Contacts of the helix formed by residues 366 - 371 (chain B) in PDB entry 6XWQ
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 LEU 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B TYR* 4.6 5.6 - - + +
321B GLN* 4.0 12.3 - - + +
324B THR* 3.6 39.7 - - + -
325B VAL* 4.2 10.1 - - + -
362B GLY 2.9 13.6 + - - +
363B ALA* 3.2 15.0 - - - +
364B ILE 3.1 0.2 - - - -
365B MET* 1.3 77.7 - - - +
367B ALA* 1.3 55.4 + - - +
369B VAL* 3.1 23.7 - - + +
370B LEU* 2.9 36.6 + - + +
387B TYR* 3.9 24.9 - - + -
390B ILE* 4.2 14.4 - - + -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA 4.0 1.4 + - - -
364B ILE 3.0 15.3 + - - +
366B LEU* 1.3 78.0 - - - +
368B MET* 1.3 62.7 + - + +
369B VAL 3.1 0.2 - - - -
371B GLN* 2.9 35.0 + - - +
377B LEU* 3.6 31.6 - - + +
387B TYR* 4.0 11.7 + - + +
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Residues in contact with MET 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B THR* 4.2 4.9 + - - -
351B ALA* 4.6 7.7 - - + +
364B ILE 4.4 1.1 + - - +
365B MET* 3.0 46.1 + - + +
367B ALA* 1.3 81.7 - - + +
369B VAL* 1.3 56.1 + - - +
371B GLN* 4.3 15.1 - - - +
372B SER* 3.7 15.9 + - - -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN* 4.1 15.7 - - + +
325B VAL* 3.6 29.2 - - + -
344B VAL* 4.3 6.3 - - + -
347B THR* 3.6 27.4 - - + +
348B ALA* 4.3 15.3 - - + +
351B ALA* 4.2 5.8 - - + -
365B MET 3.6 1.2 + - - -
366B LEU* 3.1 31.6 - - + +
368B MET* 1.3 78.9 - - - +
370B LEU* 1.3 61.6 + - - +
371B GLN 3.5 0.2 - - - -
372B SER* 2.4 23.5 + - - -
373B VAL* 3.3 11.4 + - - +
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 3.9 26.2 - - + -
328B VAL* 3.5 39.3 - - + -
366B LEU* 2.9 28.4 + - + +
367B ALA 4.0 2.2 - - - +
369B VAL* 1.3 74.5 - - - +
371B GLN* 1.3 64.6 + - - +
372B SER 3.1 2.4 + - - -
373B VAL* 3.3 7.9 - - + +
375B LEU* 3.1 38.6 + - + +
376B ASP 5.4 0.9 - - - +
377B LEU* 4.0 14.4 - - + -
383B VAL* 5.8 3.4 - - + -
387B TYR* 3.6 35.2 - - + -
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Residues in contact with GLN 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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126B GLU* 4.8 4.8 + - - +
129B PRO* 4.8 9.4 - - - +
367B ALA 2.9 17.3 + - - +
368B MET* 4.3 18.1 - - - +
370B LEU* 1.3 76.1 - - - +
372B SER* 1.3 68.0 + - - +
374B GLY 4.3 2.6 + - - -
375B LEU 3.4 15.2 - - - +
376B ASP* 5.9 1.3 - - - -
377B LEU* 4.2 17.7 - - + +
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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