Contacts of the strand formed by residues 153 - 157 (chain H) in PDB entry 3INU
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 THR 153 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151H PRO* 5.3 9.2 - - + -
152H VAL* 1.3 78.9 - - - +
154H VAL* 1.3 63.2 + - - +
209H ASN 3.3 3.3 - - - +
210H VAL* 3.4 3.5 - - - -
211H ASN* 2.9 52.4 + - - +
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Residues in contact with VAL 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H CYS* 5.8 0.2 - - + -
144H VAL* 4.3 4.0 - - + -
152H VAL* 4.1 14.8 + - + +
153H THR* 1.3 81.0 - - - +
156H SER* 1.3 68.2 + - - +
157H TRP* 3.8 12.7 - - - +
171H VAL* 5.8 1.2 - - - +
173H THR* 4.3 18.3 + - + +
187H LEU* 4.1 17.9 - - + -
189H SER* 3.5 29.8 - - - +
208H CYS* 4.4 11.2 - - + -
209H ASN 3.3 3.4 - - - +
210H VAL* 4.0 17.0 - - + -
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Residues in contact with SER 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H THR 4.3 0.2 - - - -
154H VAL* 1.3 75.6 - - - +
157H TRP* 1.3 64.8 + - - +
163H SER* 4.2 1.9 - - - -
164H GLY* 4.0 18.3 + - - -
208H CYS* 3.3 5.7 - - - +
209H ASN* 2.7 56.7 + - - +
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Residues in contact with TRP 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H LEU* 3.4 21.3 - - + -
141H GLY* 3.4 26.9 - - - -
142H CYS* 3.8 4.5 - - - -
154H VAL* 3.8 5.7 - - + +
156H SER* 1.3 78.0 - - - +
162H ASN* 1.3 70.1 + - - +
163H SER 3.2 1.6 - - - -
164H GLY* 3.1 9.2 + - - -
166H LEU* 3.2 49.9 + - + +
171H VAL* 3.8 24.8 - - + +
189H SER* 2.8 45.0 + - - -
190H VAL 4.8 1.2 + - - -
191H VAL* 4.2 16.4 - - + -
206H TYR* 4.5 1.8 - - + -
207H ILE 3.3 25.8 - - - -
208H CYS* 3.7 28.7 - - + -
225H VAL* 4.1 8.3 - - + -
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Residues in contact with ASN 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H TRP* 1.3 71.1 - - - +
163H SER* 1.3 62.5 + - - +
165H ALA* 2.8 38.7 + - + +
166H LEU* 4.0 14.0 - - - +
203H GLN* 4.4 8.5 + - - +
205H THR* 3.2 29.2 + - - +
206H TYR* 3.6 20.2 - - - -
207H ILE* 2.8 44.5 + - - +
209H ASN* 3.5 1.7 + - - +
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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