Contacts of the strand formed by residues 408 - 411 (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 VAL 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B VAL 4.5 2.6 + - - -
187B LYS* 3.9 28.1 + - + +
192B LEU* 3.9 20.4 - - + -
195B LEU* 4.0 7.0 - - + -
371B PHE* 3.2 11.0 - - - +
372B LEU* 3.0 58.8 + - + +
406B GLY 3.6 1.9 + - - +
407B MET* 1.3 76.5 - - - +
409B LEU* 1.3 66.3 + - - +
454B ASP* 5.3 1.1 - - + -
455B VAL 3.3 11.9 - - - +
456B VAL* 4.2 6.1 - - + -
465B LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 409 (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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320B MET* 4.4 11.7 - - + -
326B TRP* 3.6 45.8 - - + +
370B HIS 3.3 9.6 - - - +
371B PHE* 3.9 17.9 - - + -
372B LEU* 5.0 1.1 - - - -
399B THR* 4.9 1.6 - - + -
403B LEU* 3.9 22.4 - - + -
407B MET* 3.8 22.7 - - + -
408B VAL* 1.3 82.9 - - - +
410B THR* 1.3 69.2 + - - +
454B ASP* 3.6 2.2 - - - +
455B VAL* 2.8 36.4 + - + +
457B VAL* 4.0 11.0 - - + -
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Residues in contact with THR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 4.0 3.1 - - - +
326B TRP* 3.6 8.8 - - - -
369B GLY* 3.3 15.2 - - - -
370B HIS* 2.9 57.5 + - + +
372B LEU* 4.0 11.9 - - + -
409B LEU* 1.3 76.7 - - - +
411B VAL* 1.3 63.9 + - - +
412B GLU* 3.4 6.5 + - - -
452B GLU* 3.4 25.6 - - - +
453B GLU 3.3 6.7 - - - -
454B ASP* 3.5 16.2 - - - +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B SER* 4.4 8.0 + - - +
316B VAL* 3.9 26.7 - - + -
317B MET* 4.3 15.9 - - + -
320B MET* 3.7 28.3 - - + -
326B TRP* 4.2 3.8 - - + -
368B LEU* 3.9 4.5 - - + -
409B LEU 5.0 0.2 - - - -
410B THR* 1.3 78.2 - - - +
412B GLU* 1.3 59.8 + - - +
413B PRO* 3.5 13.4 - - + +
451B ILE 3.3 5.4 - - - +
453B GLU* 2.9 36.5 + - + +
455B VAL* 4.0 22.2 - - + -
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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