Contacts of the helix formed by residues 361 - 368 (chain B) in PDB entry 3R2W
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 VAL 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 5.3 2.0 - - + -
212B HIS* 3.0 36.0 + - + +
213B GLY* 3.3 5.3 - - - -
215B ILE* 3.6 31.0 - - + -
216B TYR* 3.1 26.4 + - + +
238B VAL* 4.7 13.5 - - + -
267B PHE* 4.8 0.3 - - - -
319B ASN* 4.6 3.8 - - - +
321B LEU* 3.5 38.6 - - + -
323B ILE* 5.2 2.5 - - + -
360B ALA* 1.3 73.1 - - - +
362B GLY* 1.3 68.9 + - - +
363B ALA 3.0 1.7 + - - -
364B ALA* 3.2 9.5 + - - +
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 4.7 0.4 - - - -
269B MET* 5.0 4.4 - - - +
293B LEU* 3.8 21.2 - - - +
317B ASN* 4.8 7.4 - - - +
319B ASN* 4.5 4.9 + - - -
321B LEU* 4.3 12.6 - - - -
360B ALA* 3.4 2.6 - - - +
361B VAL* 1.3 85.7 - - - +
363B ALA* 1.3 58.4 + - - +
364B ALA 2.7 7.5 + - - -
365B ILE* 3.1 22.5 + - - +
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Residues in contact with ALA 363 (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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293B LEU* 3.7 23.8 + - + +
338B ASP 3.5 13.1 - - - +
339B MET* 3.8 5.8 - - + -
340B GLU* 3.6 41.4 - - + +
360B ALA* 3.6 17.7 + - + +
361B VAL 3.0 2.6 + - - -
362B GLY* 1.3 74.1 - - - +
364B ALA* 1.3 60.9 + - - +
365B ILE* 3.3 1.4 + - - +
366B LYS* 3.8 15.8 + - - +
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Residues in contact with ALA 364 (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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216B TYR* 3.4 19.5 - - + +
267B PHE* 4.4 1.8 - - + -
337B ILE* 3.4 28.9 - - + -
338B ASP 4.6 1.6 - - - -
339B MET* 4.0 7.2 - - + +
361B VAL 3.2 16.0 + - - +
362B GLY 2.7 1.6 + - - -
363B ALA* 1.3 73.5 - - - +
365B ILE* 1.3 65.0 + - - +
366B LYS* 3.2 3.4 - - - -
367B SER* 2.9 22.4 + - - -
368B PHE* 3.2 14.4 - - + -
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Residues in contact with ILE 365 (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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267B PHE* 2.9 43.2 - - + +
269B MET* 3.9 14.1 - - + +
284B LEU* 3.8 24.0 - - + -
290B LYS* 5.9 0.2 - - - +
291B LEU* 3.4 38.4 - - + +
292B ARG* 4.9 0.2 - - - -
293B LEU 5.2 5.6 - - - +
362B GLY 3.1 11.7 + - - +
363B ALA 3.3 0.9 - - - +
364B ALA* 1.3 74.6 - - - +
366B LYS* 1.3 68.3 + - - +
367B SER 2.7 2.8 + - - -
368B PHE* 2.8 22.3 + - - +
371B SER* 3.4 18.5 + - - +
372B LEU 5.6 2.5 - - - +
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Residues in contact with LYS 366 (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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290B LYS* 3.4 30.3 + - + +
291B LEU 3.5 13.1 + - - +
292B ARG* 3.4 45.7 - - + +
338B ASP* 2.6 43.6 + - + +
340B GLU* 2.8 33.9 + - - -
363B ALA 3.8 10.4 + - - +
364B ALA 4.3 0.4 - - - +
365B ILE* 1.3 78.7 - - - +
367B SER* 1.3 57.7 + - - +
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Residues in contact with SER 367 (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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290B LYS* 4.4 3.8 + - - +
331B LEU* 3.8 19.2 - - - +
336B ALA 3.2 24.2 - - - -
337B ILE* 3.5 9.3 - - - +
338B ASP* 3.5 22.0 + - - -
364B ALA 2.9 14.2 + - - -
365B ILE 2.7 4.2 + - - -
366B LYS* 1.3 73.8 - - - +
368B PHE* 1.3 61.0 + - - -
369B GLU* 3.4 10.9 - - - +
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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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216B TYR* 5.3 6.5 - + - -
266B GLU* 3.6 28.5 - - + -
267B PHE* 3.8 23.1 - + + -
290B LYS* 3.1 22.5 + - - +
323B ILE* 3.5 25.6 - - + -
327B ALA* 4.1 17.7 - - + -
328B VAL* 5.1 6.7 - - + -
331B LEU* 4.0 22.9 - - + -
337B ILE* 4.3 11.2 - - + -
364B ALA* 3.2 32.3 - - + -
365B ILE 2.8 11.0 + - - +
367B SER* 1.3 78.1 - - - +
369B GLU* 1.3 67.0 + - - +
371B SER* 3.7 18.1 - - - +
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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