Contacts of the helix formed by residues 366 - 376 (chain B) in PDB entry 5Y7G
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 SER 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B PRO* 5.4 1.1 - - - -
365B CYS* 1.3 77.3 + - - +
367B VAL* 1.3 67.2 + - - +
368B GLU* 3.1 12.5 + - - -
369B TRP* 3.2 32.1 + - - -
370B ALA* 3.0 20.8 + - - +
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Residues in contact with VAL 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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365B CYS 3.9 0.4 + - - -
366B SER* 1.3 72.6 - - - +
368B GLU* 1.3 87.5 + - + +
370B ALA* 3.5 6.8 + - - +
371B VAL* 3.4 20.6 + - - +
523B VAL* 3.5 19.5 - - + -
525B GLY* 3.7 31.6 - - - +
553B VAL* 4.3 15.3 - - + -
555B TRP* 4.8 17.0 - - + -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B SER* 3.1 9.8 - - - -
367B VAL* 1.3 98.9 - - - +
369B TRP* 1.3 59.3 + - - +
370B ALA 3.1 0.3 + - - -
371B VAL* 3.2 4.9 + - - +
372B ARG* 2.8 28.7 + - - +
384B TYR* 3.1 41.3 + - + -
507B ASP* 3.2 43.3 - - + +
508B LEU* 4.4 4.9 - - + +
522B GLU* 4.8 0.3 - - - +
523B VAL* 3.6 19.7 - - + +
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Residues in contact with TRP 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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365B CYS* 4.8 8.7 - - - -
366B SER* 3.2 43.0 + - - +
368B GLU* 1.3 75.9 - - - +
370B ALA* 1.3 62.0 + - - +
372B ARG* 3.2 43.0 + - - +
373B GLU* 3.2 26.9 + - - +
384B TYR* 3.9 38.2 - + + -
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Residues in contact with ALA 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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358B LEU* 4.6 15.2 - - + +
361B PRO* 5.7 3.4 - - + -
365B CYS* 4.3 17.4 - - - +
366B SER 3.0 15.6 + - - +
367B VAL* 3.7 8.5 - - - +
368B GLU 3.1 0.6 - - - -
369B TRP* 1.3 78.8 - - - +
371B VAL* 1.3 61.3 + - - +
373B GLU* 3.7 4.6 + - - +
374B HIS* 3.3 20.6 + - - +
555B TRP* 4.9 13.0 - - + -
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Residues in contact with VAL 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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356B LEU* 3.7 21.8 - - + -
358B LEU* 3.7 22.9 - - + -
367B VAL 3.4 10.7 + - - +
368B GLU 3.2 7.0 + - - +
370B ALA* 1.3 73.0 - - - +
372B ARG* 1.3 60.0 + - - +
374B HIS* 4.0 5.8 - - - +
375B LEU* 3.0 44.3 + - + +
508B LEU* 4.3 5.5 - - + +
521B VAL* 5.3 0.2 - - + -
523B VAL* 3.8 24.5 - - + -
551B CYS* 4.2 7.2 - - + -
553B VAL* 3.8 17.9 - - + -
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Residues in contact with ARG 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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368B GLU 2.8 17.0 + - - +
369B TRP* 3.5 39.5 + - - +
370B ALA 3.2 0.6 - - - -
371B VAL* 1.3 80.1 - - - +
373B GLU* 1.3 95.1 + - - +
376B GLU* 2.6 50.3 + - - +
382B VAL* 3.5 41.5 + - + +
384B TYR* 4.1 13.9 - - + +
508B LEU* 4.2 13.0 - - + +
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Residues in contact with GLU 373 (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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369B TRP 3.2 14.4 + - - +
370B ALA* 4.2 4.7 - - - +
372B ARG* 1.3 103.8 + - - +
374B HIS* 1.3 64.7 + - - +
376B GLU* 3.5 18.3 + - - +
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Residues in contact with HIS 374 (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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356B LEU* 3.7 35.0 - - + +
358B LEU* 4.2 19.3 - - + +
370B ALA 3.3 16.5 + - - +
371B VAL* 3.6 7.9 - - - +
372B ARG 3.2 0.4 - - - -
373B GLU* 1.3 77.2 - - - +
375B LEU* 1.3 78.7 + - + +
376B GLU 3.0 14.9 + - - +
377B GLU* 4.3 6.9 - - - +
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Residues in contact with LEU 375 (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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354B LEU* 5.2 6.5 - - + -
356B LEU* 6.0 0.9 - - + -
371B VAL* 3.0 31.8 + - + +
374B HIS* 1.3 94.2 - - + +
376B GLU* 1.3 56.6 + - - +
377B GLU* 3.1 24.2 + - - +
380B CYS* 4.1 12.0 - - - -
382B VAL* 3.6 16.1 - - + +
508B LEU* 5.4 1.8 - - + -
510B GLN* 3.4 33.7 - - - +
519B ARG* 4.2 11.4 - - - +
521B VAL* 4.6 15.9 - - + -
551B CYS* 6.3 0.4 - - + -
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Residues in contact with GLU 376 (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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372B ARG* 2.6 47.1 + - - +
373B GLU* 3.5 15.1 - - - +
374B HIS 3.0 4.9 + - - +
375B LEU* 1.3 74.6 - - - +
377B GLU* 1.3 63.6 + - - +
380B CYS 3.6 17.7 - - - +
381B ALA* 4.9 3.2 - - - +
382B VAL* 3.7 18.3 - - + +
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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