Contacts of the strand formed by residues 606 - 610 (chain B) in PDB entry 1WZ2
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 606 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.3 39.9 - + - -
37B TYR 3.7 2.8 + - - -
38B ILE* 3.5 17.0 - - + -
39B THR 3.2 11.0 + - - -
486B LYS* 4.1 27.6 - - + -
488B LEU* 3.3 39.5 - - + -
604B LEU* 2.8 29.2 + - - +
605B ASP* 1.3 96.1 + - + +
607B ARG* 1.3 61.8 + - - +
608B CYS* 4.2 0.7 - - - -
637B GLY* 3.6 20.0 - - - -
638B ILE 4.3 8.3 - - - -
639B ALA* 4.1 12.8 - - + -
745B GLU 4.7 9.0 - - - -
747B PHE* 3.6 30.0 - + + -
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Residues in contact with ARG 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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39B THR* 3.5 26.8 - - - +
40B VAL 3.6 4.8 - - - -
41B ALA* 3.7 14.5 - - - +
42B PHE* 5.4 0.2 - - - -
535B TYR* 2.6 42.9 + - - -
536B MET* 3.7 13.8 - - - -
604B LEU* 3.9 14.6 - - + +
606B TRP* 1.3 74.5 - - - +
608B CYS* 1.3 75.3 + - - +
609B SER* 5.1 0.4 - - - -
617B HIS* 3.4 30.7 + - - -
618B LEU* 4.7 8.3 - - - +
621B PHE* 3.9 33.9 - - + -
637B GLY 3.3 9.8 + - - +
638B ILE* 3.4 13.1 - - + +
639B ALA 3.2 18.0 + - - -
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Residues in contact with CYS 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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38B ILE* 4.5 6.1 - - - -
39B THR 2.8 16.4 + - - +
40B VAL* 3.3 33.3 - - + +
41B ALA 3.5 3.5 + - - -
56B THR 4.7 1.6 - - - +
59B ILE* 5.3 3.4 - - + -
60B PRO* 4.1 26.0 - - + -
607B ARG* 1.3 79.3 - - - +
609B SER* 1.3 67.2 + - - +
639B ALA* 3.2 12.6 - - - +
641B ASN* 5.8 1.8 - - - +
747B PHE* 3.4 34.8 - - - -
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Residues in contact with SER 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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40B VAL* 4.6 0.4 - - - -
41B ALA* 4.7 9.0 - - - +
56B THR* 4.3 11.2 - - - +
607B ARG* 5.1 1.3 - - - -
608B CYS* 1.3 80.6 - - - +
610B GLY* 1.3 79.8 + - - +
613B LEU* 3.5 27.1 - - - +
617B HIS* 6.0 0.4 - - - -
618B LEU* 3.9 21.5 - - - -
639B ALA 3.1 4.6 + - - -
640B VAL* 2.9 27.9 - - - -
641B ASN* 3.1 10.5 + - - +
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Residues in contact with GLY 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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56B THR* 4.5 8.6 - - - +
609B SER* 1.3 93.4 + - - +
611B LYS* 1.3 65.7 + - - +
612B ASP* 3.3 9.9 - - - -
613B LEU* 3.5 7.9 + - - +
618B LEU* 4.2 1.7 - - - +
640B VAL* 3.9 5.2 - - - +
641B ASN* 3.5 19.3 - - - -
643B PHE* 5.6 3.4 - - - -
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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