Contacts of the strand formed by residues 348 - 358 (chain A) in PDB entry 1MU5
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 HIS 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.4 33.7 + + - -
100A VAL* 3.8 21.8 - - + -
235A GLY* 4.6 3.5 + - - -
309A PRO* 3.7 4.8 - - - +
344A ALA* 3.3 0.7 - - - -
345A TYR* 2.9 34.4 + - + +
346A GLN 3.5 15.5 - - - -
347A GLY* 1.3 82.9 + - - +
349A PRO* 1.3 69.6 - - + +
417A SER* 4.0 6.3 - - - +
418A THR* 2.8 30.9 + - - +
419A LYS* 3.5 36.0 - - + +
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Residues in contact with PRO 349 (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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229A VAL* 6.3 0.2 - - + -
263A GLN* 5.9 2.2 - - - +
309A PRO* 3.6 20.6 - - + +
310A SER 2.8 29.2 - - - +
311A ALA* 4.0 7.4 - - + -
313A SER* 3.5 15.9 - - - +
314A LEU* 3.8 15.9 - - + +
342A PRO* 5.6 0.7 - - + -
343A LYS 3.4 9.6 - - - +
347A GLY 4.5 0.4 - - - +
348A HIS* 1.3 85.3 - - - +
350A PHE* 1.3 56.9 + - - +
417A SER* 2.7 32.9 + - - -
418A THR* 3.3 15.3 - - - +
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 3.7 0.9 - - - -
342A PRO* 3.4 0.3 - - - +
343A LYS* 2.7 65.1 + - + +
344A ALA* 3.6 29.8 - - - -
345A TYR* 3.9 21.3 - + + -
349A PRO* 1.3 76.4 - - - +
351A ILE* 1.3 67.0 + - - +
352A VAL* 4.2 5.6 - - + -
415A LEU* 3.8 20.2 - - + -
416A CYS 3.2 13.5 - - - +
417A SER* 3.7 10.1 - - - +
435A ASP* 3.6 23.8 - - + -
436A ILE* 4.0 15.7 - - + -
439A GLU* 3.8 25.4 - - + -
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Residues in contact with ILE 351 (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 ALA* 4.7 4.7 - - + +
314A LEU* 3.8 25.8 - - + -
316A VAL* 3.7 33.2 - - + -
339A THR* 4.3 4.3 - - + -
340A ARG 3.2 22.7 - - - +
341A LYS 4.9 1.6 - - - -
342A PRO* 3.7 30.1 - - + -
343A LYS* 6.1 0.2 - - - -
350A PHE* 1.3 81.4 - - - +
352A VAL* 1.3 72.8 - - - +
353A GLU* 4.4 2.0 - - + +
414A HIS 3.7 1.7 - - - +
415A LEU* 3.7 2.6 - - - +
416A CYS* 3.0 38.1 + - - -
439A GLU* 6.0 0.2 - - - -
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Residues in contact with VAL 352 (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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340A ARG* 3.0 33.4 + - + +
350A PHE* 4.2 4.5 - - + -
351A ILE* 1.3 80.3 - - - +
353A GLU* 1.3 71.8 + - - +
413A VAL* 4.2 10.8 - - + -
414A HIS 3.3 6.3 - - - +
415A LEU* 4.0 18.6 - - + -
436A ILE 4.9 0.2 - - - +
439A GLU* 3.6 34.8 + - + +
440A ILE* 4.1 22.0 - - + -
443A ALA* 3.7 24.9 - - + -
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Residues in contact with GLU 353 (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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316A VAL* 3.5 11.2 - - + +
317A ILE* 2.7 29.0 + - - +
318A GLY* 2.9 18.2 + - - -
322A ILE* 3.8 17.0 - - + +
338A ILE* 3.1 11.7 - - - +
339A THR* 2.6 31.5 + - + +
351A ILE* 4.4 7.0 - - + +
352A VAL* 1.3 82.9 - - - +
354A ALA* 1.3 61.6 + - - +
412A MET* 4.7 0.7 - - - -
413A VAL* 3.5 2.4 - - - -
414A HIS* 2.7 57.5 + - + +
416A CYS* 5.7 0.2 - - - -
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Residues in contact with ALA 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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322A ILE* 4.5 1.0 - - - +
337A SER* 3.2 4.3 - - - -
338A ILE* 2.8 39.1 + - + +
352A VAL* 5.1 0.2 - - + -
353A GLU* 1.3 76.6 - - - +
355A GLY* 1.3 58.8 + - - +
412A MET* 3.2 17.9 - - - +
413A VAL* 4.5 7.9 - - + -
440A ILE 5.6 0.2 - - - +
443A ALA* 3.8 31.4 - - + +
444A LEU* 4.2 5.2 - - + +
447A VAL* 4.1 9.0 - - + -
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Residues in contact with GLY 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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322A ILE* 4.3 5.8 - - - -
326A LEU* 4.2 5.6 - - - -
336A ALA 3.3 11.2 - - - -
337A SER* 4.0 4.3 - - - -
354A ALA* 1.3 77.6 - - - +
356A VAL* 1.3 61.5 + - - +
411A VAL* 3.4 5.7 - - - +
412A MET* 2.7 42.2 + - - +
447A VAL* 4.4 5.8 - - - +
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Residues in contact with VAL 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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326A LEU* 3.8 4.0 - - - +
334A PHE* 4.4 11.0 - - + -
335A ALA* 3.1 5.9 - - - +
336A ALA* 2.9 47.8 + - + +
355A GLY* 1.3 75.9 - - - +
357A ALA* 1.3 67.7 + - - +
358A PHE 4.9 0.2 - - - +
397A TRP* 5.2 3.1 - - + -
409A MET* 3.8 27.8 - - + -
410A VAL 3.3 11.7 - - - +
411A VAL* 4.2 6.7 - - + -
447A VAL* 4.0 32.3 - - + +
451A LEU* 4.4 14.8 - - + -
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Residues in contact with ALA 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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326A LEU* 4.2 20.4 - - + +
330A PHE* 4.9 2.9 - - + -
332A PRO* 3.9 13.7 - - + -
334A PHE 3.2 8.7 - - - +
335A ALA* 4.3 0.4 - - + -
356A VAL* 1.3 76.7 - - - +
358A PHE* 1.3 60.5 + - - +
362A ILE* 3.7 18.5 - - + +
409A MET* 3.3 5.5 - - - +
410A VAL* 2.8 42.5 + - + +
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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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332A PRO* 3.8 1.1 - - - +
333A ASP* 2.9 27.0 + - + +
334A PHE* 2.8 22.8 + - + +
356A VAL* 5.1 0.9 - - + -
357A ALA* 1.3 76.2 - - - +
359A GLY* 1.3 69.0 + - - +
402A ILE* 4.4 20.9 - - + -
407A TYR* 4.4 14.8 - - + -
408A GLN* 3.5 21.8 - - - -
409A MET* 4.3 9.9 - - + -
451A LEU* 3.7 30.3 - - + -
454A TYR* 4.2 10.8 - + - -
455A LEU* 3.7 30.5 - - + -
458A LYS* 3.8 14.6 - - - -
459A ARG* 6.0 1.1 - - - -
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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