Contacts of the strand formed by residues 201 - 205 (chain Z) in PDB entry 1NJI
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 GLU 201 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182Z PHE* 3.6 5.5 - - - -
183Z GLU* 3.3 20.1 - - + +
185Z VAL* 3.9 21.7 - - + +
195Z GLY 4.3 2.8 - - - +
196Z VAL* 3.5 16.9 - - + +
197Z ASP* 2.6 44.4 + - - +
198Z GLY* 3.7 15.6 - - - +
200Z THR* 1.3 93.9 - - + +
202Z ALA* 1.3 61.5 + - - +
226Z ILE* 4.3 5.9 - - - +
227Z ARG 4.9 1.0 + - - -
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Residues in contact with ALA 202 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Z PHE* 3.6 34.5 - - + -
183Z GLU 3.1 7.5 + - - +
184Z GLU* 3.6 2.4 - - - -
185Z VAL* 3.1 25.3 + - - +
196Z VAL* 5.4 0.7 - - - -
201Z GLU* 1.3 75.8 - - - +
203Z VAL* 1.3 61.3 + - - +
226Z ILE* 4.6 1.8 - - - -
227Z ARG* 3.7 14.1 - - + +
229Z LEU* 3.8 24.9 - - + -
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Residues in contact with VAL 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Z VAL* 3.1 29.4 - - + +
187Z VAL* 3.5 36.6 - - + -
193Z LEU* 4.1 18.2 - - + -
196Z VAL* 5.1 5.8 - - + -
202Z ALA* 1.3 73.9 - - - +
204Z ARG* 1.3 59.2 + - - +
205Z ILE* 4.7 1.6 - - + -
217Z ILE* 5.4 0.4 - - + -
221Z ALA* 5.0 0.4 - - + -
226Z ILE* 4.1 12.3 - - + +
227Z ARG 2.9 10.5 + - - +
228Z VAL* 3.4 29.7 - - + +
229Z LEU* 2.9 27.9 + - - +
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Residues in contact with ARG 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A A 2.9 16.8 + - - -
553A G 2.5 29.7 + - - -
1324A G 3.1 24.8 - - - +
1325A G 5.1 4.4 + - - -
1333A U 3.8 15.2 + - - +
1334A C 3.3 28.9 + - - -
178Z HIS* 4.0 0.6 - - - -
184Z GLU* 2.5 49.6 + - - +
185Z VAL 2.9 13.6 + - - +
186Z ARG* 3.6 12.6 - - - +
187Z VAL* 2.9 24.9 + - - -
202Z ALA 4.3 0.2 + - - -
203Z VAL* 1.3 72.7 - - - +
205Z ILE* 1.3 61.7 + - - +
206Z ALA* 3.3 1.4 + - - -
229Z LEU* 3.5 14.9 - - + +
230Z ASN* 3.4 13.3 + - - +
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Residues in contact with ILE 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334A C 3.9 4.4 - - - +
187Z VAL* 3.3 22.7 - - + +
203Z VAL* 4.7 2.0 - - + -
204Z ARG* 1.3 70.4 - - - +
206Z ALA* 1.3 79.0 + - - +
207Z SER 3.3 1.2 + - - -
209Z VAL* 3.8 23.6 - - + -
214Z ARG* 3.5 35.4 - - + +
217Z ILE* 3.7 26.9 - - + -
218Z GLU* 4.0 22.0 - - + -
228Z VAL* 4.1 16.8 - - + -
230Z ASN* 3.0 23.5 + - - +
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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