Contacts of the helix formed by residues 491 - 496 (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 GLY 491 (chain B).
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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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Residues in contact with PHE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO* 4.1 22.9 - - + -
393B ARG* 4.0 24.7 - - + +
394B VAL* 4.6 18.2 - - - +
395B CYS* 4.7 6.1 - - + -
487B PHE 4.4 1.0 + - - -
488B GLU 5.8 1.1 - - - -
489B ALA 4.8 2.0 - - - -
490B LEU* 2.7 37.8 + - + -
491B GLY* 1.3 71.4 - - - +
493B LEU* 1.3 79.3 + - + -
495B GLU* 2.8 22.3 + - + +
496B ASP* 2.9 16.5 + - + +
498B TRP* 3.0 37.6 + + + +
554B ILE* 3.8 20.4 - - + -
558B MET* 5.0 1.6 - - - -
562B HIS* 4.6 8.7 - + - -
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Residues in contact with LEU 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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383B TRP* 5.1 9.4 - - + -
490B LEU* 3.3 29.8 - - + +
491B GLY 3.2 0.6 - - - -
492B PHE* 1.3 103.7 - - + +
494B ASN* 1.3 63.6 + - - +
495B GLU 3.4 0.2 + - - -
497B HIS* 4.0 3.1 + - - -
498B TRP* 3.4 48.3 + - + +
499B MET* 4.7 14.0 + - + -
554B ILE* 4.5 14.1 - - + -
607B VAL* 6.0 1.8 - - + -
610B ALA* 3.7 31.4 - - + -
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Residues in contact with ASN 494 (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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403B LYS* 4.2 17.6 + - - +
487B PHE* 5.6 0.4 - - + -
491B GLY* 3.3 18.5 + - - +
493B LEU* 1.3 79.4 - - - +
495B GLU* 1.3 59.8 + - - +
497B HIS* 4.9 1.0 + - - -
606B VAL* 2.3 43.5 + - + +
607B VAL* 3.3 27.4 - - - +
609B TYR* 4.6 11.5 - - - +
610B ALA* 5.6 0.4 - - - +
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Residues in contact with GLU 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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395B CYS* 5.8 5.6 - - + -
399B GLU* 5.5 16.4 - - - +
403B LYS* 4.2 23.6 + - - +
487B PHE* 4.9 7.0 - - + -
491B GLY 3.3 8.9 + - - +
492B PHE* 2.8 14.1 + - - +
494B ASN* 1.3 82.9 - - + +
496B ASP* 1.3 76.0 + - - +
497B HIS* 3.3 20.6 + - - -
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Residues in contact with ASP 496 (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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390B LYS* 6.0 2.1 - - - +
492B PHE* 2.9 11.1 + - + +
495B GLU* 1.3 90.6 - - - +
497B HIS* 1.3 77.3 + - + +
498B TRP* 3.2 29.9 + - + +
503B ASN* 4.7 2.3 + - - -
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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