Contacts of the helix formed by residues 359 - 364 (chain B) in PDB entry 5M4G
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 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B LEU* 4.0 9.6 - - + -
347B LEU* 4.0 21.8 - - + -
354B MET* 3.1 32.3 + - + +
357B ALA* 3.2 5.2 - - + +
358B HIS* 1.3 75.0 - - - +
360B GLY* 1.3 65.4 + - - +
362B VAL* 3.0 39.0 + - + +
363B PHE* 3.6 11.9 - - + -
425B ALA* 4.7 0.7 - - + -
431B ARG* 4.1 23.6 - - + +
434B PHE* 3.6 31.2 - - + -
435B LEU* 4.0 19.3 - - + -
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Residues in contact with GLY 360 (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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334B ASP* 3.7 31.0 - - - +
337B HIS* 5.6 3.8 + - - +
338B LEU* 3.8 24.7 - - - +
355B VAL* 5.8 0.2 - - - +
358B HIS 3.1 2.0 - - - -
359B LEU* 1.3 78.5 - - - +
361B ALA* 1.3 56.2 + - - +
363B PHE* 3.1 7.6 + - - +
364B MET* 3.0 23.7 + - - +
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Residues in contact with ALA 361 (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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334B ASP* 4.3 5.3 + - - +
358B HIS* 3.2 9.4 + - + +
359B LEU 3.1 1.4 - - - -
360B GLY* 1.3 74.9 - - - +
362B VAL* 1.3 63.1 + - - +
363B PHE 3.3 0.2 - - - -
364B MET 3.7 9.0 - - - -
365B PRO* 3.4 25.5 - - + +
392B PRO* 3.4 45.8 - - + +
393B GLY* 3.7 7.4 - - - +
421B LEU* 4.3 2.6 - - - +
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Residues in contact with VAL 362 (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 HIS 4.8 1.3 - - - +
359B LEU* 3.0 24.4 + - + +
361B ALA* 1.3 78.1 - - - +
363B PHE* 1.3 70.1 + - + +
365B PRO* 4.6 0.7 - - - +
416B TYR 4.3 5.5 - - - +
418B ILE* 5.0 3.8 + - - +
421B LEU* 3.6 43.8 - - + +
422B LEU* 3.8 28.6 - - + +
425B ALA* 4.1 14.8 - - + -
431B ARG* 3.5 28.3 - - - +
435B LEU* 5.9 0.4 - - + -
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Residues in contact with PHE 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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337B HIS* 5.6 4.0 - - + -
338B LEU* 4.6 5.2 - - + -
341B LEU* 3.6 32.8 - - + -
346B ILE* 4.6 5.8 - - + -
347B LEU* 4.2 20.2 - - + -
359B LEU* 3.6 20.6 - - + -
360B GLY* 3.1 6.0 + - - +
362B VAL* 1.3 86.2 - - + +
364B MET* 1.3 58.8 - - + +
365B PRO* 3.8 2.2 - - - -
414B GLY 4.3 0.7 - - - -
415B ILE* 3.4 16.0 - - + -
416B TYR* 2.9 48.9 + - - +
417B PHE* 4.0 22.0 - + - -
422B LEU* 3.9 20.9 - - + -
435B LEU* 4.0 23.6 - - + -
440B LEU* 4.9 0.4 - - + -
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Residues in contact with MET 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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330B HIS* 3.6 31.7 + - + +
333B ALA* 4.4 16.6 - - + -
334B ASP* 3.5 19.9 - - - +
337B HIS* 3.8 13.9 - - + +
360B GLY 3.0 10.3 + - - +
361B ALA* 3.6 13.9 - - - +
363B PHE* 1.3 76.3 - - - +
365B PRO* 1.3 64.7 - - - +
366B HIS* 3.3 31.3 + - + +
368B LEU* 4.8 6.7 - - - -
393B GLY* 4.4 4.2 - - - -
413B PRO* 3.8 13.0 - - - -
414B GLY 3.3 34.1 - - - +
416B TYR* 4.4 0.9 - - - -
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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