Contacts of the strand formed by residues 366 - 372 (chain B) in PDB entry 1WZ9
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 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 6.0 2.0 - - - +
9B SER* 3.7 27.1 + - - +
12B ALA* 4.3 7.6 - - + -
32B PRO* 3.7 25.9 - - + +
33B ILE* 3.6 19.2 + - - +
255B LEU* 3.6 30.7 - - + -
357B ILE* 4.2 24.2 - - + -
358B ILE 3.8 3.6 - - - +
359B ARG* 4.3 2.7 - - + +
364B ARG 4.6 3.6 - - - +
365B ASN* 1.3 73.8 + - - +
367B ILE* 1.3 58.6 + - - +
368B PHE 3.3 24.9 - - - +
369B PHE* 4.1 18.6 - - + -
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 2.8 33.8 + - - -
32B PRO* 3.6 2.0 - - - +
33B ILE* 4.0 22.3 - - + +
73B VAL* 5.3 1.3 - - + -
77B VAL* 4.2 18.6 - - + -
86B LEU* 4.8 4.9 - - + -
88B LEU* 3.7 24.7 - - + -
226B LEU* 4.0 15.9 - - + -
358B ILE* 2.8 18.5 + - + +
360B HIS* 3.9 20.9 - - + +
365B ASN* 3.9 16.2 - - + +
366B ILE* 1.3 75.4 - - - +
368B PHE* 1.3 80.9 + - + +
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Residues in contact with PHE 368 (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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29B LEU* 4.2 11.9 - - + -
30B PHE 3.4 7.2 - - - +
31B SER* 4.3 1.6 - - - -
86B LEU* 3.9 7.4 - - + -
88B LEU* 3.8 20.2 - - + -
165B ALA* 4.0 14.1 - - + -
166B TYR 4.1 5.6 - - - -
167B PHE* 3.4 35.2 - + + -
226B LEU* 5.4 0.4 - - + -
322B VAL* 3.5 33.4 - - + -
323B CME 4.7 3.1 - - - -
324B LEU* 5.0 6.7 - - + -
356B TYR* 5.2 2.0 - - + -
357B ILE* 3.3 3.7 - - - -
358B ILE* 2.8 59.9 + - + -
366B ILE* 3.3 7.2 - - - +
367B ILE* 1.3 95.0 - - + +
369B PHE* 1.3 60.7 + - - +
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Residues in contact with PHE 369 (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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12B ALA* 3.9 34.5 - - + -
13B VAL* 3.9 24.0 - - + -
16B PHE* 3.7 35.9 - + + -
28B VAL* 4.5 0.7 - - - +
29B LEU* 3.5 4.9 + - - -
30B PHE* 3.1 52.3 + + + -
32B PRO* 4.1 6.9 - - + +
250B LEU* 4.5 6.5 - - + -
255B LEU* 4.0 19.3 - - + -
355B ILE* 3.9 16.6 - - + -
356B TYR 3.7 2.9 - - - -
357B ILE* 3.6 20.4 - - + -
366B ILE* 4.1 9.9 - - + -
368B PHE* 1.3 73.4 - - - +
370B GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 370 (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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16B PHE* 3.9 7.6 - - - -
28B VAL 3.0 13.9 - - - -
29B LEU* 4.2 0.4 - - - -
355B ILE* 3.4 10.4 - - - +
356B TYR* 2.8 50.8 + - - +
369B PHE* 1.3 76.4 - - - +
371B LYS* 1.3 60.6 + - - -
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Residues in contact with LYS 371 (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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16B PHE* 4.0 16.6 - - + -
20B CME 4.2 16.3 + - - +
23B GLU 3.0 26.7 + - - -
24B PRO* 3.0 22.8 + - - +
26B GLY 3.6 14.8 - - - +
27B ASN* 3.6 7.8 - - - +
28B VAL* 2.9 40.7 + - + +
243B LEU* 4.0 22.0 - - + -
354B PHE 3.5 6.5 - - - +
355B ILE* 4.2 2.9 - - + +
356B TYR* 3.8 3.8 + - - -
370B GLY* 1.3 74.7 - - - +
372B PHE* 1.3 59.9 + - - +
373B CME 3.2 28.3 - - - -
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Residues in contact with PHE 372 (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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27B ASN* 3.7 7.0 - - - -
185B PHE* 3.7 35.2 - + - -
195B VAL* 4.9 0.7 - - + -
274B PRO* 3.9 12.8 - - + -
276B PHE* 3.4 45.5 - + + -
278B VAL* 4.3 10.8 - - + -
353B PRO* 3.1 4.2 - - - +
354B PHE* 2.7 67.7 + + + -
356B TYR* 3.9 8.2 - + + -
371B LYS* 1.3 73.4 - - - +
373B CME 1.3 60.3 + - - +
374B SER 3.6 24.0 - - - -
375B PRO* 3.8 16.8 - - + -
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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