Contacts of the helix formed by residues 467 - 475 (chain A) in PDB entry 5I94
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 PHE 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A MET* 3.1 14.1 + - + +
466A ASP* 1.3 77.3 - - - +
468A SER* 1.3 51.7 + - - +
469A GLY 3.5 0.9 - - - -
470A GLN* 3.1 33.3 + - + -
471A PHE* 2.7 61.4 + + + +
474A HIS* 5.9 2.0 - + - -
505A ASP* 5.9 3.1 - - - -
507A MET* 3.8 30.9 - - + +
509A ASN* 3.4 19.1 - - - +
514A ILE* 4.1 23.1 - - + -
518A HIS* 4.0 22.9 - + - -
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A HIS 4.1 4.2 - - - +
461A SER 3.5 24.9 - - - -
462A CYS* 3.4 11.5 - - - -
463A GLY 4.4 0.4 - - - +
464A MET* 3.1 29.7 + - - +
465A TYR 2.6 21.1 + - - -
466A ASP 3.1 3.5 - - - -
467A PHE* 1.3 75.4 - - - +
469A GLY* 1.3 59.4 + - - +
471A PHE* 3.4 2.9 + - - +
472A ALA* 2.8 29.1 + - - +
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Residues in contact with GLY 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A SER* 5.0 1.9 + - - -
466A ASP 4.6 1.0 + - - -
467A PHE 3.5 0.4 - - - -
468A SER* 1.3 78.4 - - - +
470A GLN* 1.3 57.4 + - - +
472A ALA* 3.5 7.6 + - - +
473A PHE* 3.1 27.5 + - - +
310B LYS 4.2 5.7 - - - +
311B GLU* 4.0 32.8 + - - -
312B PRO* 5.5 4.9 - - - -
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Residues in contact with GLN 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ASP 5.8 0.4 - - - +
467A PHE* 3.1 38.5 + - + +
469A GLY* 1.3 74.1 - - - +
471A PHE* 1.3 65.9 + - - +
473A PHE* 3.3 2.9 + - - +
474A HIS* 3.0 40.1 + - + +
507A MET* 5.9 3.4 - - + +
310B LYS* 3.0 35.4 + - + +
311B GLU* 3.4 21.1 + - + +
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Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A HIS 5.4 3.8 - - - +
464A MET* 3.8 35.2 - - + -
467A PHE* 2.7 42.3 + + + +
468A SER 3.5 4.7 - - - +
470A GLN* 1.3 70.1 - - - +
472A ALA* 1.3 60.7 + - - +
474A HIS* 5.2 0.2 - - - -
475A VAL* 2.7 70.4 + - + +
476A GLY 3.2 4.2 + - - -
477A LEU 3.3 27.6 - - - -
479A ALA* 3.8 23.3 - - + -
489A LEU* 4.1 4.5 - - + -
514A ILE* 4.3 7.0 - - + -
517A CYS* 4.0 20.2 - - + -
518A HIS* 5.2 0.7 - + - -
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Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A HIS* 3.9 38.4 - - + +
461A SER* 5.3 1.8 - - - -
468A SER 2.8 19.2 + - - +
469A GLY* 3.6 10.3 - - - +
470A GLN 3.3 0.2 - - - -
471A PHE* 1.3 78.1 - - - +
473A PHE* 1.3 61.3 + - - +
476A GLY* 3.1 25.3 + - - +
477A LEU 5.5 0.9 - - - +
527A HIS* 3.9 4.0 + - - -
457B SER* 5.1 3.1 + - - -
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Residues in contact with PHE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A GLY 3.1 14.1 + - - +
470A GLN 3.8 3.6 - - - +
471A PHE 3.2 0.2 - - - -
472A ALA* 1.3 81.5 - - - +
474A HIS* 1.3 86.8 - + - +
527A HIS* 3.1 18.1 + - - -
292B TYR* 3.8 12.1 - - - -
301B THR* 4.1 10.1 - - + -
305B HIS* 3.8 14.1 - + - -
310B LYS* 3.5 42.2 - - + +
453B ARG* 5.8 0.9 + - - +
454B ASN* 3.4 49.7 - - - +
457B SER* 4.4 14.5 + - - -
458B LEU* 4.0 15.5 - - + -
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Residues in contact with HIS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 5.9 1.6 - + - -
470A GLN* 3.0 36.4 + - + +
473A PHE* 1.3 96.2 - + + +
475A VAL* 1.3 61.7 + - + +
518A HIS* 3.8 29.6 - + + +
521A VAL* 4.1 6.8 - - - +
527A HIS* 3.2 16.5 - - - -
301B THR* 4.9 8.3 - - + +
310B LYS* 2.9 33.5 + - - -
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A PHE* 2.7 64.0 + - + +
474A HIS* 1.3 74.4 - - - +
476A GLY* 1.3 60.8 + - - +
477A LEU* 3.7 14.7 - - + +
489A LEU* 4.8 0.2 - - + -
517A CYS* 3.7 28.5 - - + +
518A HIS* 4.0 25.8 - - + +
521A VAL* 3.3 27.2 - - + +
527A HIS* 3.3 9.1 - - - -
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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