Contacts of the helix formed by residues 482 - 496 (chain H) in PDB entry 6X34
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 GLY 482 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237H ASP* 5.9 9.4 - - - -
479H GLN* 3.5 11.3 + - - -
480H GLU 3.8 0.6 - - - -
481H GLU* 1.3 77.7 - - - +
483H MET* 1.3 60.6 + - - +
484H LEU* 3.3 6.8 + - - -
485H SER* 4.0 8.1 + - - -
486H LEU* 3.9 11.6 + - - +
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Residues in contact with MET 483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404H ILE* 4.8 8.7 - - - +
407H THR* 3.7 20.2 - - + +
408H ALA* 5.2 5.4 - - + +
411H TYR* 3.7 30.7 - - + -
478H PHE* 3.5 64.4 - - + +
481H GLU* 3.2 14.6 - - + +
482H GLY* 1.3 75.7 - - - +
484H LEU* 1.3 62.9 + - + +
485H SER 3.4 0.2 - - - -
486H LEU* 3.1 22.0 - - + +
487H VAL* 2.9 34.5 + - + +
525H ILE* 6.5 0.2 - - + -
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Residues in contact with LEU 484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478H PHE* 4.3 11.0 - - + +
479H GLN* 3.6 45.3 - - + +
482H GLY* 3.3 3.1 - - - -
483H MET* 1.3 78.5 - - + +
485H SER* 1.3 61.6 + - - +
487H VAL* 3.1 13.2 - - + +
488H LEU* 2.9 36.2 + - + +
529H LEU* 6.3 2.5 - - + -
530H ILE* 4.7 9.6 - - + -
536H ASN* 4.1 33.2 - - + +
539H LEU* 4.6 20.4 - - + -
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Residues in contact with SER 485 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482H GLY* 4.0 9.1 + - - -
483H MET 3.4 0.2 - - - -
484H LEU* 1.3 78.2 - - - +
486H LEU* 1.3 56.8 + - - +
488H LEU* 3.3 18.3 + - - +
489H ASN* 2.9 29.3 + - - +
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Residues in contact with LEU 486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H ALA* 4.4 14.1 - - + +
411H TYR* 3.5 45.1 - - + -
412H ASN* 3.9 17.7 - - - +
415H ILE* 3.5 28.7 - - + -
482H GLY 3.9 4.4 + - - +
483H MET* 3.1 31.1 + - + +
484H LEU 3.1 0.4 - - - -
485H SER* 1.3 78.5 - - - +
487H VAL* 1.3 59.5 + - - +
489H ASN* 3.1 9.2 + - - +
490H CYS* 3.0 29.4 + - - -
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Residues in contact with VAL 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411H TYR* 3.7 34.8 - - + +
478H PHE* 6.2 0.9 - - + -
483H MET* 2.9 19.7 + - + +
484H LEU* 3.1 22.4 + - + +
486H LEU* 1.3 72.3 - - - +
488H LEU* 1.3 69.3 + - + +
490H CYS* 3.5 9.4 - - - +
491H ILE* 2.9 33.6 + - + +
522H LEU* 4.7 11.4 - - + +
525H ILE* 6.3 4.7 - - + -
526H LEU* 4.8 16.2 - - + -
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Residues in contact with LEU 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484H LEU* 2.9 30.6 + - + +
485H SER* 3.6 19.3 - - - +
487H VAL* 1.3 79.2 - - + +
489H ASN* 1.3 55.6 + - - +
491H ILE* 3.1 12.1 - - + +
492H ASP* 2.9 30.8 + - - +
526H LEU* 4.1 24.5 - - + -
539H LEU* 6.1 4.0 - - + -
540H PHE* 4.2 28.0 - - + -
546H TRP* 5.1 6.7 - - + -
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Residues in contact with ASN 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H ILE* 3.5 34.0 - - + +
485H SER 2.9 14.2 + - - +
