Contacts of the helix formed by residues 472 - 478 (chain B) in PDB entry 4EG8
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 TYR 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B GLN* 5.6 0.2 - - - -
367B ASP 4.8 0.2 + - - -
368B GLU* 2.7 47.3 + - + +
449B VAL* 3.0 29.0 + - - +
450B SER* 4.1 6.5 - - - +
451B ARG* 3.4 51.8 - - + +
456B LEU* 4.7 3.8 - - + -
470B CAS 3.3 2.5 + - - -
471B VAL* 1.3 80.1 - - - +
473B VAL* 1.3 88.2 + - + +
474B TRP* 3.2 32.3 + + - +
475B LEU 3.7 1.3 + - - -
476B ASP* 3.3 15.6 + - - +
812B 0P6 3.5 26.2 - + - -
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Residues in contact with VAL 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ASP* 3.7 5.8 - - - +
472B TYR* 1.3 92.6 - - + +
474B TRP* 1.3 94.8 + - + +
477B ALA* 2.6 35.2 + - + +
478B LEU* 3.9 0.3 + - - +
811B GOL 3.3 22.6 + - - +
812B 0P6 3.0 55.0 - - + +
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Residues in contact with TRP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B LEU* 3.7 21.0 - - + +
448B SER 3.4 23.3 + - - -
449B VAL* 4.4 7.4 - - + -
451B ARG* 5.5 0.6 - - - +
472B TYR* 3.2 26.1 + + - -
473B VAL* 1.3 100.3 - - + +
475B LEU* 1.3 62.5 + - - +
478B LEU* 3.2 31.8 + - + +
522B PHE* 3.4 55.9 - + + -
526B TYR* 3.7 22.7 - + + -
530B PHE* 3.9 25.9 - - + -
811B GOL 4.5 10.1 - - - -
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B VAL* 3.4 16.3 - - + +
344B LEU* 3.9 22.6 - - + +
345B TRP* 3.6 31.9 - - + +
348B LEU* 3.9 13.7 - - + -
354B ILE* 3.7 21.8 - - + -
449B VAL* 4.0 16.4 - - + +
471B VAL* 3.8 18.6 - - + -
472B TYR 3.7 2.4 + - - -
473B VAL 3.6 0.2 - - - -
474B TRP* 1.3 77.9 - - - +
476B ASP* 1.3 55.6 + - - +
479B THR* 2.7 23.0 + - - +
530B PHE* 3.7 37.2 - - + -
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Residues in contact with ASP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B HIS* 2.7 30.0 + - - +
332B THR* 3.8 9.0 - - - -
337B HIS* 2.8 52.1 + - - -
341B VAL* 4.1 5.4 - - - -
461B ILE* 3.6 12.9 + - + +
471B VAL* 4.2 10.3 - - + +
472B TYR 3.3 19.0 + - - +
474B TRP 3.2 0.6 - - - -
475B LEU* 1.3 78.2 - - - +
477B ALA* 1.3 63.6 + - - +
479B THR 3.6 3.3 + - - -
812B 0P6 2.7 22.1 + - - +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 3.5 17.6 - - + +
287B ASP* 3.5 28.7 - - - +
332B THR* 4.7 0.4 - - - -
473B VAL* 2.6 27.6 + - + +
476B ASP* 1.3 73.6 - - - +
478B LEU* 1.3 64.7 + - - +
480B ASN* 2.9 29.5 + - - +
811B GOL 4.1 12.8 - - - +
812B 0P6 4.6 0.4 - - - +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B TRP* 3.2 28.9 + - + +
477B ALA* 1.3 76.3 - - - +
479B THR* 1.3 57.1 + - - +
480B ASN* 3.0 7.9 + - - +
481B TYR* 3.2 26.7 + - + -
522B PHE* 3.5 28.5 - - + +
523B HIS* 3.6 41.1 - - + +
526B TYR* 4.3 5.4 - - + -
527B TRP* 3.6 29.4 - - + +
530B PHE* 4.1 19.5 - - + -
811B GOL 3.7 17.0 - - - +
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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