Contacts of the strand formed by residues 350 - 357 (chain E) 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 VAL 350 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 4.5 8.3 - - + -
167D ASN* 2.5 52.2 + - + +
169D GLU* 4.2 1.6 - - - +
299E PHE* 3.8 6.3 - - + -
301E THR* 3.5 40.4 - - + +
303E ASP* 4.6 9.6 - - + +
304E ILE* 3.6 27.6 - - + -
331E TRP* 4.0 2.7 - - + -
332E LYS 3.2 13.9 - - - +
334E GLY 3.4 2.9 - - - +
349E ASN* 1.3 80.7 - - - +
351E THR* 1.3 63.6 + - - +
352E ILE* 4.9 0.4 - - + -
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Residues in contact with THR 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ARG* 4.4 15.9 - - - +
38D VAL* 6.0 0.2 - - + -
167D ASN* 4.6 1.8 - - - +
169D GLU* 3.4 18.3 + - - +
331E TRP* 3.4 2.9 - - - -
332E LYS* 3.0 34.3 + - - +
334E GLY 3.2 13.7 + - - -
335E LYS 4.3 0.7 - - - -
336E MET* 3.4 30.9 + - - -
350E VAL* 1.3 78.0 + - - +
352E ILE* 1.3 71.1 + - - +
353E LEU* 3.5 17.2 + - + +
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Residues in contact with ILE 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ARG* 5.7 1.3 - - - +
34D ARG* 6.0 0.3 - - - -
38D VAL* 5.4 1.0 - - - +
165D PHE* 3.3 37.8 - - + -
167D ASN* 5.5 0.2 - - - +
304E ILE* 3.3 39.0 - - + -
329E VAL* 3.5 27.6 - - + -
330E CYS 3.8 4.3 - - - +
331E TRP* 3.5 9.4 - - + -
350E VAL* 4.9 0.2 - - + -
351E THR* 1.3 78.5 - - - +
353E LEU* 1.3 66.2 + - - +
354E GLY 4.3 8.7 - - - +
355E ARG* 3.6 24.2 - - - +
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Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ARG* 6.1 0.9 - - - +
38D VAL* 4.0 27.5 - - + +
41D MET* 4.8 9.0 - - + -
42D PHE* 4.0 20.4 - - + -
318E LEU* 3.4 46.2 - - + -
330E CYS* 2.9 18.6 + - - +
331E TRP* 4.7 3.6 - - - -
332E LYS* 4.5 2.9 - - + -
336E MET* 3.4 33.7 - - + -
351E THR* 3.6 18.2 - - + +
352E ILE* 1.3 79.0 - - - +
354E GLY* 1.3 57.8 + - - +
396E PRO* 5.1 6.1 - - - +
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Residues in contact with GLY 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 4.5 3.5 - - - -
329E VAL* 3.8 3.3 - - - +
330E CYS* 2.9 36.3 + - - +
352E ILE* 3.9 2.4 - - - -
353E LEU* 1.3 81.1 - - - +
355E ARG* 1.3 65.7 + - - +
356E PHE* 5.1 0.2 - - - -
396E PRO* 5.1 8.3 - - - -
397E HIS* 4.7 16.4 - - - -
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Residues in contact with ARG 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ARG* 3.5 28.0 - - - +
165D PHE* 4.4 21.2 - - - +
304E ILE 5.0 5.5 + - - -
327E ALA* 4.4 10.5 - - + +
328E ILE 3.6 5.4 - - - +
329E VAL* 4.1 21.3 - - + +
352E ILE* 3.6 26.0 - - + +
354E GLY* 1.3 77.5 - - - +
356E PHE* 1.3 63.1 + - - +
357E ASP* 3.7 23.0 + - - +
396E PRO* 5.9 0.2 - - - +
397E HIS* 2.7 34.6 + - - +
398E LYS 4.0 1.6 + - - +
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Residues in contact with PHE 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 5.8 2.5 - + - -
315E LEU* 5.5 2.0 - - + -
320E LEU* 4.2 23.3 - - + -
327E ALA* 3.6 1.2 - - - -
328E ILE* 2.8 46.4 + - + +
330E CYS* 4.3 11.0 - - + -
354E GLY 4.8 1.8 - - - -
355E ARG* 1.3 73.6 - - - +
357E ASP* 1.3 65.3 + - - +
358E TYR* 3.6 5.7 - - - -
377E LEU* 4.0 11.4 - - + -
389E TRP* 3.7 48.3 - + + +
390E ASP 4.5 6.7 - - - -
391E LEU* 3.6 31.4 - - + -
397E HIS* 3.3 38.6 - + + -
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Residues in contact with ASP 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E ASN 4.1 7.1 - - - +
327E ALA* 4.0 8.0 - - - +
355E ARG* 3.7 22.2 + - - +
356E PHE* 1.3 70.5 - - - +
358E TYR* 1.3 60.0 + - - +
387E TYR* 5.0 2.4 - - - -
389E TRP* 3.3 22.0 + - - +
397E HIS 6.0 0.4 - - - -
398E LYS* 4.4 26.7 + - - +
401E CYS* 5.2 2.1 - - - +
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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