Contacts of the helix formed by residues 482 - 496 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B ASP* 5.9 9.4 - - - -
479B GLN* 3.5 10.9 + - - -
480B GLU 3.8 0.6 - - - -
481B GLU* 1.3 77.0 - - - +
483B MET* 1.3 61.5 - - - +
484B LEU* 3.3 5.7 + - - -
485B SER* 4.0 8.9 + - - -
486B LEU* 3.9 11.3 + - - +
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Residues in contact with MET 483 (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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404B ILE* 4.8 9.4 - - - +
407B THR* 3.7 20.0 - - + +
408B ALA* 5.2 5.4 - - + +
411B TYR* 3.7 30.5 - - + -
478B PHE* 3.5 63.5 - - + +
481B GLU* 3.2 13.6 - - + +
482B GLY* 1.3 76.5 - - - +
484B LEU* 1.3 62.5 + - + +
485B SER 3.4 0.2 - - - -
486B LEU* 3.1 22.2 - - + +
487B VAL* 2.9 34.8 + - + +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B PHE* 4.3 10.5 - - + +
479B GLN* 3.6 45.5 - - + +
482B GLY* 3.3 3.1 - - - -
483B MET* 1.3 77.9 - - + +
485B SER* 1.3 61.5 + - - +
487B VAL* 3.1 13.3 - - + +
488B LEU* 2.9 36.8 + - + +
529B LEU* 6.3 2.7 - - + -
530B ILE* 4.7 10.3 - - + -
536B ASN* 4.1 32.3 - - + +
539B LEU* 4.6 20.2 - - + -
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B GLY* 4.0 9.2 + - - -
484B LEU* 1.3 78.2 - - - +
486B LEU* 1.3 57.4 + - - +
488B LEU* 3.3 17.8 + - - +
489B ASN* 2.9 29.3 + - - +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA* 4.4 13.7 - - + +
411B TYR* 3.5 46.4 - - + -
412B ASN* 3.9 17.9 - - - +
415B ILE* 3.5 28.3 - - + -
482B GLY 3.9 4.9 + - - +
483B MET* 3.1 31.7 + - + +
484B LEU 3.1 0.6 - - - -
485B SER* 1.3 77.5 - - - +
487B VAL* 1.3 57.6 + - - +
489B ASN* 3.1 8.8 + - - +
490B CYS* 3.0 30.1 + - - -
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 3.7 34.8 - - + +
478B PHE* 6.2 1.3 - - + -
483B MET* 2.9 19.3 + - + +
484B LEU* 3.1 22.2 + - - +
486B LEU* 1.3 72.9 - - - +
488B LEU* 1.3 67.6 + - + +
490B CYS* 3.3 9.8 + - - +
491B ILE* 2.9 33.8 + - + +
522B LEU* 4.8 11.4 - - + -
525B ILE* 6.3 5.2 - - + -
526B LEU* 4.8 15.7 - - + -
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 2.9 30.1 + - + +
485B SER* 3.6 18.8 - - - +
486B LEU 3.2 0.2 - - - -
487B VAL* 1.3 80.8 - - + +
489B ASN* 1.3 57.3 + - - +
491B ILE* 3.1 13.2 - - + +
492B ASP* 2.9 31.1 + - - +
526B LEU* 4.1 25.4 - - + -
539B LEU* 6.1 4.3 - - + -
540B PHE* 4.2 26.7 - - + -
546B TRP* 5.1 5.6 - - + -
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Residues in contact with ASN 489 (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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415B ILE* 3.5 33.5 - - + +
485B SER 2.9 13.5 + - - +
486B LEU* 3.1 10.5 + - - +
488B LEU* 1.3 76.1 - - - +
490B CYS* 1.3 58.4 + - - +
492B ASP* 3.4 4.9 + - - +
493B ARG* 2.9 57.7 + - - +
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Residues in contact with CYS 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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411B TYR* 4.6 18.4 - - - -
414B PHE* 4.6 22.3 - - + -
415B ILE* 3.8 23.8 - - - -
486B LEU* 3.0 38.6 + - - -
487B VAL* 3.5 11.0 - - - +
488B LEU 3.3 0.4 - - - -
489B ASN* 1.3 78.8 - - - +
491B ILE* 1.3 58.7 + - - +
493B ARG* 3.3 4.8 + - - +
494B LEU* 2.9 30.0 + - - +
522B LEU* 4.7 12.8 - - + -
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Residues in contact with ILE 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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487B VAL* 2.9 17.2 + - + +
488B LEU* 3.1 24.0 - - + +
490B CYS* 1.3 74.7 - - - +
492B ASP* 1.3 56.9 + - - +
494B LEU* 3.3 7.0 + - + +
495B ASN* 2.9 31.9 + - - +
522B LEU* 3.7 39.3 - - + +
523B TYR* 4.4 23.0 + - + +
526B LEU* 3.7 26.5 - - + -
546B TRP* 3.5 33.0 - - + -
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Residues in contact with ASP 492 (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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488B LEU 2.9 18.3 + - - +
489B ASN* 3.8 6.7 - - - +
491B ILE* 1.3 78.2 - - - +
493B ARG* 1.3 60.5 + - + +
495B ASN* 3.2 5.4 + - - +
496B VAL* 2.9 30.1 + - - +
546B TRP* 4.7 18.2 - - + +
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Residues in contact with ARG 493 (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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415B ILE* 5.2 7.1 + - + +
418B LEU* 4.7 20.7 - - + +
419B ASP* 4.1 28.9 - - - +
422B SER* 4.9 11.8 + - - -
489B ASN* 2.9 48.0 + - - +
490B CYS* 3.9 4.9 - - - +
492B ASP* 1.3 77.2 - - + +
494B LEU* 1.3 59.1 + - - +
496B VAL* 3.2 26.7 - - - +
497B TYR* 4.3 7.4 - - - -
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PHE* 4.4 22.2 - - + -
418B LEU* 6.3 2.9 - - + -
490B CYS 2.9 16.7 + - - +
491B ILE* 3.8 6.7 - - + +
492B ASP 3.1 0.4 - - - -
493B ARG* 1.3 80.7 - - - +
495B ASN* 1.3 59.9 + - - +
496B VAL 3.4 0.4 + - - -
497B TYR* 4.0 11.3 + - + +
503B PHE* 4.6 17.9 - - + -
515B TRP* 3.4 47.2 + - + +
518B ILE* 3.6 31.4 - - + -
519B VAL* 3.7 19.7 - - + +
522B LEU* 5.2 7.9 - - + -
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Residues in contact with ASN 495 (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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491B ILE 2.9 17.6 + - - +
492B ASP* 3.6 5.2 - - - +
494B LEU* 1.3 73.2 - - - +
496B VAL* 1.3 59.6 + - - +
497B TYR 2.9 18.6 - - - +
515B TRP* 5.1 7.3 - - - -
519B VAL* 6.3 0.4 - - - +
523B TYR* 3.3 25.0 + - - +
546B TRP* 5.8 5.6 - - + +
550B LYS* 4.7 18.4 + - - +
553B ARG* 2.9 55.3 + - - +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B SER* 5.7 4.9 - - - -
492B ASP 2.9 13.5 + - - +
493B ARG* 3.2 26.9 - - - +
495B ASN* 1.3 77.8 - - - +
497B TYR* 1.3 77.8 + - + +
553B ARG* 5.3 0.3 + - - -
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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