Contacts of the helix formed by residues 484 - 494 (chain B) in PDB entry 6PUO
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 484 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LEU* 4.6 11.2 - - + -
473B PHE* 4.5 10.5 - - + -
477B TRP* 4.5 15.7 - - + -
479B TRP* 3.8 29.6 - - + +
480B LYS 4.2 5.4 - - - +
481B PRO* 3.6 12.8 + - + +
482B SER 3.2 1.4 - - - -
483B ASP* 1.3 85.6 - - + +
485B HIS* 1.3 67.2 + - + +
486B PRO* 3.4 4.1 - - - -
487B THR* 3.5 8.3 + - - +
488B MET* 3.1 25.1 + - + +
503B PHE* 3.7 42.8 - - + +
506B ASN* 5.1 6.1 - - + +
508B VAL* 5.3 9.0 - - + -
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Residues in contact with HIS 485 (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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481B PRO 3.6 19.1 + - - -
482B SER* 3.9 25.5 + - - +
484B LEU* 1.3 74.6 - - - +
486B PRO* 1.3 68.6 - - + +
488B MET* 4.2 1.8 - - + -
489B THR* 3.0 25.1 + - - -
508B VAL* 3.8 20.7 - - + +
509B GLN 5.1 1.2 + - - -
512B GLU* 4.1 24.3 - - + +
513B PHE* 3.7 35.8 + + + +
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Residues in contact with PRO 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLY* 5.7 2.5 - - - -
319B VAL* 4.8 10.3 - - + +
457B LYS* 6.4 0.4 - - + -
482B SER 4.9 1.8 - - - +
483B ASP* 4.6 6.1 - - - +
484B LEU* 3.7 7.0 - - - +
485B HIS* 1.3 90.2 - - + +
487B THR* 1.3 64.2 + - + +
489B THR* 3.0 29.0 + - - +
490B ALA* 3.2 5.4 + - - +
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Residues in contact with THR 487 (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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319B VAL* 4.3 5.6 - - + -
453B ASP* 5.2 2.9 - - + +
456B LEU* 4.0 20.2 - - + +
457B LYS* 3.9 28.3 - - + -
460B VAL* 4.7 14.6 - - - +
483B ASP 5.7 1.8 - - - +
484B LEU* 3.5 11.6 + - - +
486B PRO* 1.3 77.7 - - + +
488B MET* 1.3 58.0 + - - +
490B ALA* 3.0 11.2 + - - +
491B ALA* 2.7 34.7 + - - +
503B PHE* 3.5 21.1 - - - -
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Residues in contact with MET 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 3.1 17.3 + - + +
485B HIS* 4.1 6.3 - - + +
487B THR* 1.3 82.0 + - - +
489B THR* 1.3 57.0 + - - +
491B ALA* 3.0 3.7 + - - +
492B LEU* 2.8 35.8 + - + +
500B VAL* 3.8 33.4 - - + +
503B PHE* 3.5 36.6 - - + -
504B LEU* 5.0 2.7 - - + -
508B VAL* 4.4 20.0 - - + -
510B LEU* 4.2 24.5 - - + -
513B PHE* 4.0 23.6 - - + -
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Residues in contact with THR 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLY* 5.5 4.9 - - - +
485B HIS 3.0 14.2 + - - -
486B PRO* 3.0 14.1 + - - +
488B MET* 1.3 78.0 - - - +
490B ALA* 1.3 55.9 + - - +
492B LEU* 3.0 21.0 + - - +
493B ILE* 3.0 23.7 + - + +
513B PHE* 3.7 16.1 - - - -
518B THR* 4.4 8.7 - - + +
521B TYR* 4.0 31.6 - - + -
522B LEU* 4.4 11.7 - - + -
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Residues in contact with ALA 490 (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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316B ARG 4.4 4.3 - - - +
317B GLY* 4.6 6.1 - - - -
318B GLY 4.2 15.9 - - - +
319B VAL* 3.9 34.8 - - + -
460B VAL* 5.3 8.5 - - + +
486B PRO 3.2 2.4 + - - +
487B THR* 3.0 8.8 + - - +
489B THR* 1.3 79.7 - - - +
491B ALA* 1.3 61.1 + - - +
492B LEU 3.5 0.2 + - - -
493B ILE* 4.6 1.0 - - - +
494B SER* 3.5 24.3 + - - -
496B LYS* 4.9 1.4 + - - -
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Residues in contact with ALA 491 (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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460B VAL* 4.4 10.5 - - + +
487B THR 2.7 16.9 + - - +
488B MET* 3.0 12.3 + - - +
490B ALA* 1.3 73.0 - - - +
492B LEU* 1.3 61.5 + - - +
494B SER* 4.4 4.0 - - - -
495B ASN* 4.0 0.5 + - - -
496B LYS* 3.5 33.5 + - + +
499B PHE* 3.9 28.5 - - + -
500B VAL* 4.2 8.5 - - + +
503B PHE* 4.2 6.7 - - + -
637B LEU* 5.8 0.3 - - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B MET* 2.8 19.8 + - + +
489B THR* 3.0 7.5 + - - +
491B ALA* 1.3 80.7 - - - +
493B ILE* 1.3 65.5 + - - +
495B ASN* 3.8 5.0 + - - -
500B VAL* 4.1 24.5 - - + -
513B PHE* 4.4 18.4 - - + -
522B LEU* 4.2 26.5 - - + -
625B LEU* 4.3 19.7 - - + -
628B TRP* 3.5 23.3 - - + -
634B ARG* 4.6 1.2 + - - -
637B LEU* 4.0 28.6 - - + +
641B ILE* 5.6 6.1 - - + -
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Residues in contact with ILE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLY* 4.5 19.7 - - - -
489B THR* 3.0 17.3 + - + +
490B ALA* 4.6 3.4 - - - +
492B LEU* 1.3 78.5 - - - +
494B SER* 1.3 60.1 + - - +
495B ASN 3.1 5.9 + - - -
521B TYR* 4.3 11.4 - - + -
522B LEU* 3.8 24.9 - - + -
525B ASN* 3.4 52.0 - - + +
628B TRP* 4.6 6.7 - - + -
634B ARG* 3.3 22.5 + - - -
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Residues in contact with SER 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 6.5 0.7 - - - -
490B ALA 3.5 16.2 + - - -
491B ALA* 4.5 0.5 + - - -
492B LEU 3.5 0.4 - - - -
493B ILE* 1.3 78.4 - - - +
495B ASN* 1.3 68.2 + - - +
496B LYS* 2.5 44.5 + - - +
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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