
143C ALA* 3.8 20.6 - - + -
144C GLN* 3.6 14.1 - - + +
154C GLY 3.6 14.4 - - - +
155C LYS* 1.3 85.2 - - - +
157C ILE* 1.3 75.0 + - - +
158C PHE* 4.7 0.4 - - + -
187C ASN 3.1 6.9 + - - +
188C VAL* 3.3 17.3 - - + -
189C LEU 2.8 31.0 + - - -
217C PHE* 3.9 3.7 - - - -
219C LEU* 3.2 17.0 - - + +
221C ILE* 3.8 23.1 - - + -
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Residues in contact with ILE 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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156C ILE* 1.3 77.6 - - - +
158C PHE* 1.3 59.2 + - - +
159C ILE* 4.6 0.9 - - + -
189C LEU* 3.2 13.0 - - + +
205C TYR* 6.3 0.9 - - + -
206C VAL* 3.8 22.4 - - + -
209C LYS* 3.9 22.7 - - + -
210C PHE* 3.9 18.6 - - + -
217C PHE* 3.7 29.4 - - + -
219C LEU 2.9 8.0 + - - +
220C LEU* 3.4 13.7 - - + -
221C ILE 2.7 32.6 + - - -
85D PHE* 3.3 30.7 - - + -
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Residues in contact with PHE 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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136C SER* 4.0 20.0 - - - -
137C HIS* 4.9 2.2 - + - -
140C CYS* 3.7 24.0 - - - -
156C ILE* 4.7 0.4 - - + -
157C ILE* 1.3 75.0 - - - +
159C ILE* 1.3 81.6 + - - +
160C ASP* 3.8 14.8 - - + -
165C PHE* 3.9 28.0 - + + -
188C VAL* 4.1 12.6 - - + -
189C LEU 2.6 13.4 + - - +
190C TYR* 3.2 18.6 - + + -
191C ALA 3.0 25.3 + - - +
221C ILE* 3.5 27.1 - - + -
223C ASP* 3.9 23.6 - - + -
85D PHE* 4.2 1.0 - - - -
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Residues in contact with ILE 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 ILE* 4.6 2.9 - - + -
158C PHE* 1.3 82.5 - - - +
160C ASP* 1.3 63.0 + - - +
161C THR* 4.7 3.4 - - + -
191C ALA 3.2 8.1 - - - +
193C ALA* 4.1 23.1 - - + -
199C GLN* 4.8 5.8 - - + +
202C LEU* 4.2 26.2 - - + -
203C LEU* 4.4 20.6 - - + -
206C VAL* 4.3 17.5 - - + -
220C LEU* 4.5 7.2 - - + -
221C ILE 2.9 12.1 + - - +
222C ILE* 3.5 18.8 - - + +
223C ASP 3.0 27.4 + - - +
85D PHE* 4.2 12.1 - - + -
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Residues in contact with ASP 160 (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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158C PHE* 3.8 7.6 - - + -
159C ILE* 1.3 73.6 - - - +
161C THR* 1.3 61.6 + - - +
162C GLU* 2.9 25.7 + - - +
163C ASN* 2.9 10.6 + - - -
164C THR* 3.2 12.6 + - - -
165C PHE* 3.1 23.5 + - - +
190C TYR* 2.4 42.9 + - + +
191C ALA 3.0 7.0 + - - +
192C ARG* 2.7 18.6 + - - -
193C ALA 3.0 13.4 + - - -
223C ASP* 3.4 5.0 - - - +
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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