Contacts of the helix formed by residues 606 - 612 (chain B) in PDB entry 2WSC
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 VAL 606 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504B ASN* 6.1 5.2 - - + -
597B LYS* 5.9 5.2 - - + -
600B THR* 4.5 7.4 - - - +
601B LEU* 3.6 42.4 - - + +
605B ASN* 1.3 83.4 - - - +
607B SER* 1.3 58.7 + - - +
608B GLN 2.5 18.4 + - - +
609B PHE* 3.3 11.3 + - + +
610B ASN* 3.1 22.1 + - - +
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Residues in contact with SER 607 (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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605B ASN* 4.1 7.5 + - - +
606B VAL* 1.3 79.2 - - - +
608B GLN* 1.3 64.2 + - - +
610B ASN* 3.0 32.5 + - - +
611B GLU* 3.3 26.3 + - - +
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Residues in contact with GLN 608 (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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596B TRP* 4.9 9.4 - - + +
600B THR* 3.6 21.1 - - + -
605B ASN* 3.4 32.5 + - - +
606B VAL 2.5 5.9 + - - -
607B SER* 1.3 79.9 + - - +
609B PHE* 1.3 57.9 - - - +
611B GLU* 4.4 4.9 + - - -
612B SER* 2.9 47.5 + - - +
622B ASP* 4.5 18.8 + - - +
626B LEU* 4.8 8.1 - - - +
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Residues in contact with PHE 609 (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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515B GLY* 4.3 6.5 - - - -
516B ASP* 3.3 32.1 - - - -
519B VAL* 4.7 2.7 - - + -
593B TYR* 3.4 35.9 - + - -
596B TRP* 3.4 44.0 - + + -
597B LYS* 3.8 27.6 - - + +
600B THR* 4.4 13.6 + - - +
606B VAL* 3.3 8.2 + - + +
608B GLN* 1.3 76.0 - - - +
610B ASN* 1.3 78.3 + - - +
612B SER 4.0 5.6 - - - -
613B SER* 2.7 40.9 + - - -
619B TRP* 4.3 4.9 - + - -
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Residues in contact with ASN 610 (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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513B GLY* 5.9 1.2 + - - -
515B GLY* 4.7 6.8 + - - +
516B ASP* 5.7 0.5 - - - +
606B VAL* 3.1 17.6 + - - +
607B SER* 3.0 33.2 + - - +
609B PHE* 1.3 91.6 - - - +
611B GLU* 1.3 61.5 + - + +
612B SER 3.0 3.3 + - - -
613B SER* 3.5 4.3 + - - -
614B THR* 3.9 9.2 + - - -
65F SER* 4.9 13.4 + - - +
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Residues in contact with GLU 611 (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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444B LEU* 5.8 0.3 - - - +
452B GLN* 4.5 2.6 - - - +
607B SER* 3.3 27.2 + - - +
608B GLN* 4.2 6.8 + - - +
610B ASN* 1.3 74.8 - - + +
612B SER* 1.3 62.2 + - - +
613B SER 3.6 1.6 - - - -
614B THR* 3.5 17.1 - - + +
615B TYR* 3.1 17.2 + - - -
65F SER 4.6 4.5 - - - +
66F ASP* 2.9 45.3 - - + +
68F LEU* 4.5 11.4 - - + -
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Residues in contact with SER 612 (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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596B TRP* 2.0 41.7 - - - -
608B GLN* 2.9 27.9 + - - +
609B PHE 3.5 3.8 - - - -
610B ASN 3.0 1.8 + - - -
611B GLU* 1.3 83.3 + - - +
613B SER* 1.3 49.9 - - - +
615B TYR* 3.2 24.4 + - - -
618B GLY 4.5 1.3 + - - -
619B TRP 5.8 0.2 - - - -
621B ARG* 4.2 0.3 + - - -
622B ASP* 2.8 29.4 + - - -
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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