Contacts of the strand formed by residues 381 - 386 (chain A) in PDB entry 4MSL
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 TYR 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ALA* 4.6 1.8 - - + -
324A ASN* 4.7 0.5 + - - -
329A PHE* 3.8 30.8 - + - -
371A PHE* 3.7 22.7 - + + -
372A THR 3.2 6.5 - - - +
373A ASN* 3.4 40.5 + - + -
374A VAL* 4.2 0.4 - - - -
379A GLY* 3.3 30.1 + - - -
380A VAL* 1.3 77.2 - - - +
382A ILE* 1.3 64.9 + - - +
396A ILE* 3.3 3.6 - - - +
397A THR* 2.8 45.2 + - + +
400A GLN* 4.1 12.8 + - + -
404A TRP* 3.6 10.3 - - + -
1B NAG 2.7 36.0 + - + +
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Residues in contact with ILE 382 (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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370A ASP* 3.7 3.7 - - + +
371A PHE* 3.7 1.7 - - - -
372A THR* 2.9 56.3 + - + +
374A VAL* 3.9 15.0 - - + +
381A TYR* 1.3 79.5 - - - +
383A THR* 1.3 64.4 + - - +
394A THR* 4.3 5.6 - - + -
395A MET 3.2 8.3 - - - +
396A ILE* 3.8 27.4 - - + -
404A TRP* 4.2 1.3 - - - -
407A LEU* 4.7 7.6 - - + -
429A ILE* 3.7 40.8 - - + -
445A PRO* 4.4 9.4 - - + -
455A VAL* 6.3 2.5 - - + -
482A TRP* 5.7 5.2 - - + -
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Residues in contact with THR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 4.4 2.0 - - + -
357A LEU* 3.5 31.6 - - + -
360A HIS* 2.5 33.5 + - + +
369A THR* 4.2 0.2 + - - -
370A ASP* 3.8 9.1 + - - -
371A PHE* 3.4 18.2 + - - -
382A ILE* 1.3 78.3 - - - +
384A SER* 1.3 66.9 + - - +
385A VAL* 4.9 0.4 - - + -
394A THR* 3.1 9.0 - - - +
395A MET* 2.8 35.6 + - + -
404A TRP* 3.6 16.2 - - + -
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Residues in contact with SER 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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360A HIS* 3.2 13.0 - - - -
361A LEU* 3.1 32.0 + - - -
370A ASP* 2.5 37.9 + - - +
383A THR* 1.3 81.3 + - - +
385A VAL* 1.3 62.5 + - - +
392A ILE* 3.7 21.9 - - - +
393A GLN 3.4 4.0 - - - -
394A THR* 4.4 4.3 + - - -
429A ILE 4.7 0.5 + - - -
465A ILE* 4.0 7.1 - - - +
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.7 26.9 - - + -
358A ASP 3.7 19.5 - - - +
359A ARG* 3.2 7.6 - - + +
360A HIS* 4.5 0.7 - - - -
361A LEU* 4.3 2.7 - - - +
383A THR* 4.9 0.2 - - + -
384A SER* 1.3 80.1 - - - +
386A LEU* 1.3 65.1 + - - +
387A SER* 3.8 0.4 + - - -
392A ILE* 3.4 8.2 - - - +
393A GLN* 2.8 58.6 + - + +
395A MET* 3.8 24.2 - - + -
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Residues in contact with LEU 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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338A THR 4.5 8.5 - - - +
339A GLY 5.2 2.5 - - - +
340A PHE* 3.8 34.5 - - + -
359A ARG* 2.7 49.6 + - + +
361A LEU* 4.7 13.9 - - + +
385A VAL* 1.3 76.3 - - - +
387A SER* 1.3 66.1 + - - +
390A ASN* 3.7 35.4 - - - +
391A SER 3.3 19.1 - - - +
392A ILE* 4.4 9.4 - - + -
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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