Contacts of the strand formed by residues 465 - 470 (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 ILE 465 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358O THR* 3.1 30.3 - - - +
360O VAL* 2.5 41.5 - - + -
394O THR* 4.4 5.6 - - + -
463O SER* 3.0 29.4 - - - +
464O GLU* 1.3 82.4 + - - +
466O GLU* 1.3 67.1 + - - +
467O ILE* 4.0 15.8 + - + +
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Residues in contact with GLU 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353O PHE* 4.4 21.7 - - + -
357O LYS* 3.3 38.8 + - + +
358O THR 2.9 8.7 + - - -
359O ILE* 3.3 11.4 - - + -
360O VAL 2.9 25.5 + - - +
456O ARG* 2.9 37.6 + - - +
458O GLY* 4.3 9.6 + - - -
465O ILE* 1.3 76.1 - - - +
467O ILE* 1.3 65.8 + - - +
468O PHE* 3.8 21.4 - - + -
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Residues in contact with ILE 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360O VAL* 3.6 27.1 - - + -
362O THR* 3.8 26.7 - - + -
456O ARG* 3.0 5.1 - - - +
457O ASP* 2.8 63.6 + - + +
458O GLY 5.5 0.8 - - - +
463O SER* 5.7 3.1 - - - +
465O ILE* 4.0 17.2 + - + +
466O GLU* 1.3 78.5 + - - +
468O PHE* 1.3 63.4 + - - +
469O ARG* 4.3 3.6 - - - +
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Residues in contact with PHE 468 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284O ILE* 3.9 12.1 - - + -
349O LEU* 3.5 48.0 - - + -
353O PHE* 3.9 16.8 - + - -
359O ILE* 3.6 22.2 - - + -
360O VAL 2.9 11.1 + - - +
361O PHE* 3.7 21.7 - + + +
362O THR* 3.1 26.0 + - - +
391O PHE* 5.5 0.7 - - - +
454O LEU* 4.7 15.9 - - + -
455O THR 3.3 7.9 - - - +
456O ARG* 3.5 37.5 - - + -
466O GLU* 3.8 16.2 - - + -
467O ILE* 1.3 74.2 - - - +
469O ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 469 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 3.4 27.3 - - - +
362O THR* 3.4 32.2 + - + +
363O HIS* 3.2 29.9 + - - +
364O SER* 4.2 2.8 + - - -
365O SER* 3.7 31.3 - - - +
454O LEU* 3.4 8.4 - - - +
455O THR* 2.9 39.7 + - - +
457O ASP* 2.7 39.8 + - - +
467O ILE* 4.3 4.4 - - + +
468O PHE* 1.3 74.4 - - - +
470O PRO* 1.3 76.9 - - + +
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Residues in contact with PRO 470 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O GLN* 3.8 32.5 - - + +
362O THR 3.3 17.7 - - - +
363O HIS* 4.3 3.1 - - - -
364O SER* 4.4 17.6 + - - +
371O ILE 4.7 8.0 - - - +
387O SER* 4.3 2.0 - - - +
391O PHE* 3.6 40.8 - - + -
453O LEU 3.5 7.0 - - - +
454O LEU* 3.8 4.0 - - + -
455O THR* 4.9 1.4 + - - +
469O ARG* 1.3 91.2 - - + +
471O GLY* 1.3 59.4 + - - +
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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