Contacts of the helix formed by residues 484 - 494 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A LEU* 4.6 11.4 - - + -
473A PHE* 4.5 10.1 - - + -
477A TRP* 4.5 15.9 - - + -
479A TRP* 3.8 30.5 - - + +
480A LYS 4.2 4.9 - - - +
481A PRO* 4.0 12.8 - - + +
482A SER 3.2 0.8 - - - -
483A ASP* 1.3 87.1 - - + +
485A HIS* 1.3 66.6 + - + +
486A PRO* 3.4 4.4 - - - -
487A THR* 3.5 8.2 + - - +
488A MET* 3.1 25.1 + - + +
503A PHE* 3.7 43.1 - - + +
506A ASN* 5.1 5.8 - - + +
508A VAL* 5.3 9.0 - - + -
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Residues in contact with HIS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A PRO 3.6 17.8 + - - -
482A SER* 3.9 25.1 + - - +
483A ASP 3.7 0.2 - - - -
484A LEU* 1.3 74.7 - - - +
486A PRO* 1.3 68.1 - - + +
488A MET* 4.4 1.6 - - + -
489A THR* 3.0 25.1 + - - -
508A VAL* 3.8 20.9 - - + +
509A GLN 5.1 1.4 + - - -
512A GLU* 4.1 24.3 - - + +
513A PHE* 3.7 35.4 + + + +
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLY* 5.7 3.3 - - - -
319A VAL* 4.8 8.5 - - + +
457A LYS* 6.4 0.7 - - + -
482A SER 4.9 2.0 - - - +
483A ASP* 4.6 6.1 - - - +
484A LEU* 3.7 7.6 - - - +
485A HIS* 1.3 89.7 - - + +
487A THR* 1.3 65.6 - - + +
489A THR* 3.0 28.4 + - - +
490A ALA* 3.2 5.0 + - - +
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Residues in contact with THR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 4.3 5.4 - - + -
453A ASP* 5.2 2.7 - - + +
456A LEU* 4.0 19.8 - - + +
457A LYS* 3.9 29.2 - - + -
460A VAL* 4.7 15.3 - - - +
483A ASP 5.7 2.0 - - - +
484A LEU* 3.5 11.0 + - - +
486A PRO* 1.3 77.5 - - + +
488A MET* 1.3 57.6 + - - +
490A ALA* 3.0 10.8 + - - +
491A ALA* 2.7 34.3 + - - +
503A PHE* 3.5 21.1 - - - -
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Residues in contact with MET 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A LEU* 3.1 17.4 + - + +
485A HIS* 4.1 5.8 - - + +
487A THR* 1.3 82.0 + - - +
489A THR* 1.3 56.8 + - - +
491A ALA* 3.0 5.5 + - - +
492A LEU* 2.8 35.9 + - + +
500A VAL* 3.8 32.8 - - + +
503A PHE* 3.5 35.7 - - + -
504A LEU* 5.0 2.0 - - + -
508A VAL* 4.4 20.2 - - + -
510A LEU* 4.2 24.7 - - + -
513A PHE* 4.0 24.5 - - + -
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLY* 5.5 5.2 - - - +
485A HIS 3.0 14.9 + - - -
486A PRO* 3.0 15.0 + - - +
488A MET* 1.3 78.5 - - - +
490A ALA* 1.3 55.5 + - - +
492A LEU* 3.0 20.9 + - - +
493A ILE* 3.0 23.5 + - + +
513A PHE* 3.7 17.3 - - + -
518A THR* 4.4 8.8 - - + +
521A TYR* 4.0 31.4 - - + -
522A LEU* 4.4 11.0 - - + -
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ARG 4.4 4.0 - - - +
317A GLY* 4.6 6.1 - - - -
318A GLY 4.2 16.6 - - - +
319A VAL* 3.9 34.1 - - + -
460A VAL* 5.3 7.8 - - + +
486A PRO 3.2 2.2 + - - +
487A THR* 3.0 9.5 + - - +
489A THR* 1.3 79.5 - - - +
491A ALA* 1.3 60.3 + - - +
492A LEU 3.5 0.2 + - - -
493A ILE* 4.6 1.4 - - - +
494A SER* 3.5 24.8 + - - -
496A LYS* 4.9 1.2 + - - -
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A VAL* 4.4 10.5 - - + -
487A THR 2.7 16.7 + - - +
488A MET* 3.0 13.2 + - - +
490A ALA* 1.3 74.3 - - - +
492A LEU* 1.3 60.9 + - - +
493A ILE 3.6 0.2 - - - -
494A SER* 4.4 3.8 - - - -
495A ASN* 4.0 0.7 + - - -
496A LYS* 3.5 33.1 + - + +
499A PHE* 3.9 28.3 - - + -
500A VAL* 4.2 8.4 - - + +
503A PHE* 4.2 6.3 - - + -
637A LEU* 5.8 0.3 - - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A MET* 2.8 21.3 + - + +
489A THR* 3.0 7.3 + - - +
491A ALA* 1.3 79.3 - - - +
493A ILE* 1.3 66.2 + - - +
495A ASN* 3.8 4.9 + - - -
500A VAL* 4.1 23.3 - - + -
513A PHE* 4.4 17.9 - - + -
522A LEU* 4.2 26.5 - - + -
625A LEU* 4.3 20.4 - - + -
628A TRP* 3.5 24.6 - - + -
634A ARG* 4.6 1.2 + - - -
637A LEU* 4.0 29.2 - - + +
641A ILE* 5.6 6.3 - - + -
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Residues in contact with ILE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLY* 4.5 20.4 - - - -
489A THR* 3.0 18.7 + - + +
490A ALA* 4.6 3.4 - - - +
492A LEU* 1.3 77.6 - - - +
494A SER* 1.3 60.4 + - - +
495A ASN 3.1 5.3 + - - -
521A TYR* 4.3 11.4 - - + -
522A LEU* 3.8 24.7 - - + -
525A ASN* 3.4 52.3 - - + +
628A TRP* 4.6 6.1 - - + -
634A ARG* 3.3 21.5 + - - -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ARG* 6.5 0.4 - - - -
490A ALA 3.5 16.1 + - - -
491A ALA 4.5 0.3 + - - -
492A LEU 3.5 0.2 - - - -
493A ILE* 1.3 78.6 - - - +
495A ASN* 1.3 68.5 + - - +
496A LYS* 2.5 44.0 + - - +
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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