Contacts of the strand formed by residues 413 - 418 (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 ILE 413 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366K MET* 3.1 10.5 - - - +
367K ARG 5.2 0.2 - - - +
380K GLY* 3.1 47.9 + - - +
381K ASN 3.1 9.3 + - - +
384K GLY* 3.7 32.3 - - - +
385K LYS 4.0 6.5 - - - +
386K LEU* 4.0 14.6 - - + -
409K CYS* 4.4 6.3 - - - -
412K ALA* 1.3 70.7 - - - +
414K ARG* 1.3 63.2 + - - +
415K GLN 3.7 20.9 - - - +
416K THR* 4.7 1.1 - - + -
427K ALA* 3.8 15.0 - - + -
428K VAL 3.6 8.7 - - - +
429K CYS* 3.5 18.6 - - - -
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Residues in contact with ARG 414 (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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96K LEU 3.3 28.0 - - - +
97K PHE* 3.4 35.3 - - + +
363K ILE* 3.9 3.5 - - - +
364K TRP 3.2 9.3 + - - -
365K TYR* 3.2 25.8 + - + +
366K MET* 3.5 17.4 - - - -
367K ARG* 2.8 29.3 + - - +
412K ALA 4.5 1.8 - - - +
413K ILE* 1.3 72.6 - - - +
415K GLN* 1.3 60.7 + - - +
428K VAL* 3.2 8.0 + - + +
430K ASP* 2.7 32.0 + - - +
7T M3L 3.1 23.9 + - - +
8T PHE* 3.1 41.4 - - - +
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Residues in contact with GLN 415 (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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97K PHE 4.0 10.8 - - - +
98K GLY* 3.1 8.5 - - - -
99K VAL* 2.7 44.9 + - + +
100K GLN* 3.5 18.7 - - - +
149K THR* 5.8 0.4 + - - -
195K GLU* 4.6 6.9 + - - -
197K LYS* 6.2 0.6 - - - +
313K ARG* 4.1 19.6 - - - +
367K ARG* 3.7 27.0 + - + +
368K PHE 5.5 0.2 - - - -
369K SER* 5.2 2.7 - - - -
413K ILE* 3.5 9.7 - - - +
414K ARG* 1.3 81.9 - - - +
416K THR* 1.3 80.7 + - - +
427K ALA* 3.7 0.5 - - - -
428K VAL* 3.5 25.6 + - + +
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Residues in contact with THR 416 (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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99K VAL* 3.7 3.5 - - - +
100K GLN* 4.3 0.7 + - - -
367K ARG 4.1 2.7 + - - +
368K PHE 4.1 0.2 - - - -
369K SER* 3.1 37.6 + - - -
378K ALA* 3.7 13.5 + - + +
379K LEU* 4.1 2.5 - - - +
380K GLY 4.0 15.7 - - - +
386K LEU* 3.7 30.1 - - + -
413K ILE* 4.7 0.9 - - + -
415K GLN* 1.3 94.7 + - - +
417K SER* 1.3 65.8 + - - +
425K LEU* 4.0 13.5 - - + -
426K ILE 3.5 6.5 - - - +
427K ALA* 4.7 2.9 - - + -
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Residues in contact with SER 417 (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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99K VAL* 3.8 18.4 - - - -
100K GLN* 3.5 15.1 + - - -
101K PHE* 3.0 39.4 + - - +
103K TRP* 5.1 1.9 + - - -
369K SER* 3.6 5.6 - - - -
416K THR* 1.3 77.7 - - - +
418K PHE* 1.3 64.6 + - - +
425K LEU* 3.6 7.1 - - - -
426K ILE* 3.0 34.0 + - - -
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Residues in contact with PHE 418 (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* 4.2 10.5 - + - -
101K PHE* 3.4 9.3 - - - +
103K TRP* 2.8 23.4 + - + -
369K SER* 3.8 14.3 + - - -
370K MET 3.5 6.0 + - - +
371K ASP* 3.4 37.2 - - + -
376K MET* 3.7 43.7 - - + -
377K LEU 4.6 0.9 - - - -
378K ALA* 3.7 32.3 - - + -
388K VAL* 4.7 4.9 - - + -
417K SER* 1.3 74.4 + - - +
419K SER* 1.3 69.5 + - - +
422K SER* 4.4 8.1 - - - +
424K ILE 3.7 6.3 - - - -
425K LEU* 3.8 27.8 - - + -
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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