Contacts of the helix formed by residues 368 - 373 (chain K) in PDB entry 4R2G
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 368 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42H SER 4.5 0.5 - - - +
43H PHE* 3.7 13.0 - - + -
44H LEU* 3.1 28.9 + - - +
59H ARG* 2.5 36.8 + - - -
367K GLY* 1.3 75.1 - - - -
369K PRO* 1.3 62.9 - - + +
370K GLU* 3.3 15.9 - - - +
371K ILE* 2.9 31.9 + - + +
372K VAL* 2.9 13.6 + - - +
425K ASN* 3.6 16.0 + - - +
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Residues in contact with PRO 369 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367K GLY 3.8 4.0 - - - +
368K ASP* 1.3 87.8 - - + +
370K GLU* 1.3 68.1 + - - +
372K VAL* 4.6 5.4 - - + +
373K MET* 3.1 39.2 + - + +
384K TYR* 3.5 25.6 - - + -
421K LYS* 3.7 20.6 - - - +
425K ASN* 4.6 4.7 - - - +
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Residues in contact with GLU 370 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PHE* 3.8 30.1 - - + -
257K THR* 2.8 14.0 + - - +
368K ASP* 3.0 10.6 + - - +
369K PRO* 1.3 79.4 - - - +
371K ILE* 1.3 58.8 + - - +
373K MET 3.7 1.3 - - - -
375K SER* 2.2 38.7 + - - +
384K TYR* 2.6 35.5 + - + +
421K LYS* 4.8 2.8 + - - +
424K ILE* 4.1 2.3 - - + -
425K ASN* 3.1 49.3 + - - +
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Residues in contact with ILE 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PHE* 3.5 35.0 - - + -
44H LEU 3.0 28.5 - - - +
45H THR* 3.5 24.7 - - + -
257K THR* 3.7 8.3 + - + -
258K GLN* 3.3 16.5 + - - +
364K SER* 4.1 6.5 + - - +
366K GLY 4.6 2.9 - - - +
367K GLY* 4.4 2.0 - - - -
368K ASP* 2.9 21.9 + - + +
370K GLU* 1.3 85.2 - - - +
372K VAL* 1.3 63.6 + - + +
373K MET 3.1 2.8 - - - +
471K GLY* 4.8 9.1 - - - +
472K GLY 3.6 21.8 - - - +
473K GLY* 3.8 4.3 - - - -
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Residues in contact with VAL 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K GLN* 3.2 12.7 + - - +
363K HIS* 6.0 1.6 - - + +
364K SER* 3.8 27.9 + - - +
366K GLY* 3.4 27.8 - - - +
367K GLY 3.4 18.8 - - - +
368K ASP 2.9 21.4 + - - +
369K PRO* 4.7 3.8 - - + +
371K ILE* 1.3 78.9 - - + +
373K MET* 1.3 66.7 + - + +
386K ASN* 5.2 2.1 - - - +
387K SER* 4.2 4.2 + - - -
515K NAG 5.6 6.5 - - + -
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Residues in contact with MET 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257K THR* 2.9 14.6 + - - -
258K GLN* 3.3 5.8 - - - -
369K PRO* 3.1 26.7 + - + +
370K GLU 3.3 7.1 - - - +
371K ILE 3.8 1.0 - - - -
372K VAL* 1.3 86.3 - - + +
374K HIS* 1.3 58.9 + - - +
375K SER 2.8 9.5 + - - +
384K TYR* 3.6 43.5 - - + +
385K CYS 3.0 22.4 - - - +
386K ASN* 4.6 10.1 - - - +
387K SER* 4.9 1.6 - - - -
419K ARG* 3.7 29.8 - - - +
421K LYS* 5.3 1.3 - - - -
515K NAG 3.5 29.4 - - + -
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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