Contacts of the strand formed by residues 283 - 289 (chain A) in PDB entry 6N8P
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 ILE 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.2 19.6 - - - +
248A CYS* 3.2 24.4 - - + +
249A HIS 3.4 6.7 + - - +
252A GLY 3.3 30.1 - - - +
253A SER 3.9 12.8 - - - +
254A TYR* 4.3 7.9 - - + -
274A PRO* 4.1 12.3 - - + -
282A ALA* 1.3 71.5 - - - +
284A THR* 1.3 63.1 + - - +
285A ARG 3.4 21.1 - - - +
286A ILE* 4.6 0.2 - - + -
300A PHE* 3.6 27.4 - - + -
301A GLN 3.4 10.3 - - - +
303A GLY* 3.6 19.5 - - - +
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Residues in contact with THR 284 (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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234A GLU* 3.9 20.2 - - - +
235A ASN* 3.2 20.1 + - - +
282A ALA* 4.4 13.2 - - + +
283A ILE* 1.3 73.2 - - - +
285A ARG* 1.3 63.6 + - - +
301A GLN* 3.1 39.2 + - + +
302A GLY* 5.8 1.1 - - - -
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Residues in contact with ARG 285 (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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235A ASN* 3.7 21.9 + - - +
237A TRP* 4.1 23.6 - - - -
248A CYS* 3.9 2.9 - - - -
283A ILE* 3.4 5.7 - - - +
284A THR* 1.3 83.6 + - - +
286A ILE* 1.3 70.2 + - - +
287A LEU* 3.9 15.7 - - + +
300A PHE* 3.3 2.4 - - - -
301A GLN* 3.0 26.0 + - - +
334A GLY* 5.7 0.2 - - - -
335A PHE* 2.5 65.7 + - + +
336A THR* 4.7 5.9 + - - +
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Residues in contact with ILE 286 (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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235A ASN* 4.2 5.4 + - - +
236A ILE 4.7 2.5 - - - +
237A TRP* 3.5 22.5 - - + +
246A VAL* 3.6 35.9 - - + +
248A CYS* 3.6 22.4 - - + +
254A TYR* 3.5 44.6 - - + -
285A ARG* 1.3 79.3 - - - +
287A LEU* 1.3 79.4 + - - +
298A THR* 4.4 6.5 - - + -
299A ILE 3.2 12.1 - - - +
300A PHE* 3.7 13.7 - - + -
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Residues in contact with LEU 287 (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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237A TRP* 3.7 36.3 - - + -
285A ARG* 3.9 27.4 - - - +
286A ILE* 1.3 87.1 - - - +
288A TRP* 1.3 61.0 + - - +
289A LEU* 4.0 17.5 - - + -
297A PHE 4.3 0.4 - - - -
298A THR* 3.7 6.4 - - - +
299A ILE* 2.6 40.7 + - + +
335A PHE* 3.9 24.0 - - + -
336A THR 5.6 0.2 - - - -
337A VAL* 3.8 32.3 - - + +
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Residues in contact with TRP 288 (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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237A TRP* 3.2 28.6 + - + +
239A GLN* 3.6 47.8 - - + +
244A LEU* 3.9 14.5 - - + +
246A VAL* 3.8 30.3 - - + -
254A TYR* 5.5 2.5 - + - -
256A GLN* 3.5 29.8 - - - -
287A LEU* 1.3 73.2 - - - +
289A LEU* 1.3 60.4 + - - +
290A THR* 4.2 7.2 + - + +
296A PRO* 3.6 36.1 - - + -
297A PHE 3.6 3.4 - - - -
298A THR* 3.2 33.4 - - + -
348A ASP* 4.0 4.3 - - - +
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Residues in contact with LEU 289 (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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237A TRP* 4.1 24.9 - - + +
287A LEU* 4.1 13.7 - - + -
288A TRP* 1.3 77.7 - - - +
290A THR* 1.3 62.1 + - - +
291A THR* 5.3 0.2 - - - -
296A PRO* 3.2 6.2 - - - +
297A PHE* 2.7 45.8 + - + +
299A ILE* 4.1 13.2 - - + -
337A VAL* 3.6 36.1 - - + -
339A THR* 4.4 7.9 - - + -
348A ASP* 3.4 27.1 - - + +
350A PRO* 3.9 18.4 - - + -
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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