Contacts of the strand formed by residues 433 - 439 (chain K) in PDB entry 5LS6
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 SER 433 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K SER* 5.9 0.9 - - - -
88K LEU 3.3 10.3 - - - -
89K LYS* 4.2 14.6 - - - +
96K LEU* 4.3 0.2 - - - +
428K VAL* 3.6 1.4 - - - -
429K CYS* 2.9 29.5 + - - +
431K ASP* 2.5 33.9 + - - -
432K ALA* 1.3 79.7 - - - +
434K ILE* 1.3 61.7 + - - +
435K TRP* 2.9 36.5 + - - -
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Residues in contact with ILE 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K SER* 3.3 5.2 - - - -
88K LEU* 2.7 62.6 + - + +
90K GLU* 4.6 4.3 - - + -
96K LEU* 3.6 27.8 - - + -
113K PHE* 4.3 5.2 - - + -
115K THR* 4.1 3.6 - - + -
124K TYR* 3.6 34.8 - - + +
132K ILE* 5.2 1.8 - - + -
426K ILE* 3.6 33.0 - - + -
427K ALA 3.6 4.9 - - - +
428K VAL* 4.0 4.9 - - + -
432K ALA 4.3 1.1 - - - +
433K SER* 1.3 71.9 - - - +
435K TRP* 1.3 77.0 + - - +
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Residues in contact with TRP 435 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K CYS* 4.2 12.6 - - - -
86K ASN 3.7 4.7 - - - +
87K SER* 3.1 34.3 - - - -
386K LEU* 5.6 0.2 - - + -
406K HIS* 3.2 28.0 - + + -
408K LYS* 3.5 14.6 - - + -
409K CYS* 3.2 58.1 - - + -
410K GLY 4.8 0.4 - - - -
425K LEU 3.9 0.5 - - - +
426K ILE* 3.4 9.9 - - - +
427K ALA* 3.0 43.9 + - + +
429K CYS* 3.6 13.4 - - - -
431K ASP* 5.1 1.3 - - - -
433K SER* 2.9 32.3 + - - -
434K ILE* 1.3 82.0 - - - +
436K ARG* 1.3 59.9 + - - +
437K TRP* 3.5 22.4 - + + +
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Residues in contact with ARG 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K CYS* 3.5 6.2 - - - -
85K VAL* 2.9 32.3 + - + +
86K ASN 3.1 18.4 + - - +
126K CYS* 4.0 9.6 - - - +
127K HIS 3.5 10.7 + - - -
128K SER* 4.7 4.4 - - - +
129K GLN* 4.9 2.0 - - - +
130K GLY* 3.4 27.7 - - - +
131K GLU 2.9 28.5 + - - -
132K ILE* 3.9 22.6 - - + +
424K ILE* 3.4 44.1 - - + +
425K LEU 3.6 2.7 - - - -
426K ILE* 3.6 9.4 - - + -
435K TRP* 1.3 73.5 - - - +
437K TRP* 1.3 60.6 + - - +
438K ASP* 2.8 34.8 + - - +
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Residues in contact with TRP 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K PHE* 3.6 22.2 - - + -
83K LYS* 3.3 11.0 - - - -
84K CYS* 3.6 38.1 - - + -
384K GLY 5.5 0.4 - - - -
386K LEU* 3.4 28.7 - - + +
404K LEU* 3.3 53.8 - - + -
405K THR 3.4 20.6 - - - -
406K HIS* 4.3 11.7 - - + -
409K CYS* 5.3 8.1 - - - -
424K ILE* 4.5 0.2 - - - -
425K LEU* 2.8 53.6 + - + +
427K ALA* 5.1 1.1 - - + -
435K TRP* 3.5 26.0 - + + +
436K ARG* 1.3 77.2 - - - +
438K ASP* 1.3 61.1 + - - +
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Residues in contact with ASP 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K PHE* 2.9 8.2 - - - -
83K LYS* 2.8 34.5 + - + +
85K VAL* 3.1 23.2 - - + +
129K GLN* 5.4 5.2 - - - +
423K SER* 3.3 9.1 - - - +
424K ILE* 3.7 12.1 - - - +
436K ARG* 2.8 45.0 + - - +
437K TRP* 1.3 76.5 - - - +
439K ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K TYR* 3.6 30.3 - - + +
81K SER 3.2 13.9 - - - +
82K PHE* 3.2 33.3 - - + -
83K LYS* 4.9 2.3 + - - +
376K MET* 3.8 11.7 - - - +
422K SER* 3.1 53.0 - - - +
423K SER* 3.2 9.4 + - - +
438K ASP* 1.3 78.7 - - - +
440K LEU* 1.3 73.1 + - - +
441K ARG* 3.5 2.9 + - - -
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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
------------------------------------------------------------
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