Contacts of the helix formed by residues 479 - 486 (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 THR 479 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B HIS* 3.8 3.4 - - - -
340B VAL* 3.6 27.6 - - + -
341B VAL* 4.1 15.3 - - + -
344B LEU* 3.5 26.0 - - + +
474B TRP 4.2 0.2 + - - -
475B LEU* 2.7 29.7 + - - +
476B ASP 3.6 6.4 + - - -
477B ALA 3.1 0.8 - - - -
478B LEU* 1.3 75.7 - - - +
480B ASN* 1.3 64.3 + - - +
481B TYR 3.0 0.7 - - - -
482B LEU* 2.9 17.6 + - + -
483B THR* 3.0 8.6 + - - +
527B TRP* 4.1 9.1 - - - -
530B PHE* 6.0 0.2 - - - -
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Residues in contact with ASN 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER 5.0 0.3 - - - +
248B ILE* 3.2 44.1 - - + +
283B LEU* 3.6 13.3 - - - +
330B ILE* 3.4 19.7 - - + +
332B THR* 4.8 1.6 - - + -
337B HIS* 3.5 18.3 - - + -
477B ALA 2.9 23.1 + - - +
478B LEU* 3.0 1.4 + - - +
479B THR* 1.3 77.8 - - - +
481B TYR* 1.3 92.4 + - - +
483B THR 3.3 0.3 + - - -
484B GLY* 2.9 27.7 + - - -
811B GOL 5.7 0.6 + - - -
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Residues in contact with TYR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.5 12.0 - - + -
245B THR* 3.4 26.5 - - + -
246B SER 3.3 20.7 + - - -
247B PRO* 3.7 17.3 - - - +
248B ILE 4.7 0.2 + - - -
283B LEU* 4.1 5.6 - - + -
478B LEU* 3.2 24.9 - - + +
479B THR 3.0 0.2 - - - -
480B ASN* 1.3 104.6 + - - +
482B LEU* 1.3 61.1 + - - +
485B SER* 3.2 22.9 + - - -
508B PHE* 4.0 5.4 - - + -
513B HIS* 3.4 26.5 - + + -
514B VAL 5.1 0.2 + - - -
515B ILE* 4.5 2.4 - - - +
523B HIS* 2.6 42.6 + + - -
527B TRP* 3.9 15.5 - + + -
811B GOL 4.9 2.0 + - - -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.8 19.5 - - + -
344B LEU* 4.5 10.8 - - + -
479B THR* 2.9 19.1 + - + +
481B TYR* 1.3 76.2 - - - +
483B THR* 1.3 66.4 + - - +
485B SER* 2.6 28.7 + - - +
486B ARG* 3.4 13.4 + - - +
502B PHE* 4.6 4.7 - - + -
508B PHE* 3.7 31.2 - - + -
527B TRP* 4.3 8.1 - - + -
536B LEU* 3.8 20.9 - - + -
802B GOL 3.3 34.3 - - - +
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Residues in contact with THR 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.7 17.0 - - + -
334B ASN* 6.3 0.2 - - - -
336B GLN* 4.1 5.8 - - + +
337B HIS* 2.9 46.4 + - + +
340B VAL* 3.3 27.4 - - + +
479B THR 3.0 7.4 + - - -
480B ASN 3.3 6.9 + - - -
482B LEU* 1.3 75.0 - - - +
484B GLY* 1.3 58.2 + - - +
486B ARG* 2.9 21.7 + - - +
487B LEU* 3.2 25.5 + - + +
498B LEU* 4.2 0.6 - - + +
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Residues in contact with GLY 484 (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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243B PHE* 4.8 0.4 - - - -
281B PHE* 3.6 12.5 - - - -
283B LEU* 4.0 21.1 - - - -
330B ILE* 3.9 7.4 - - - +
480B ASN 2.9 19.0 + - - -
481B TYR 4.1 0.2 - - - -
483B THR* 1.3 72.5 - - - +
485B SER* 1.3 56.9 + - - +
486B ARG 3.0 0.9 + - - -
487B LEU* 3.4 12.9 + - - +
507B ARG* 2.9 24.3 + - - -
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.9 10.7 - - - -
481B TYR 3.2 14.0 + - - -
482B LEU* 2.6 23.6 + - - +
484B GLY* 1.3 76.2 - - - +
486B ARG* 1.3 61.0 + - - +
502B PHE* 4.3 5.4 - - - +
505B LEU* 3.6 18.5 - - - +
507B ARG* 3.7 19.2 - - - +
508B PHE* 3.3 43.2 - - - +
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Residues in contact with ARG 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.7 23.6 - - - +
343B GLU* 3.1 40.0 + - - -
482B LEU* 3.7 15.3 - - - +
483B THR 2.9 9.9 + - - +
485B SER* 1.3 81.1 - - - +
487B LEU* 1.3 58.7 + - - +
488B ARG 3.7 0.5 + - - -
498B LEU* 3.5 22.4 - - + +
499B VAL* 2.9 58.3 + - + +
500B ASP* 3.4 23.8 + - - +
502B PHE* 3.7 28.9 - - - -
505B LEU* 3.6 7.8 - - - +
802B GOL 3.3 23.9 + - - -
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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
------------------------------------------------------------
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