Contacts of the strand formed by residues 407 - 412 (chain A) in PDB entry 4WMJ
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 CYS 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A HIS* 4.7 0.4 - - - -
340A ALA* 3.4 16.2 - - - +
342A LEU* 3.7 23.8 - - + -
398A VAL* 4.2 22.0 - - - -
405A ILE* 3.3 18.6 + - - -
406A PRO* 1.3 73.6 - - - +
408A ASP* 1.3 64.3 + - - +
409A PHE* 3.6 24.0 - - + -
439A LEU* 5.0 0.7 - - - -
476A PRO 3.4 5.5 + - - -
477A THR* 3.2 10.9 - - + +
478A ASN 2.9 25.5 + - - +
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A LEU* 4.9 5.1 - - - +
339A HIS* 3.0 27.9 + - - -
340A ALA 2.8 9.7 + - - -
341A LEU* 3.6 7.8 - - + +
342A LEU* 2.8 33.3 + - - +
407A CYS* 1.3 73.9 - - - +
409A PHE* 1.4 57.5 + - - +
410A LEU* 3.6 6.8 - - + +
478A ASN* 2.8 37.7 - - + +
480A ILE* 4.7 6.3 - - + -
497A TYR* 2.7 36.3 + - - +
500A LYS* 4.6 1.7 + - - -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.5 18.4 - - + -
344A TYR* 3.5 38.6 - + - -
395A TYR* 3.6 16.8 - + - -
407A CYS* 3.6 29.2 - - + -
408A ASP* 1.4 71.4 - - - +
410A LEU* 1.3 56.0 + - - +
432A PHE* 3.5 22.2 - + + -
435A GLN* 3.7 19.1 - - + -
436A THR* 3.4 24.2 - - + -
439A LEU* 4.0 11.7 - - + -
477A THR* 3.7 17.5 - - + -
478A ASN 2.8 10.0 + - - +
479A SER* 3.3 2.7 - - - +
480A ILE* 2.8 31.7 + - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU* 5.0 2.2 - - + -
342A LEU 3.2 8.4 + - - +
343A PRO* 3.9 27.6 - - + -
344A TYR* 2.7 33.6 + - - +
348A LEU* 6.2 1.6 - - + -
351A PHE* 4.6 15.7 - - + -
408A ASP* 3.6 19.1 - - + +
409A PHE* 1.3 78.5 - - - +
411A ALA* 1.3 61.4 + - - +
432A PHE* 3.6 2.3 - - - -
480A ILE* 3.1 40.6 - - + +
485A PHE* 4.5 10.5 - - + -
493A LEU* 4.3 16.4 - - + -
497A TYR* 4.4 20.6 - - + +
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A TYR* 4.3 7.4 - - + +
410A LEU* 1.3 76.7 - - - +
412A PRO* 1.3 71.3 - - + +
429A LEU* 3.9 13.0 - - + -
432A PHE* 3.7 34.3 - - + -
480A ILE 2.9 7.3 + - - +
481A VAL* 3.3 9.8 - - + +
482A VAL* 3.1 22.2 + - - +
485A PHE* 4.1 10.0 - - - -
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Residues in contact with PRO 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A TYR 3.9 13.5 - - - +
345A ASP* 4.2 8.1 - - - +
411A ALA* 1.3 89.3 - - + +
413A ALA* 1.3 61.1 + - - +
414A GLN 3.4 20.9 - - - +
415A THR* 5.2 1.3 - - - -
425A HIS* 2.9 35.7 + - + -
429A LEU* 3.6 7.8 - - - +
482A VAL* 3.2 8.3 - - + +
484A LYS* 3.9 13.5 - - - -
485A PHE* 3.6 31.4 - - + +
552B LEU* 4.4 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