Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 4LG8
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 LEU 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A THR* 2.6 26.7 + - - +
324A SER* 3.8 13.0 - - - -
325A SER 3.0 21.6 + - - +
326A ASP* 3.7 1.7 + - - +
328A GLN 4.1 10.3 - - - +
329A TYR 3.6 28.3 - - - +
330A TRP* 3.8 11.7 - - + +
351A CYS 3.8 13.9 - - - +
352A SER* 1.3 72.5 - - - +
354A THR* 1.3 54.4 + - - +
367A THR* 4.0 31.0 - - + +
368A GLY 3.2 7.0 - - - +
369A THR* 3.8 24.0 - - + -
375A LYS* 4.5 7.4 - - + -
377A TRP* 5.6 2.2 - - + +
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Residues in contact with THR 354 (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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310A THR* 3.3 26.0 - - - +
326A ASP* 5.3 2.2 - - - +
352A SER* 5.1 0.4 - - - -
353A LEU* 1.3 73.3 - - - +
355A CYS* 1.3 64.0 + - - +
368A GLY 2.8 22.2 + - - -
369A THR 3.8 1.1 - - - -
370A MET* 3.6 48.7 - - + +
394A PRO* 4.8 1.3 - - + -
395A ILE* 2.7 31.8 + - - +
396A THR* 4.6 4.9 - - - +
612A UNX 4.2 5.7 - - - -
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Residues in contact with CYS 355 (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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310A THR 4.0 3.6 - - - +
324A SER* 3.3 12.5 + - - -
354A THR* 1.3 83.5 - - - +
356A ALA* 1.3 62.9 + - - +
367A THR* 3.2 8.5 - - - -
368A GLY 3.2 33.3 + - - +
395A ILE* 3.7 25.6 - - - -
396A THR 4.3 7.2 - - - +
397A SER* 4.0 8.7 - - - -
398A ILE* 3.9 15.5 - - - -
607A UNX 3.6 8.5 - - - -
613A UNX 3.5 14.8 - - - -
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Residues in contact with ALA 356 (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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311A GLY* 4.1 6.0 - - - -
312A LEU 4.2 3.6 + - - +
313A SER* 3.7 8.5 - - - -
322A LEU* 3.9 24.7 - - + +
323A SER* 4.4 0.7 - - - -
324A SER* 3.7 23.7 + - - +
355A CYS* 1.3 78.1 - - - +
357A GLN* 1.3 80.8 + - - +
366A GLY 3.3 9.4 - - - +
367A THR* 4.3 4.7 - - + -
398A ILE* 4.6 1.1 - - - +
613A UNX 3.1 6.5 - - - -
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Residues in contact with GLN 357 (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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312A LEU 4.1 0.6 + - - -
313A SER* 3.6 13.1 + - - -
322A LEU* 4.0 2.0 - - - -
356A ALA* 1.3 86.4 + - - +
358A PHE* 1.3 63.1 + - - +
365A PHE* 3.2 4.6 - - - +
366A GLY 2.9 32.0 + - - -
398A ILE* 3.3 38.7 - - + +
399A ALA* 4.8 3.1 - - - -
400A PHE* 3.3 17.0 + - + +
603A UNX 4.1 0.4 - - - -
604A UNX 3.1 24.2 - - - -
607A UNX 3.6 5.3 - - - -
613A UNX 3.3 10.5 - - - -
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Residues in contact with PHE 358 (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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313A SER* 3.1 27.8 + - - +
314A LEU 3.8 4.9 - - - +
315A HIS* 3.5 51.1 - + + -
316A ALA 5.5 1.3 - - - +
321A LEU 4.7 0.2 - - - -
322A LEU* 3.3 30.7 - - + -
332A PHE* 3.6 27.1 - + - -
357A GLN* 1.3 77.4 - - - +
359A HIS* 1.3 67.7 + - - +
360A PRO* 3.7 1.8 - - + +
362A GLY* 4.4 6.7 - - - -
364A ILE 3.8 13.0 - - - -
365A PHE* 3.8 22.7 - + + -
379A LEU* 4.1 10.8 - - + -
400A PHE* 3.4 14.3 - - - +
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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