Contacts of the helix formed by residues 479 - 491 (chain B) in PDB entry 6WCZ
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 TRP 479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413B ILE 4.6 9.2 - - - +
414B PHE* 4.2 20.5 - + - -
415B GLU* 4.8 14.4 - - + +
416B GLU* 2.5 40.4 + - - +
432B PHE* 5.8 2.4 - - + +
435B LEU* 3.6 33.2 - - + -
436B VAL* 4.5 6.1 - - + -
439B GLU* 5.6 4.9 - - + -
450B SER* 3.6 30.7 - - - -
452B VAL 4.6 1.8 + - - +
477B TYR 4.1 0.8 + - - -
478B MET* 1.3 101.5 - - + +
480B LEU* 1.3 77.1 + - - +
481B GLY* 3.2 26.3 + - - +
482B ALA* 3.4 22.6 + - + -
483B ARG* 3.0 16.6 + - - +
485B LEU* 6.2 0.7 - - + -
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Residues in contact with LEU 480 (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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400B PHE* 5.0 14.8 - - + -
404B VAL* 6.1 2.7 - - + -
411B GLY 3.5 13.2 - - - +
413B ILE 4.1 4.5 - - - +
414B PHE* 3.7 31.4 - - + -
423B ALA* 3.7 28.3 - - + +
426B ALA* 5.5 3.1 - - + -
432B PHE* 6.6 0.4 - - + -
479B TRP* 1.3 82.1 - - + +
481B GLY* 1.3 57.1 + - - +
483B ARG* 3.0 36.4 + - + +
484B PHE* 2.8 26.3 + - - +
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Residues in contact with GLY 481 (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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432B PHE* 6.0 3.1 - - - -
436B VAL* 3.7 17.9 - - - +
479B TRP* 3.2 32.2 + - - +
480B LEU* 1.3 78.6 - - - +
482B ALA* 1.3 59.0 + - - +
484B PHE* 2.9 21.7 + - - +
485B LEU* 3.0 16.7 + - - +
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Residues in contact with ALA 482 (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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439B GLU* 5.9 0.7 - - + -
443B HIS* 5.8 0.2 - - + -
450B SER 3.3 26.0 - - - +
451B CYS* 4.2 12.6 - - - -
478B MET* 3.8 24.4 - - + +
479B TRP* 3.4 9.4 - - + -
481B GLY* 1.3 71.5 - - - +
483B ARG* 1.3 61.2 + - - +
485B LEU* 3.6 15.8 - - + +
486B GLU* 2.9 25.6 + - - +
569B VAL* 5.7 1.7 - - - +
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Residues in contact with ARG 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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400B PHE* 5.0 8.4 - - + -
409B ALA* 4.5 18.6 - - - +
411B GLY* 3.2 28.3 + - - +
413B ILE 4.5 5.7 + - - +
477B TYR* 4.3 27.1 - - - +
478B MET* 2.6 36.2 + - + +
479B TRP 3.0 14.4 + - - +
480B LEU* 3.0 32.6 + - + +
482B ALA* 1.3 77.7 - - - +
484B PHE* 1.3 56.6 + - - +
486B GLU* 3.3 22.5 - - - +
487B PHE* 3.0 24.9 + - - +
604B GLY 5.2 11.9 + - - -
605B GLN* 5.5 3.8 - - + +
606B VAL* 5.5 2.3 - - - +
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Residues in contact with PHE 484 (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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396B THR 4.5 0.4 - - - -
397B LYS* 3.7 44.4 - - + -
400B PHE* 3.5 41.5 - + + -
433B TRP* 4.7 12.1 - + - -
436B VAL* 3.9 15.0 - - + -
440B ARG* 4.4 19.7 - - - -
480B LEU 2.8 11.9 + - - +
481B GLY* 2.9 10.5 + - - +
483B ARG* 1.3 74.6 - - - +
485B LEU* 1.3 74.5 + - + +
487B PHE* 2.8 12.9 + + - -
488B GLU* 2.8 46.8 + - + +
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Residues in contact with LEU 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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436B VAL* 3.8 18.8 - - + +
