Contacts of the helix formed by residues 484 - 494 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456C LEU* 4.6 11.7 - - + -
473C PHE* 4.5 10.3 - - + -
477C TRP* 4.5 16.4 - - + -
479C TRP* 3.8 30.3 - - + +
480C LYS 4.2 5.2 - - - +
481C PRO* 3.6 12.1 + - + +
482C SER 3.2 1.6 - - - -
483C ASP* 1.3 86.9 - - + +
485C HIS* 1.3 66.2 + - + +
486C PRO* 3.4 3.3 - - - -
487C THR* 3.5 9.1 + - - +
488C MET* 3.1 26.2 + - + +
503C PHE* 3.7 43.1 - - + +
506C ASN* 5.1 4.9 - - + +
508C VAL* 5.3 8.7 - - + -
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Residues in contact with HIS 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C PRO 3.6 18.4 + - - -
482C SER* 3.9 25.1 + - - +
484C LEU* 1.3 74.4 - - - +
486C PRO* 1.3 68.8 - - + +
488C MET* 4.4 1.6 - - + -
489C THR* 3.0 25.1 + - - -
508C VAL* 3.8 21.1 - - + +
509C GLN 5.1 0.8 + - - -
512C GLU* 4.1 23.4 - - + +
513C PHE* 3.7 35.5 + + + +
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Residues in contact with PRO 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C GLY* 5.7 2.8 - - - -
319C VAL* 4.8 8.9 - - + +
457C LYS* 6.4 0.7 - - + -
482C SER 4.9 2.5 - - - +
483C ASP* 4.6 5.4 - - - +
484C LEU* 3.7 7.2 - - - +
485C HIS* 1.3 90.7 - - + +
487C THR* 1.3 65.3 + - + +
489C THR* 3.0 28.4 + - - +
490C ALA* 3.2 5.4 + - - +
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Residues in contact with THR 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C VAL* 4.3 5.4 - - + -
453C ASP* 5.2 2.7 - - + +
456C LEU* 4.0 19.3 - - + +
457C LYS* 3.9 28.9 - - + -
460C VAL* 4.7 16.3 - - - +
483C ASP 5.7 1.8 - - - +
484C LEU* 3.5 11.2 + - - +
486C PRO* 1.3 78.2 - - + +
488C MET* 1.3 56.6 + - - +
490C ALA* 3.0 11.3 + - - +
491C ALA* 2.7 34.5 + - - +
503C PHE* 3.5 21.4 - - - -
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Residues in contact with MET 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 3.1 18.2 + - + +
485C HIS* 4.1 7.0 - - + +
487C THR* 1.3 81.0 + - - +
489C THR* 1.3 56.4 + - - +
491C ALA* 3.0 3.7 + - - +
492C LEU* 2.8 36.6 + - + +
500C VAL* 3.8 33.2 - - + +
503C PHE* 3.5 35.2 - - + -
504C LEU* 5.0 2.0 - - + -
508C VAL* 4.4 20.2 - - + -
510C LEU* 4.2 24.7 - - + -
513C PHE* 4.0 24.5 - - + -
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Residues in contact with THR 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLY* 5.5 4.7 - - - +
485C HIS 3.0 14.1 + - - -
486C PRO* 3.0 14.4 + - - +
488C MET* 1.3 78.7 - - - +
490C ALA* 1.3 55.4 + - - +
492C LEU* 3.0 21.2 + - - +
493C ILE* 3.0 24.5 + - + +
513C PHE* 3.7 16.8 - - - -
518C THR* 4.4 9.0 - - + +
521C TYR* 4.0 31.0 - - + -
522C LEU* 4.4 10.8 - - + -
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Residues in contact with ALA 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C ARG 4.4 4.0 - - - +
317C GLY* 4.6 6.1 - - - -
318C GLY 4.2 15.9 - - - +
319C VAL* 3.9 33.7 - - + -
460C VAL* 5.3 8.1 - - + +
486C PRO 3.2 2.7 + - - +
487C THR* 3.0 11.4 + - - +
489C THR* 1.3 77.8 - - - +
491C ALA* 1.3 60.3 + - - +
492C LEU 3.5 0.2 + - - -
493C ILE* 4.6 1.6 - - - +
494C SER* 3.5 24.3 + - - -
496C LYS* 4.9 1.2 + - - -
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Residues in contact with ALA 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C VAL* 4.4 10.5 - - + +
487C THR 2.7 15.8 + - - +
488C MET* 3.0 13.2 + - - +
490C ALA* 1.3 74.3 - - - +
492C LEU* 1.3 60.1 + - - +
494C SER* 4.4 3.8 - - - -
495C ASN 4.0 0.5 + - - -
496C LYS* 3.5 33.1 + - + +
499C PHE* 3.9 27.6 - - + -
500C VAL* 4.2 8.4 - - + +
503C PHE* 4.2 6.7 - - + -
637C LEU* 5.8 0.5 - - - +
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C MET* 2.8 19.8 + - + +
489C THR* 3.0 6.9 + - - +
491C ALA* 1.3 79.3 - - - +
493C ILE* 1.3 66.1 + - - +
495C ASN* 3.8 5.1 + - - -
500C VAL* 4.1 23.8 - - + -
513C PHE* 4.4 18.8 - - + -
522C LEU* 4.2 26.5 - - + -
625C LEU* 4.3 20.2 - - + -
628C TRP* 3.5 23.6 - - + -
634C ARG* 4.6 1.2 + - - -
637C LEU* 4.0 29.4 - - + +
641C ILE* 5.6 6.5 - - + -
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Residues in contact with ILE 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C GLY* 4.5 20.2 - - - -
489C THR* 3.0 16.6 + - + +
490C ALA* 4.6 3.1 - - - +
492C LEU* 1.3 78.1 - - - +
494C SER* 1.3 61.0 + - - +
495C ASN 3.1 5.6 + - - -
521C TYR* 4.3 11.4 - - + -
522C LEU* 3.8 24.2 - - + -
525C ASN* 3.4 52.0 - - + +
628C TRP* 4.6 6.1 - - + -
634C ARG* 3.3 22.1 + - - +
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Residues in contact with SER 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ARG* 6.5 0.9 - - - -
490C ALA 3.5 16.1 + - - -
491C ALA 4.5 0.3 + - - -
492C LEU 3.5 0.4 - - - -
493C ILE* 1.3 78.9 - - - +
495C ASN* 1.3 68.3 + - - +
496C LYS* 2.5 44.4 + - - +
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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