Contacts of the strand formed by residues 413 - 418 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366B MET* 3.4 4.5 - - - +
367B ARG 4.6 0.7 - - - +
380B GLY* 2.7 39.1 + - - +
381B ASN 2.9 13.7 + - - +
384B GLY* 3.2 39.0 - - - +
385B LYS 3.5 18.6 - - - +
386B LEU* 4.1 10.5 - - + -
409B CYS* 4.4 4.9 - - - -
412B ALA* 1.3 68.6 - - - +
414B ARG* 1.3 65.8 + - - +
415B GLN* 3.2 5.9 + - - +
416B THR* 4.6 2.7 - - + -
427B ALA* 3.6 29.4 - - + -
428B VAL 3.5 10.8 - - - +
429B CYS* 3.6 17.9 - - - -
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Residues in contact with ARG 414 (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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96B LEU 3.3 26.5 - - - +
97B PHE* 3.5 35.8 - - + +
363B ILE* 3.6 2.0 - - - +
364B TRP 3.3 6.8 + - - -
365B TYR* 3.0 25.5 + - + +
366B MET* 3.0 29.9 - - - -
367B ARG* 3.0 30.9 + - - +
412B ALA 3.4 4.2 + - - +
413B ILE* 1.3 73.0 - - - +
415B GLN* 1.3 61.4 + - - +
428B VAL* 3.0 6.0 + - + +
429B CYS 4.9 0.4 - - - -
430B ASP* 3.2 27.0 + - - +
7Q M3L 2.8 33.7 + - - +
8Q PHE* 3.2 29.9 - - - +
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE 4.1 10.1 - - - +
98B GLY* 3.3 8.2 - - - -
99B VAL* 2.7 62.7 + - + +
100B GLN* 3.9 17.2 + - - +
149B THR* 5.6 3.6 + - - -
195B GLU* 5.1 4.0 + - - -
313B ARG* 4.7 11.1 - - - +
367B ARG* 3.8 32.1 - - + +
368B PHE 4.7 4.9 + - - +
369B SER* 5.5 2.0 - - - -
413B ILE* 3.2 3.2 + - - -
414B ARG* 1.3 82.1 - - + +
416B THR* 1.3 74.7 + - - +
427B ALA* 3.7 1.0 - - - +
428B VAL* 3.4 18.0 + - + +
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Residues in contact with THR 416 (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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99B VAL* 4.0 0.4 - - - -
100B GLN* 5.1 0.5 + - - -
367B ARG 4.4 4.0 + - - +
369B SER* 3.0 33.6 + - - -
378B ALA* 3.1 25.6 + - - +
379B LEU* 4.3 0.2 - - - -
380B GLY* 3.5 20.0 - - - +
386B LEU* 3.4 29.8 - - + -
413B ILE* 4.6 3.6 - - + -
415B GLN* 1.3 92.4 + - - +
417B SER* 1.3 63.0 + - - +
425B LEU* 4.0 10.3 - - - +
426B ILE 3.6 10.8 - - - -
427B ALA* 4.5 1.1 - - + +
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Residues in contact with SER 417 (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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99B VAL* 3.4 27.1 + - - +
100B GLN* 3.4 10.5 + - - +
101B PHE* 2.8 43.1 + - - +
103B TRP* 5.4 0.7 + - - -
369B SER* 3.8 4.0 - - - -
416B THR* 1.3 77.9 - - - +
418B PHE* 1.3 60.0 + - - +
425B LEU* 3.8 3.8 - - - -
426B ILE 2.9 34.3 + - - -
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Residues in contact with PHE 418 (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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82B PHE* 4.1 6.7 - + - -
101B PHE* 2.9 14.2 - - - +
103B TRP* 3.1 20.6 + - + -
369B SER* 4.1 5.0 + - - -
370B MET* 3.4 11.5 + - - +
371B ASP* 3.3 40.8 - - + -
376B MET* 3.2 48.0 - - + -
378B ALA* 3.9 29.2 - - + -
388B VAL* 4.5 4.5 - - + -
417B SER* 1.3 72.6 + - - +
419B SER* 1.3 68.0 + - - +
422B SER* 4.5 7.2 - - - -
424B ILE 3.7 15.0 - - - +
425B LEU* 3.9 22.9 - - + -
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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
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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