Contacts of the strand formed by residues 340 - 345 (chain D) in PDB entry 5MG3
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 GLN 340 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D SER* 3.3 3.3 - - - -
332D SER* 3.1 31.9 + - - +
333D GLN 4.2 0.2 + - - -
334D ASP* 3.4 36.3 - - + +
336D TYR* 3.6 27.4 - - + +
338D GLN* 2.8 27.8 + - - +
339D PRO* 1.3 77.1 + - - +
341D VAL* 1.4 61.5 + - - +
342D ASN* 3.6 13.5 - - - +
407D ARG* 4.1 8.9 + - - +
408D ILE 4.3 4.6 - - - +
409D THR* 4.9 0.5 - - - -
410D GLY* 3.3 25.7 + - - -
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Residues in contact with VAL 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D SER* 5.4 0.7 - - - -
330D THR 3.7 9.6 - - - +
331D SER* 3.9 14.1 - - - -
339D PRO 4.3 0.8 + - - -
340D GLN* 1.4 70.1 - - - +
342D ASN* 1.3 72.5 + - - +
408D ILE* 2.9 48.3 + - + +
409D THR 4.6 2.5 + - - +
411D ILE* 4.0 31.6 - - + -
420D LEU* 4.7 9.6 - - + +
421D SER* 4.8 12.8 - - - +
424D LEU* 3.8 28.9 - - + -
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Residues in contact with ASN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D SER* 3.2 7.2 - - - -
330D THR* 2.8 47.1 + - + +
331D SER* 4.3 0.2 - - - -
332D SER* 2.7 29.2 + - - -
340D GLN* 3.6 12.3 + - - +
341D VAL* 1.3 83.6 + - - +
343D ILE* 1.3 65.9 + - - +
405D SER* 4.8 9.4 - - - +
406D PHE 3.5 10.0 + - - +
407D ARG* 3.6 28.7 - - - +
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Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D PHE* 6.5 0.2 - - + -
326D ILE* 4.0 23.3 - - + -
328D ASP 3.6 10.1 - - - +
329D SER* 3.9 9.4 - - - -
342D ASN* 1.3 78.1 - - - +
344D SER* 1.4 60.6 + - - +
345D LEU* 3.6 25.5 + - + -
367D THR* 4.5 11.7 - - + +
405D SER* 3.5 3.5 + - - -
406D PHE* 2.7 50.8 + - + +
408D ILE* 3.8 32.7 - - + +
424D LEU* 4.2 22.7 - - + +
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Residues in contact with SER 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ILE* 3.6 3.6 - - - +
327D THR* 2.8 37.6 + - - -
328D ASP* 2.8 42.8 + - - +
329D SER* 4.4 0.6 - - - +
330D THR* 6.4 1.8 - - - -
342D ASN 4.3 0.2 - - - -
343D ILE* 1.4 68.7 - - - +
345D LEU* 1.3 57.4 + - - +
404D ASN* 3.4 11.3 + - - +
405D SER* 4.9 0.2 - - - +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D PHE* 5.5 3.1 - - + -
321D LEU* 4.0 17.7 - - + -
325D HIS* 3.4 9.6 - - + +
326D ILE* 3.8 19.3 - - + -
327D THR* 4.6 4.0 - - - -
343D ILE* 3.6 23.8 - - + -
344D SER* 1.3 74.1 + - - +
346D ASP* 1.3 66.7 + - - +
349D GLY* 5.0 1.3 - - - -
350D GLY 4.5 4.7 - - - +
353D MET* 3.9 22.2 - - + -
403D GLY 3.7 22.4 - - - +
404D ASN* 2.9 32.1 + - - +
406D PHE* 3.8 28.3 - - + -
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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