Contacts of the strand formed by residues 225 - 228 (chain B) in PDB entry 1NVT
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 VAL 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B LEU* 4.5 6.1 - - + -
123B ILE* 4.4 19.3 - - + -
195B ASP 3.2 15.1 + - - +
196B ILE* 3.4 18.9 - - + -
197B ILE* 3.1 26.5 + - - +
223B ASP 5.2 2.5 - - - +
224B MET* 1.3 80.7 - - - +
226B VAL* 1.3 66.9 + - - +
248B LYS* 3.5 27.1 - - + +
250B ILE* 4.0 26.5 - - + -
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.7 32.1 - - + +
220B LEU* 4.1 5.2 - - + -
224B MET* 4.1 9.6 - - + -
225B VAL* 1.3 80.8 - - - +
227B MET* 1.3 62.4 + - - +
238B LEU* 4.0 28.5 - - + -
239B LEU* 3.7 11.9 - - + +
242B ALA* 3.8 28.0 - - + -
247B ALA* 4.4 11.2 - - + -
248B LYS 2.9 9.9 + - - +
249B THR* 3.4 2.8 - - - -
250B ILE 3.0 24.7 + - - +
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Residues in contact with MET 227 (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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115B ALA* 4.0 27.4 - - + +
118B ALA* 4.9 6.5 - - - -
119B LEU* 4.2 29.2 - - + -
196B ILE* 5.4 1.3 - - + -
197B ILE 2.9 11.5 + - - +
198B ILE* 3.1 34.8 - - + +
199B ASN* 2.8 24.3 + - - +
225B VAL* 4.1 1.0 - - - +
226B VAL* 1.3 76.9 - - - +
228B ASP* 1.3 70.0 + - - +
229B LEU* 4.0 22.0 - - + -
238B LEU* 5.0 0.2 - - - +
250B ILE* 3.2 36.3 - - + +
251B ASN 4.5 2.9 - - - +
255B MET* 5.7 2.5 - - + -
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Residues in contact with ASP 228 (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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199B ASN* 2.9 34.0 - - + +
203B ILE 4.7 1.0 - - - +
226B VAL 4.1 0.4 + - - -
227B MET* 1.3 75.1 - - - +
229B LEU* 1.3 69.5 + - - +
230B ILE* 3.1 25.1 + - - +
236B THR* 2.8 27.1 + - - +
238B LEU* 3.8 12.4 - - + +
239B LEU* 3.9 24.7 - - + -
250B ILE 2.9 5.9 + - - -
251B ASN 3.0 4.3 - - - +
252B GLY* 2.9 25.1 + - - -
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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