Contacts of the helix formed by residues 473 - 482 (chain B) in PDB entry 6IY6
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 LEU 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLN* 3.9 16.4 - - + -
199B GLN* 3.6 32.1 - - + +
202B ILE* 3.6 28.9 - - + -
203B CYS* 3.5 30.1 - - - -
287B VAL* 3.0 40.2 + - + +
289B LEU* 4.2 13.2 - - + -
471B ILE 3.6 4.2 + - - -
472B GLY* 1.3 69.5 - - - +
474B GLU* 1.3 58.8 + - - +
476B VAL* 3.4 7.0 + - - +
477B THR* 2.7 32.6 + - - +
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Residues in contact with GLU 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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199B GLN* 3.7 10.3 - - - +
285B GLU 4.9 0.5 - - - +
286B PHE* 3.5 20.7 - - + +
287B VAL* 3.1 49.9 + - - +
472B GLY 4.2 0.3 - - - -
473B LEU* 1.3 73.0 + - + +
475B ARG* 1.3 53.2 + - - +
477B THR 3.3 1.4 + - - -
478B MET* 2.9 24.6 + - - +
486B VAL* 4.6 11.0 - - + +
489B THR* 2.8 43.9 + - - +
490B SER* 4.1 21.4 + - - +
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Residues in contact with ARG 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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273B ARG* 5.9 7.0 - - - +
370B THR* 6.3 1.2 - - - +
423B GLU* 3.3 36.5 + - - +
424B GLU* 2.7 31.2 + - - +
425B ILE* 4.6 11.4 - - + +
472B GLY* 2.8 21.3 + - - +
474B GLU* 1.3 71.0 - - - +
476B VAL* 1.3 59.7 + - - +
478B MET* 3.4 22.7 + - + +
479B LEU* 3.1 42.8 + - + +
486B VAL* 4.4 13.2 - - + +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.0 24.7 - - + -
310B MET* 4.2 11.7 - - + -
313B ILE* 5.3 1.8 - - + -
314B PHE* 4.9 4.0 - - + -
317B LEU* 6.4 0.2 - - + -
420B MET* 3.7 23.7 - - + +
425B ILE* 4.3 21.3 - - + -
471B ILE* 3.9 33.0 - - + -
472B GLY 2.8 21.6 + - - +
473B LEU* 3.7 8.3 - - - +
475B ARG* 1.3 69.3 - - - +
477B THR* 1.3 58.8 + - - +
479B LEU 3.4 0.7 + - - -
480B PHE* 2.9 30.2 + - + +
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Residues in contact with THR 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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195B VAL* 4.0 24.7 - - + +
198B LEU* 4.1 15.3 - - + -
199B GLN* 3.3 22.0 + - + +
202B ILE* 3.4 18.7 - - - +
473B LEU 2.7 19.9 + - - -
474B GLU 3.3 7.8 + - - -
476B VAL* 1.3 75.2 - - - +
478B MET* 1.3 62.6 + - - +
480B PHE* 3.8 3.1 - - - +
481B LEU* 3.3 33.2 + - + +
489B THR* 3.6 17.5 - - + -
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Residues in contact with MET 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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423B GLU* 3.8 11.0 - - - +
474B GLU 2.9 17.0 + - - +
475B ARG* 3.5 21.3 - - + +
477B THR* 1.3 76.4 - - - +
479B LEU* 1.3 75.9 + - + +
481B LEU 3.5 0.5 + - - -
482B GLY 2.9 8.3 + - - -
483B LEU* 2.9 53.6 + - + +
484B HIS 3.5 16.6 - - - +
485B ASN 3.6 2.5 - - - +
486B VAL* 3.4 48.5 - - + -
489B THR* 3.4 18.3 - - + +
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Residues in contact with LEU 479 (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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337B PHE* 4.0 2.1 - - - -
420B MET* 3.4 37.2 - - + +
421B ARG* 2.7 44.8 + - + +
423B GLU* 3.3 41.1 - - + +
425B ILE* 3.6 25.8 - - + -
475B ARG* 3.1 23.7 + - + +
476B VAL 4.1 1.8 - - - +
478B MET* 1.3 85.9 - - + +
480B PHE* 1.3 55.6 + - - +
482B GLY* 3.7 4.0 - - - +
483B LEU 4.9 4.0 - - - +
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Residues in contact with PHE 480 (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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198B LEU* 4.5 2.0 - - + -
202B ILE* 5.5 0.2 - - + -
314B PHE* 3.6 39.7 - + + -
317B LEU* 3.7 43.3 - - + -
318B GLN* 4.1 19.3 - - + -
325B ILE* 4.0 22.2 - - + -
334B CYS* 4.9 0.2 - - - -
337B PHE* 3.7 31.0 + + + +
420B MET* 3.8 8.0 - - + +
421B ARG* 3.1 21.0 + - - -
476B VAL* 2.9 20.5 + - + +
477B THR* 3.8 6.7 - - - +
478B MET 3.3 0.4 - - - -
479B LEU* 1.3 77.9 - - - +
481B LEU* 1.3 69.2 - - + +
482B GLY 3.3 0.7 - - - -
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Residues in contact with LEU 481 (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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195B VAL* 3.9 31.6 - - + -
198B LEU* 4.1 20.4 - - + -
325B ILE* 4.4 22.2 - - + +
328B VAL* 4.1 18.3 - - + +
332B PHE* 4.7 2.9 - - - +
334B CYS* 3.4 21.2 - - - +
477B THR* 3.3 30.3 + - + +
480B PHE* 1.3 93.5 - - + +
482B GLY* 1.3 61.5 + - - +
483B LEU* 3.4 23.3 + - + +
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Residues in contact with GLY 482 (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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332B PHE* 5.8 1.7 - - - +
333B PRO 5.4 1.0 - - - +
334B CYS* 3.7 13.6 - - - +
421B ARG* 3.7 22.9 - - - -
478B MET 2.9 7.1 + - - -
479B LEU* 3.6 3.5 + - - -
480B PHE 3.3 4.0 + - - -
481B LEU* 1.3 79.3 - - - +
483B LEU* 1.3 64.6 + - - +
484B HIS* 5.0 9.7 + - - -
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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