Contacts of the strand formed by residues 409 - 417 (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 MET 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A VAL* 3.8 18.8 - - + -
357A ALA 3.3 10.3 - - - +
358A PHE* 4.3 5.6 - - + -
362A ILE* 4.0 4.0 - - - +
363A PRO 4.5 0.6 + - - -
367A GLU 5.7 0.2 + - - -
368A PRO* 3.4 16.2 - - + +
369A ILE* 2.9 28.6 + - - +
397A TRP* 3.7 44.6 - - + -
402A ILE* 4.1 6.7 - - + -
407A TYR* 3.5 37.0 + - + -
408A GLN* 1.3 76.7 - - - +
410A VAL* 1.3 73.9 + - - +
411A VAL* 4.0 3.8 - - + -
451A LEU* 4.0 14.1 - - - -
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Residues in contact with VAL 410 (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* 4.3 10.1 - - + -
330A PHE* 3.8 33.2 - - + -
356A VAL* 3.3 7.8 - - - +
357A ALA* 2.8 39.5 + - + +
362A ILE* 3.8 16.6 - - + +
369A ILE* 3.4 24.9 - - + +
371A LEU* 3.5 32.1 - - + -
409A MET* 1.3 77.7 - - - +
411A VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 411 (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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355A GLY 3.4 6.7 - - - +
356A VAL* 4.2 6.5 - - + -
368A PRO* 4.4 7.4 - - + -
369A ILE 2.7 14.2 + - - +
370A VAL* 3.4 4.9 - - + +
371A LEU* 2.8 26.2 + - - +
392A VAL* 4.0 17.5 - - + -
397A TRP* 3.9 27.1 - - + -
409A MET* 4.0 18.8 - - + -
410A VAL* 1.3 80.5 - - - +
412A MET* 1.3 71.1 + - - +
413A VAL* 4.5 2.5 - - + -
444A LEU* 3.5 27.4 - - + -
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Residues in contact with MET 412 (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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196A ILE* 6.4 0.9 - - + -
197A ILE* 4.0 13.5 - - + -
317A ILE* 3.9 18.6 - - + -
322A ILE* 3.7 38.6 - - + -
326A LEU* 4.8 12.3 - - + -
353A GLU 4.4 0.4 - - - +
354A ALA* 3.2 11.7 - - - +
355A GLY 2.7 48.1 + - - +
371A LEU* 3.3 17.9 - - + +
373A TYR* 3.9 19.1 - - + -
411A VAL* 1.3 76.8 - - - +
413A VAL* 1.3 75.0 + - - +
414A HIS* 4.1 9.6 - - + -
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Residues in contact with VAL 413 (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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352A VAL* 4.2 12.8 - - + -
353A GLU 3.5 8.5 - - - +
354A ALA* 4.5 4.3 - - + -
370A VAL* 5.9 0.2 - - + -
371A LEU 3.0 8.2 + - - +
372A ARG* 3.6 1.4 - - - -
373A TYR* 2.9 25.5 + - - +
388A ILE* 3.7 45.9 - - + +
411A VAL* 4.5 4.7 - - + -
412A MET* 1.3 84.7 - - - +
414A HIS* 1.3 66.7 + - - +
415A LEU 4.8 0.7 - - - +
440A ILE* 4.2 15.7 - - + -
444A LEU* 3.8 28.7 - - + -
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Residues in contact with HIS 414 (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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315A SER 4.1 3.8 - - - -
317A ILE* 3.5 20.3 - - + +
351A ILE 3.7 1.4 - - - +
352A VAL* 3.3 5.9 - - - +
353A GLU* 2.7 68.1 + - + +
373A TYR* 3.4 22.4 - - + -
375A ASN* 3.5 6.9 + - - -
376A LYS* 2.9 47.9 + - + -
412A MET* 4.1 7.4 - - + -
413A VAL* 1.3 77.4 - - - +
415A LEU* 1.3 63.8 + - - +
416A CYS* 3.6 25.7 - - + +
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Residues in contact with LEU 415 (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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350A PHE* 3.8 36.6 - - + -
351A ILE 3.7 5.6 - - - +
352A VAL* 4.0 11.0 - - + +
373A TYR 2.9 11.3 + - - +
374A ALA* 3.2 4.3 - - - -
375A ASN 2.8 23.1 + - - -
388A ILE* 5.4 3.6 - - + +
413A VAL* 4.2 1.9 - - + +
414A HIS* 1.3 74.4 - - - +
416A CYS* 1.3 63.1 + - - +
417A SER* 5.1 1.1 - - - -
420A ILE* 3.7 22.3 - - + +
421A PRO* 4.3 9.6 - - + -
430A ILE* 4.1 31.4 - - + -
436A ILE* 3.9 25.4 - - + -
440A ILE* 5.4 4.7 - - + -
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Residues in contact with CYS 416 (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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103A GLN* 3.3 24.2 - - - +
314A LEU* 3.8 8.1 - - - +
315A SER 3.8 12.1 - - - -
316A VAL* 4.2 9.6 - - - -
350A PHE* 3.2 3.8 - - - +
351A ILE* 3.0 57.0 + - - -
353A GLU* 5.7 0.2 - - - -
375A ASN* 3.0 7.4 - - - +
414A HIS* 3.6 22.0 - - + +
415A LEU* 1.3 75.2 - - - +
417A SER* 1.3 66.1 + - - +
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Residues in contact with SER 417 (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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103A GLN* 4.5 3.4 - - - +
314A LEU* 3.7 11.5 - - - +
345A TYR* 4.3 3.5 - - - -
348A HIS* 4.0 5.9 - - - +
349A PRO 2.7 24.4 + - - -
350A PHE* 3.7 10.6 - - - +
375A ASN* 2.8 29.1 + - - +
415A LEU* 5.1 2.0 - - - -
416A CYS* 1.3 76.9 - - - +
418A THR* 1.3 65.4 + - - +
419A LYS* 3.1 23.3 + - - -
420A ILE* 3.8 14.4 - - - +
421A PRO* 5.9 0.2 - - - -
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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