Contacts of the helix formed by residues 550 - 558 (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 ASN 550 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B MET* 3.2 29.3 + - - +
376B ASN* 4.1 7.9 - - - +
379B SER* 2.5 38.2 + - - -
383B TRP* 4.2 3.1 + - - -
546B PHE 3.3 15.6 + - - +
547B ASP* 3.3 15.8 + - - +
548B LEU 3.2 0.4 - - - -
549B GLU* 1.3 78.3 - - - +
551B GLU* 1.3 60.8 - - - +
553B LEU* 3.3 28.3 - - - +
614B PHE* 5.5 3.5 - - + -
618B VAL* 5.7 0.6 - - - +
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Residues in contact with GLU 551 (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* 3.1 41.2 - - - -
547B ASP 3.1 13.0 + - - +
548B LEU* 3.2 17.7 + - + +
549B GLU 3.2 1.0 - - - -
550B ASN* 1.3 74.7 - - - +
552B ALA* 1.3 56.4 + - - +
553B LEU 2.8 13.1 + - - -
554B ILE* 3.7 5.6 + - + +
610B ALA* 4.7 5.9 - - - +
611B LEU* 3.3 30.3 + - + +
614B PHE* 3.1 35.5 - - - -
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Residues in contact with ALA 552 (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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548B LEU 3.7 4.4 + - - +
549B GLU 3.7 11.2 + - - +
550B ASN 3.3 2.2 - - - -
551B GLU* 1.3 75.3 - - - +
553B LEU* 1.3 57.4 + - + +
554B ILE* 3.2 3.6 - - - -
555B THR* 2.4 44.0 + - + +
567B LEU* 5.9 2.5 - - + -
570B ILE* 3.9 27.3 - - + +
575B GLN* 4.8 5.6 - - - +
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Residues in contact with LEU 553 (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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376B ASN* 3.5 22.9 - - - +
379B SER* 3.9 0.7 - - - -
380B SER* 3.7 29.8 - - - +
383B TRP* 3.4 25.3 - - + +
549B GLU 5.5 2.2 - - - +
550B ASN* 3.3 32.5 - - - +
551B GLU 2.8 6.3 + - - -
552B ALA* 1.3 70.0 - - - +
554B ILE* 1.3 62.7 + - - +
555B THR 3.1 1.6 - - - -
556B ASN* 3.1 39.1 + - - +
557B GLN* 4.5 2.6 + - - +
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Residues in contact with ILE 554 (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* 3.5 42.8 - - + -
392B PRO* 4.5 13.0 - - + -
490B LEU* 4.7 11.0 - - + -
492B PHE* 3.8 31.9 - - + -
493B LEU* 4.5 10.5 - - + -
551B GLU 3.7 9.6 + - - +
552B ALA* 4.9 1.3 - - - -
553B LEU* 1.3 76.1 - - - +
555B THR* 1.3 66.8 + - + +
556B ASN 3.1 0.4 - - - -
557B GLN* 3.1 21.3 + - - +
558B MET* 3.5 27.4 + - + +
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Residues in contact with THR 555 (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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552B ALA* 2.4 37.8 + - + +
553B LEU* 4.3 0.5 - - - -
554B ILE* 1.3 78.9 - - + +
556B ASN* 1.3 63.8 + - - +
558B MET* 3.6 22.6 + - + -
563B ARG* 2.3 47.1 + - + +
566B ALA 5.4 0.4 - - - -
567B LEU* 3.8 39.1 - - + +
570B ILE* 5.5 1.8 - - + -
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Residues in contact with ASN 556 (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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380B SER* 6.1 1.0 - - - -
553B LEU* 3.3 40.1 + - - +
554B ILE 3.1 1.4 - - - -
555B THR* 1.3 81.7 + - - +
557B GLN* 1.3 62.7 + - + +
558B MET 3.7 0.2 - - - -
563B ARG* 4.0 7.5 + - - +
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Residues in contact with GLN 557 (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* 3.3 40.0 + - - +
384B LYS* 3.9 6.3 - - - +
386B LEU 5.2 0.2 - - - -
387B GLY* 3.4 22.4 - - - -
390B LYS 4.5 1.9 - - - +
391B ARG* 5.2 4.0 - - + +
392B PRO* 3.3 37.4 - - + +
553B LEU 4.9 2.9 - - - +
554B ILE* 3.1 15.3 + - + +
556B ASN* 1.3 87.5 - - + +
558B MET* 1.3 62.4 + - - +
559B GLU* 5.2 3.1 - - - +
563B ARG* 4.0 0.4 - - - -
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Residues in contact with MET 558 (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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392B PRO* 3.6 23.3 - - + -
490B LEU* 4.7 7.9 - - + -
492B PHE* 5.0 2.9 - - - -
554B ILE* 3.5 23.6 - - + +
555B THR* 3.6 34.9 + - + +
557B GLN* 1.3 82.1 - - - +
559B GLU* 1.3 68.1 + - - +
560B GLU* 5.3 0.3 - - - +
562B HIS* 3.4 31.4 - - - +
563B ARG* 2.4 43.8 + - + +
566B ALA* 3.7 26.9 - - + -
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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