Contacts of the helix formed by residues 368 - 373 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 3.3 20.4 - - + -
44B LEU* 2.9 31.8 + - - +
59B ARG* 2.8 43.0 + - - -
367O GLY* 1.3 71.9 - - - -
369O PRO* 1.3 66.8 - - + +
370O GLU* 3.1 15.3 - - - +
371O ILE* 2.9 8.0 + - + +
372O VAL* 2.9 26.5 + - - +
425O ASN* 4.2 7.3 + - - -
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Residues in contact with PRO 369 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367O GLY 3.7 3.8 - - - +
368O ASP* 1.3 86.0 - - + +
370O GLU* 1.3 68.9 + - - +
372O VAL* 3.9 5.4 - - + +
373O MET* 3.2 43.9 + - + +
384O TYR* 3.4 20.9 - - + -
421O LYS* 4.7 14.1 - - - +
425O ASN* 4.0 10.1 - - - +
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Residues in contact with GLU 370 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.8 28.0 - - + -
257O THR* 2.7 18.4 + - - +
368O ASP* 3.3 12.6 - - - +
369O PRO* 1.3 76.7 - - - +
371O ILE* 1.3 53.7 + - - +
373O MET 3.1 3.5 - - - +
375O SER* 2.6 28.4 + - - +
384O TYR* 2.4 39.3 + - + +
421O LYS* 5.6 0.7 - - - +
424O ILE* 3.8 2.1 - - + -
425O ASN* 2.8 58.0 + - - +
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Residues in contact with ILE 371 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.4 40.8 - - + -
44B LEU 3.6 24.9 - - - +
45B THR* 3.6 20.9 - - + -
257O THR* 4.2 5.8 - - + -
258O GLN* 4.1 8.2 + - - +
364O SER* 4.0 8.0 + - - +
366O GLY 4.0 13.7 - - - +
368O ASP 2.9 15.8 + - - +
370O GLU* 1.3 80.9 - - - +
372O VAL* 1.3 65.0 + - + +
373O MET 3.2 3.8 - - - -
470O PRO 4.7 6.8 - - - +
471O GLY* 5.4 4.9 - - - +
472O GLY 3.7 22.9 - - - +
473O GLY* 3.8 4.0 - - - -
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Residues in contact with VAL 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258O GLN* 3.0 12.1 + - - -
364O SER* 3.8 25.2 + - - +
366O GLY* 3.4 13.9 - - - -
367O GLY 3.2 36.3 - - - +
368O ASP 2.9 17.4 + - - +
369O PRO* 4.4 5.6 - - + +
371O ILE* 1.3 79.6 - - - +
373O MET* 1.3 60.3 + - + +
387O SER* 4.5 2.6 + - - -
515O NAG 3.4 30.1 - - + +
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Residues in contact with MET 373 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257O THR* 3.1 11.8 + - - -
258O GLN* 2.8 11.8 - - - +
369O PRO* 3.2 33.5 + - + +
370O GLU 3.1 7.0 - - - +
371O ILE 3.9 0.5 - - - -
372O VAL* 1.3 84.6 - - + +
374O HIS* 1.3 63.1 + - - +
375O SER 3.0 7.5 + - - -
384O TYR* 3.6 37.7 - - + +
385O CYS 3.1 13.7 - - - +
386O ASN* 4.4 12.3 - - - +
387O SER* 5.0 1.3 - - - +
419O ARG* 4.0 31.0 - - - +
421O LYS* 5.9 2.5 - - - -
515O NAG 4.0 22.9 - - + -
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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