Contacts of the helix formed by residues 422 - 429 (chain Y) 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 THR 422 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255Y ARG 4.0 17.3 - - - +
256Y ARG* 4.0 28.3 - - + -
263Y THR* 6.4 0.7 - - + -
348Y LYS* 3.3 35.1 + - + -
419Y GLN 3.9 4.4 + - - -
420Y VAL 3.5 0.2 - - - -
421Y GLN* 1.4 81.2 - - + +
423Y LEU* 1.4 49.9 + - - +
424Y MET 3.6 2.2 - - - -
425Y MET* 3.2 15.5 + - + +
426Y SER* 2.9 34.3 + - - -
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Residues in contact with LEU 423 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y LEU* 4.2 23.8 - - + -
26Y VAL* 4.4 5.8 - - + -
181Y ARG* 3.9 18.4 - - - +
182Y GLY 4.1 9.2 - - - +
183Y ILE* 3.5 48.0 - - + -
419Y GLN 3.8 10.9 + - - +
420Y VAL* 3.6 17.7 + - - +
421Y GLN 3.5 2.6 + - - -
422Y THR* 1.4 70.5 - - - +
424Y MET* 1.4 54.7 + - - +
426Y SER* 4.5 10.1 - - - +
427Y SER* 2.7 48.8 + - - +
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Residues in contact with MET 424 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y ARG* 5.8 5.8 - - - -
181Y ARG* 3.9 20.5 - - - +
256Y ARG* 4.2 20.0 - - - +
420Y VAL 5.3 0.2 + - - -
422Y THR 3.6 0.2 - - - -
423Y LEU* 1.4 74.5 - - - +
425Y MET* 1.3 67.4 + - - +
427Y SER* 3.7 2.2 - - - -
428Y GLN* 2.9 46.1 + - + +
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Residues in contact with MET 425 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256Y ARG* 3.2 52.0 - - + +
257Y VAL* 4.0 17.5 - - + +
258Y TYR* 4.6 11.0 - - + -
422Y THR* 3.2 18.9 + - + +
424Y MET* 1.3 86.5 - - - +
426Y SER* 1.4 50.2 + - - +
428Y GLN* 3.7 2.0 - - - +
429Y TYR* 2.7 71.4 + - + +
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Residues in contact with SER 426 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C ASP* 3.9 13.5 + - - +
183Y ILE* 5.7 1.4 - - - +
422Y THR* 2.9 19.7 + - - -
423Y LEU* 4.0 12.7 - - - +
425Y MET* 1.4 67.8 - - - +
427Y SER* 1.3 66.7 + - - +
429Y TYR 3.1 19.5 + - - +
430Y GLU* 4.7 1.2 - - - -
431Y SER* 3.6 17.7 + - - -
434Y LYS* 3.4 27.9 - - - -
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Residues in contact with SER 427 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ASP* 5.3 5.5 - - - +
181Y ARG* 3.1 48.5 + - - -
182Y GLY 5.5 0.2 + - - -
423Y LEU* 2.7 29.3 + - - +
424Y MET* 3.7 5.6 - - - -
426Y SER* 1.3 76.3 - - - +
428Y GLN* 1.4 67.1 + - - +
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Residues in contact with GLN 428 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y LEU* 5.9 5.1 - - - +
424Y MET* 2.9 44.3 + - + +
425Y MET* 3.7 6.1 - - - +
427Y SER* 1.4 79.2 + - - +
429Y TYR* 1.4 94.6 + - + +
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Residues in contact with TYR 429 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425Y MET* 2.7 51.5 + - + +
426Y SER* 3.1 16.0 - - - +
427Y SER 3.5 0.4 - - - -
428Y GLN* 1.4 107.4 + - + +
430Y GLU* 1.4 68.1 + - - +
431Y SER* 4.4 0.2 - - - -
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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