439B GLU* 3.8 35.2 - - + -
440B ARG* 3.6 35.9 - - + +
443B HIS* 4.2 13.9 - - + +
479B TRP* 6.2 0.2 - - + -
481B GLY 3.0 14.1 + - - +
482B ALA* 3.3 13.2 + - + +
484B PHE* 1.3 80.4 - - + +
486B GLU* 1.3 54.7 + - - +
488B GLU* 4.6 3.6 - - + +
489B ALA* 2.6 41.5 + - - +
569B VAL* 4.7 12.2 - - + +
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Residues in contact with GLU 486 (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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482B ALA 2.9 14.3 + - - +
483B ARG* 3.3 22.0 - - - +
485B LEU* 1.3 75.9 - - - +
487B PHE* 1.3 57.6 + - - +
489B ALA* 3.7 2.6 - - - +
490B LEU* 2.9 29.8 + - + +
491B GLY 3.4 3.1 + - - -
569B VAL* 5.0 8.5 - - + +
574B TYR* 5.1 1.6 - - + +
605B GLN* 3.2 25.2 - - + +
606B VAL* 2.5 27.0 + - - +
607B VAL* 2.5 50.8 + - + +
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Residues in contact with PHE 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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395B CYS* 3.2 32.4 - - + -
396B THR 3.7 10.8 - - - -
399B GLU* 4.6 7.6 - - + -
400B PHE* 3.6 44.4 - + + -
403B LYS* 3.3 46.0 - - + -
483B ARG 3.0 14.0 + - - +
484B PHE* 2.8 22.2 + + - +
486B GLU* 1.3 77.3 - - - +
488B GLU* 1.3 59.6 + - - +
491B GLY* 2.7 40.6 + - - +
495B GLU* 4.9 7.4 - - + -
606B VAL* 4.9 12.8 - - + -
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Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 3.8 19.4 - - - +
395B CYS* 3.2 39.0 + - - +
396B THR* 5.1 0.4 - - - -
440B ARG* 4.5 22.0 + - - +
484B PHE* 2.8 38.6 + - + +
485B LEU* 4.7 4.0 - - + +
487B PHE* 1.3 75.0 - - - +
489B ALA* 1.3 63.5 + - - +
490B LEU* 4.6 0.3 - - - -
491B GLY 4.8 0.2 + - - -
492B PHE* 5.8 1.4 - - - -
562B HIS* 4.0 10.4 + - - -
565B LEU* 3.6 25.9 - - - +
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Residues in contact with ALA 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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485B LEU 2.6 24.3 + - - +
486B GLU* 3.7 2.5 - - - +
487B PHE 3.2 0.2 - - - -
488B GLU* 1.3 82.2 + - - +
490B LEU* 1.3 71.3 + - + +
492B PHE* 4.7 0.6 - - - -
562B HIS* 3.7 14.2 + - - -
565B LEU* 3.7 22.2 - - + +
566B ALA* 3.7 10.0 - - - +
569B VAL* 3.7 27.1 - - + -
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Residues in contact with LEU 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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486B GLU* 2.9 6.2 + - + +
489B ALA* 1.3 94.2 - - + +
491B GLY* 1.3 59.3 + - - +
492B PHE* 2.7 39.0 + - + -
493B LEU* 3.3 20.5 - - + +
554B ILE* 4.7 20.0 - - + -
558B MET* 4.7 2.7 - - + -
566B ALA* 3.7 21.8 - - + -
569B VAL* 4.1 12.1 - - + -
570B ILE* 4.1 17.9 - - + -
574B TYR* 6.3 0.7 - - + -
607B VAL* 3.7 26.4 - - + +
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Residues in contact with GLY 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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395B CYS* 4.6 4.4 - - - -
486B GLU 3.4 2.0 + - - -
487B PHE* 2.7 40.4 + - - -
488B GLU 4.8 0.4 + - - -
489B ALA 3.9 0.2 - - - -
490B LEU* 1.3 68.9 - - - +
492B PHE* 1.3 61.8 + - - +
493B LEU 3.2 1.8 - - - -
494B ASN* 3.3 36.1 + - - +
495B GLU* 3.3 9.2 + - - +
606B VAL* 5.8 0.4 - - - -
607B VAL* 3.9 4.3 - - - -
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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