Contacts of the strand formed by residues 383 - 389 (chain A) in PDB entry 3MOS
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 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ILE* 4.3 9.0 - - + -
334A ARG* 2.9 45.0 + - + +
335A ILE* 3.5 25.7 - - + -
336A ILE* 3.1 19.6 + - - +
382A THR* 1.3 75.3 - - - +
384A PRO* 1.4 63.2 - - - +
385A PHE* 3.9 6.9 - - + -
409A ASN 5.4 1.3 - - - +
411A ASN* 3.9 19.7 - - - +
462A ALA* 4.1 17.5 - - + +
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Residues in contact with PRO 384 (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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336A ILE* 3.5 11.2 - - + +
338A LEU* 3.8 18.8 - - + -
373A ALA* 3.5 34.3 - - + +
376A CYS* 4.2 2.5 - - + -
377A ALA* 3.8 12.8 - - + +
382A THR* 3.4 22.9 - - - +
383A VAL* 1.4 86.0 - - + +
385A PHE* 1.3 62.2 + - - +
386A CYS 4.1 0.4 - - - -
409A ASN 4.0 9.9 - - - +
410A ILE* 4.2 4.0 - - + -
411A ASN* 3.1 30.4 + - - +
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Residues in contact with PHE 385 (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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321A TYR* 3.5 26.5 + + - +
325A LEU* 3.8 24.0 - - + -
328A LEU* 4.6 0.9 - - + -
335A ILE* 4.2 10.5 - - + -
336A ILE 2.8 13.6 + - - +
337A ALA* 3.2 5.0 - - - +
338A LEU* 3.0 25.4 + - - +
383A VAL* 3.9 19.7 - - + -
384A PRO* 1.3 79.1 - - - +
386A CYS* 1.3 59.4 + - - +
387A SER* 5.0 0.3 + - - -
411A ASN* 3.3 39.5 - - + -
412A LEU 6.0 0.2 - - - -
413A CYS* 5.6 1.3 - - + -
458A VAL* 3.6 39.5 - - + -
461A ALA* 4.3 7.2 - - + -
462A ALA* 3.9 13.9 - - + -
470A ILE* 4.4 9.9 - - + -
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Residues in contact with CYS 386 (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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321A TYR* 4.2 1.2 + - - -
338A LEU* 3.2 13.0 - - - -
369A MET* 3.9 33.9 - - + -
370A VAL* 4.6 4.5 - - - -
373A ALA* 3.2 34.8 - - - -
385A PHE* 1.3 73.1 - - - +
387A SER* 1.3 62.8 + - - +
393A PHE* 3.9 10.7 - - + -
410A ILE* 5.4 1.1 - - - -
411A ASN 2.8 14.1 + - - +
412A LEU* 3.4 8.1 - - + -
413A CYS* 2.8 27.9 + - - +
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Residues in contact with SER 387 (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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321A TYR* 4.2 17.4 + - - -
337A ALA* 6.1 0.2 - - - +
338A LEU 2.9 9.7 + - - -
339A ASP* 2.7 48.9 + - - -
340A GLY 3.4 2.3 + - - -
346A THR* 4.1 12.3 - - - -
348A SER* 3.5 13.3 - - - -
369A MET* 3.4 4.2 - - - +
385A PHE 5.0 0.5 + - - -
386A CYS* 1.3 76.0 - - - +
388A THR* 1.3 68.6 + - - +
393A PHE* 4.1 0.9 - - - -
413A CYS* 3.2 14.6 - - - -
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Residues in contact with THR 388 (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 GLY* 4.8 4.8 + - - -
342A THR* 3.3 23.2 + - - +
346A THR* 3.7 9.2 - - - +
366A GLU* 4.2 20.0 + - + +
369A MET* 3.9 9.4 - - + -
387A SER* 1.3 75.4 - - - +
389A PHE* 1.3 78.6 + - - +
392A PHE* 3.9 16.6 - - - +
393A PHE* 3.7 35.2 - - + +
413A CYS 3.4 2.6 + - - +
414A GLY* 3.3 4.9 - - - -
415A SER* 3.0 21.0 + - - -
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Residues in contact with PHE 389 (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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342A THR* 4.0 25.4 - - + -
345A SER* 3.7 28.7 - - - -
388A THR* 1.3 83.9 + - - +
390A ALA* 1.3 66.0 + - - +
391A ALA* 4.1 7.4 - - + +
392A PHE* 2.9 35.1 + + + +
393A PHE 3.5 5.4 + - - -
415A SER* 3.6 14.6 - - - +
416A HIS* 3.5 42.2 - + + -
424A ASP* 4.6 7.0 - - - -
428A GLN* 3.7 37.5 - - + -
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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