Contacts of the helix formed by residues 414 - 418 (chain B) in PDB entry 5MBV
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 ASP 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 5.1 1.6 - - - +
23B ALA 3.2 28.1 + - - +
24B SER* 4.3 0.9 - - - -
25B ALA 4.1 0.2 + - - -
29B LYS* 5.9 2.5 - - + +
387B GLN* 3.1 22.3 + - - +
413B GLY* 1.3 72.7 - - - -
415B PRO* 1.3 65.5 - - - +
416B LYS* 2.3 33.6 + - - -
417B GLN* 2.8 50.8 + - + +
803B TYR* 3.3 22.5 + - - -
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Residues in contact with PRO 415 (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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22B GLU* 3.9 17.3 - - + +
387B GLN* 4.1 9.6 - - + -
413B GLY 3.9 1.8 - - - +
414B ASP* 1.3 90.9 - - - +
416B LYS* 1.3 61.1 + - + +
417B GLN 3.4 0.9 + - - -
418B ALA 3.8 3.9 + - - -
427B ILE* 3.9 11.8 - - + +
430B TYR* 3.4 44.9 - - + +
434B ARG* 6.2 0.2 - - - -
472B GLU 5.7 0.2 - - - +
473B ILE* 3.6 39.0 - - + +
474B PRO* 5.7 0.9 - - + +
800B ARG* 3.3 18.5 - - - -
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Residues in contact with LYS 416 (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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22B GLU* 5.3 4.6 + - - +
24B SER* 4.2 12.8 + - - +
414B ASP* 2.3 32.3 + - - +
415B PRO* 1.3 79.6 - - + +
417B GLN* 1.3 57.0 + - - +
418B ALA 3.5 0.4 - - - -
468B PHE* 3.5 36.1 - - + -
473B ILE* 4.1 13.5 - - + -
474B PRO 4.5 11.0 + - - +
475B PHE* 4.5 13.7 - - + +
476B ILE* 5.8 6.3 - - - +
800B ARG* 3.3 32.8 - - - +
803B TYR* 3.4 53.2 + - + -
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Residues in contact with GLN 417 (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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23B ALA 4.8 1.0 + - - -
24B SER 4.3 2.0 + - - -
25B ALA* 3.3 36.7 - - + +
26B GLY 4.8 0.2 - - - +
29B LYS* 4.2 18.8 - - - +
385B GLU* 4.2 2.6 - - - +
387B GLN* 4.0 8.5 + - + +
414B ASP* 2.8 35.9 + - + +
416B LYS* 1.3 77.8 - - - +
418B ALA* 1.3 58.2 + - - +
419B ILE* 3.3 6.7 + - - +
420B TYR* 5.9 0.3 - - - -
745B LYS* 3.4 47.2 + - + +
803B TYR* 4.1 8.7 - - + -
804B VAL* 3.9 16.6 - - + +
808B ARG* 4.1 7.4 - - - +
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Residues in contact with ALA 418 (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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387B GLN* 3.5 38.9 - - + +
388B ASP* 4.9 1.6 - - - +
415B PRO 3.8 5.1 + - - +
416B LYS 3.5 3.0 - - - -
417B GLN* 1.3 74.3 - - - +
419B ILE* 1.3 61.9 + - - +
420B TYR* 3.5 7.4 - - + +
421B ALA* 5.4 0.7 + - - +
425B ALA* 5.6 5.2 - - + -
426B ASP 6.5 0.2 - - - -
427B ILE* 4.9 4.3 - - + +
797B GLU* 4.7 1.4 - - - +
800B ARG* 3.2 42.2 + - - +
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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