486H LEU* 3.4 10.3 - - - +
488H LEU* 1.3 76.7 - - - +
490H CYS* 1.3 57.3 + - - +
492H ASP* 3.4 5.4 + - - +
493H ARG* 2.9 57.7 + - - +
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Residues in contact with CYS 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411H TYR* 4.6 18.2 - - - -
414H PHE* 4.6 22.0 - - + -
415H ILE* 3.8 24.9 - - - -
486H LEU* 3.0 37.7 + - - -
487H VAL* 3.5 10.8 - - - +
488H LEU 3.3 0.2 - - - -
489H ASN* 1.3 78.8 - - - +
491H ILE* 1.3 58.7 + - - +
493H ARG* 3.3 4.4 + - - +
494H LEU* 2.9 30.7 + - - +
522H LEU* 4.7 13.2 - - + -
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Residues in contact with ILE 491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487H VAL* 2.9 17.0 + - + +
488H LEU* 3.1 23.6 - - + +
490H CYS* 1.3 75.3 - - - +
492H ASP* 1.3 56.5 + - - +
494H LEU* 3.3 6.6 + - + +
495H ASN* 2.9 32.1 + - - +
522H LEU* 3.7 40.2 - - + +
523H TYR* 4.4 21.7 + - + -
526H LEU* 3.7 27.4 - - + -
546H TRP* 3.5 33.4 - - + -
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Residues in contact with ASP 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488H LEU 2.9 17.9 + - - +
489H ASN* 3.8 7.2 - - - +
491H ILE* 1.3 77.6 - - - +
493H ARG* 1.3 58.6 + - + +
495H ASN* 3.2 4.6 + - - +
496H VAL* 2.9 30.3 + - - +
546H TRP* 4.7 17.9 - - + +
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Residues in contact with ARG 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H ILE* 5.2 6.5 + - + +
418H LEU* 4.7 20.7 - - + +
419H ASP* 4.1 29.5 - - - +
422H SER* 4.9 11.8 + - - -
489H ASN* 2.9 47.4 + - - +
490H CYS* 3.9 4.5 - - - +
492H ASP* 1.3 77.9 - - + +
494H LEU* 1.3 59.2 + - - +
496H VAL* 3.2 26.4 - - - +
497H TYR* 4.3 7.1 - - - -
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Residues in contact with LEU 494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414H PHE* 4.4 22.2 - - + -
418H LEU* 6.3 3.1 - - + -
490H CYS 2.9 17.2 + - - +
491H ILE* 3.8 5.8 - - - +
492H ASP 3.1 0.2 - - - -
493H ARG* 1.3 80.6 - - - +
495H ASN* 1.3 60.5 + - - +
496H VAL 3.4 0.6 + - - -
497H TYR* 4.0 10.3 + - + +
503H PHE* 4.6 17.9 - - + -
515H TRP* 3.4 48.1 + - + +
518H ILE* 3.6 31.6 - - + -
519H VAL* 3.7 20.6 - - + +
522H LEU* 5.2 7.4 - - + -
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Residues in contact with ASN 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491H ILE 2.9 17.8 + - - +
492H ASP* 3.6 4.9 - - - +
494H LEU* 1.3 73.7 - - - +
496H VAL* 1.3 60.2 + - - +
497H TYR 2.9 18.8 - - - +
515H TRP* 5.1 7.7 - - - -
519H VAL* 6.3 0.8 - - - +
523H TYR* 3.3 24.7 + - - +
546H TRP* 5.8 5.8 - - + +
550H LYS* 4.7 16.8 - - - +
553H ARG* 2.9 54.8 + - - +
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Residues in contact with VAL 496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422H SER* 5.7 4.5 - - - -
492H ASP 2.9 12.9 + - - +
493H ARG* 3.2 27.1 - - - +
495H ASN* 1.3 76.7 - - - +
497H TYR* 1.3 78.6 + - + +
553H ARG* 5.1 0.7 + - - -
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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