Contacts of the strand formed by residues 272 - 278 (chain A) in PDB entry 1NV9
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 TYR 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ILE* 4.1 5.4 - - + +
248A GLY 4.1 0.2 - - - +
249A GLU* 3.5 34.7 + - - +
252A VAL* 3.8 32.1 - - + -
264A PHE* 3.1 39.1 + - + -
265A LEU 3.4 15.5 - - - -
266A LYS* 3.9 32.0 - - + +
270A GLY 3.6 3.6 + - - -
271A LYS* 1.3 76.3 - - - +
273A ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLU* 3.0 51.1 + - + +
200A TYR* 3.8 18.8 + - - -
246A GLU* 3.3 25.7 + - + -
247A ILE* 2.5 45.6 + - - +
249A GLU* 5.1 14.6 - - - +
265A LEU 2.7 10.9 + - - -
267A ASP* 2.7 31.5 + - + +
271A LYS* 3.3 7.6 + - - +
272A TYR* 1.3 76.1 + - - +
274A PHE* 1.3 82.9 + - + +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLU 4.2 4.7 - - - -
108A GLU* 3.7 19.7 - - + -
109A LEU* 3.5 43.3 - - + -
112A LEU* 3.9 19.1 - - + -
244A LEU* 4.3 13.2 - - + -
245A MET 3.4 5.2 - - - +
246A GLU* 3.8 23.8 - - + -
247A ILE* 3.7 7.0 - - - +
264A PHE* 3.1 7.4 - - - +
265A LEU* 2.7 51.0 + - + +
266A LYS 4.8 1.3 - - - -
267A ASP* 4.4 11.9 - - + -
273A ARG* 1.3 113.0 - - + +
275A LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TYR* 4.0 15.7 - - + -
233A PHE* 4.1 18.6 - - + -
243A VAL* 3.7 2.2 - - + +
244A LEU* 3.3 10.1 - - - +
245A MET* 2.9 37.2 + - + +
247A ILE* 3.7 25.3 - - + +
255A LEU* 4.0 23.3 - - + -
259A VAL* 5.3 2.0 - - + -
262A THR* 3.4 39.5 - - + +
263A VAL 3.6 3.1 - - - -
264A PHE* 3.8 19.5 - - + -
274A PHE* 1.3 73.3 - - - +
276A LEU* 1.3 58.5 - - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.0 25.6 - - + -
242A ILE* 3.9 23.1 - - + -
243A VAL 3.4 7.9 - - - +
244A LEU* 4.1 12.6 - - + -
261A ASP 4.8 0.2 - - - +
262A THR* 3.5 1.6 - - - +
263A VAL* 2.8 53.3 + - + +
265A LEU* 4.3 25.4 - - + -
274A PHE 4.0 0.8 + - - -
275A LEU* 1.3 73.1 - - - +
277A LEU* 1.3 63.0 - - - +
278A ASN* 4.2 15.8 + - + +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A PHE* 4.0 24.7 - - + -
238A THR* 3.9 22.2 - - - +
241A LYS 3.8 0.9 - - - +
242A ILE* 3.4 2.1 - - - -
243A VAL* 2.8 51.3 + - + +
259A VAL* 4.1 9.0 - - + -
261A ASP* 3.9 24.2 - - + +
262A THR* 3.0 25.4 - - + +
275A LEU* 5.8 0.2 - - + -
276A LEU* 1.3 73.3 - - - +
278A ASN* 1.3 60.3 + - - +
279A ARG* 3.8 32.9 + - + +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.9 4.3 - - - +
120A TYR* 3.2 29.8 + - - -
241A LYS 4.3 1.3 - - - -
242A ILE* 3.8 14.4 - - + +
261A ASP 5.6 0.8 + - - -
276A LEU* 3.9 18.3 + - + +
277A LEU* 1.3 73.0 - - - +
279A ARG* 1.3 59.7 + - - +
280A ARG* 3.0 35.0 + - - +
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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