Contacts of the strand formed by residues 266 - 270 (chain C) in PDB entry 3NIG
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 ALA 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C ALA* 2.9 35.9 + - + +
260C TRP* 3.5 34.3 - - + -
265C GLY* 1.3 75.1 - - - +
267C VAL* 1.3 69.6 + - - +
268C GLU* 5.0 4.0 - - + -
279C ARG* 4.3 11.0 - - + -
280C LEU 3.1 14.8 - - - +
289C PHE* 3.7 7.9 + - - +
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Residues in contact with VAL 267 (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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254C VAL* 3.8 25.4 - - + -
255C VAL 3.3 11.0 - - - +
256C GLY* 4.3 1.3 - - - -
266C ALA* 1.3 80.1 - - - +
268C GLU* 1.3 68.8 + - - +
269C ILE* 5.3 0.4 - - + +
279C ARG* 3.6 0.3 - - - -
280C LEU* 2.8 38.8 + - + +
289C PHE* 3.7 7.6 - - + -
290C GLY* 3.7 12.6 - - - -
293C VAL* 4.0 11.0 - - + -
306C LEU* 4.2 17.0 - - + -
308C VAL* 3.6 33.4 - - + -
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Residues in contact with GLU 268 (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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230C TYR* 2.7 33.3 + - - -
235C TRP* 3.0 32.8 + - + +
253C TYR 3.7 0.7 - - - +
254C VAL* 3.4 4.3 - - - +
255C VAL* 2.9 36.1 + - + +
257C ALA* 6.3 0.7 - - + -
260C TRP* 4.5 2.2 + - - -
266C ALA* 5.0 4.9 - - + +
267C VAL* 1.3 81.0 - - - +
269C ILE* 1.3 65.4 + - - +
270C LEU* 4.1 18.4 + - + +
276C ARG* 3.6 15.2 + - - -
278C HIS 3.4 5.6 - - - +
279C ARG* 3.0 30.7 + - + -
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Residues in contact with ILE 269 (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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244C PHE* 4.0 45.3 - - + -
252C GLU* 4.3 8.1 - - + -
253C TYR 3.2 8.3 - - - +
254C VAL* 4.3 11.9 - - + -
267C VAL* 5.3 0.9 - - + -
268C GLU* 1.3 77.9 - - - +
270C LEU* 1.3 65.2 + - - +
277C LEU* 2.8 34.2 + - + +
278C HIS* 3.0 26.0 + - + +
280C LEU* 5.0 4.0 - - + -
306C LEU* 4.3 13.7 - - + -
340C LEU* 3.6 32.8 - - + -
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Residues in contact with LEU 270 (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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195C LEU* 4.6 0.2 - - + -
235C TRP* 3.4 32.1 - - + -
252C GLU* 3.2 10.0 - - - +
253C TYR* 2.8 36.5 + - + +
255C VAL* 3.6 21.1 - - + -
268C GLU* 4.1 20.4 - - + +
269C ILE* 1.3 78.4 - - - +
271C ASP* 1.3 67.4 + - - +
274C TYR* 4.1 22.2 - - + +
275C GLN 3.2 11.2 - - - +
276C ARG* 3.6 29.4 - - + +
277C LEU* 3.8 6.3 - - - -
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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