Contacts of the strand formed by residues 381 - 389 (chain A) in PDB entry 3N9V
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 GLY 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A LEU* 4.9 0.2 - - - -
347A ILE* 3.5 10.7 - - - +
369A VAL 3.3 10.5 - - - -
370A GLY* 4.4 0.2 - - - -
371A THR* 3.2 18.3 + - - -
380A LYS* 1.3 74.8 - - - +
382A GLY* 1.3 58.1 + - - -
399A SER* 3.3 3.1 - - - -
400A HIS 2.8 36.2 + - - +
418A ILE* 3.8 7.7 - - - +
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Residues in contact with GLY 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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344A LEU* 4.1 2.0 - - - +
347A ILE* 4.3 2.4 - - - +
368A THR* 3.8 0.3 - - - -
369A VAL 2.8 32.6 + - - +
381A GLY* 1.3 74.4 - - - -
383A VAL* 1.3 69.0 + - - +
397A VAL* 5.1 0.4 - - - -
398A ASN 3.4 9.2 - - - -
399A SER* 4.0 1.1 - - - -
418A ILE* 3.9 19.7 - - - +
422A MET* 3.9 7.2 - - - -
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Residues in contact with VAL 383 (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 ILE* 4.0 11.4 - - + -
343A ARG 4.3 1.3 - - - -
344A LEU* 3.7 19.7 - - + +
347A ILE* 3.7 28.9 - - + +
349A LEU* 3.9 26.4 - - + +
367A GLU 3.4 8.7 - - - +
368A THR* 3.5 20.6 - - + -
382A GLY* 1.3 79.9 - - - +
384A ALA* 1.3 63.6 + - - +
397A VAL* 3.4 3.1 - - - +
398A ASN* 2.8 40.9 + - + +
422A MET* 3.9 2.2 - - - -
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Residues in contact with ALA 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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342A ILE* 4.1 1.7 - - - +
349A LEU* 4.5 0.7 - - - -
366A ALA* 3.1 7.4 - - - +
367A GLU 2.9 30.8 + - - +
383A VAL* 1.3 77.0 - - - +
385A ILE* 1.3 63.8 + - - +
395A CYS* 4.3 1.3 - - - -
396A VAL 3.3 11.9 - - - +
397A VAL* 4.3 14.4 - - + -
422A MET* 3.8 16.8 - - + -
424A PHE* 3.7 25.3 - - + -
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Residues in contact with ILE 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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340A LYS* 3.7 45.8 - - + +
342A ILE* 3.7 12.8 - - + -
349A LEU* 3.8 30.9 - - + +
351A LEU* 3.8 38.4 - - + +
364A VAL* 4.2 3.8 - - + -
365A GLU 3.4 8.5 - - - +
366A ALA* 4.2 0.9 - - + -
384A ALA* 1.3 77.3 - - - +
386A ARG* 1.3 68.2 + - - +
387A PHE* 4.3 3.4 - - + -
394A ILE 4.2 0.2 - - - +
395A CYS* 3.6 2.1 - - - -
396A VAL* 3.0 36.2 + - + +
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Residues in contact with ARG 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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363A GLU* 2.8 56.1 + - - +
364A VAL* 3.3 0.7 - - - -
365A GLU* 2.9 45.9 + - - +
385A ILE* 1.3 76.6 - - - +
387A PHE* 1.3 78.7 + - - +
388A GLN* 4.0 2.0 - - - +
393A SER* 3.9 16.4 - - - -
394A ILE 3.1 13.0 - - - +
395A CYS* 3.9 10.5 - - + -
424A PHE* 3.6 31.3 - - + -
434A LEU* 3.7 24.7 - - - +
438A ASN 5.1 0.6 + - - -
439A HIS* 3.0 36.0 + - + +
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Residues in contact with PHE 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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267A PHE* 4.4 10.3 - + - -
296A VAL* 4.6 2.9 - - + -
351A LEU* 3.6 41.1 - - + -
361A ILE* 3.5 33.2 - - + -
362A SER 3.7 6.7 - - - +
363A GLU 3.6 8.3 - - - -
364A VAL* 3.9 16.8 - - + -
385A ILE* 4.3 3.6 - - + -
386A ARG* 1.3 91.7 - - - +
388A GLN* 1.3 65.1 + - - +
389A PHE* 4.0 3.4 - + + -
393A SER* 3.6 2.1 - - - -
394A ILE* 2.8 78.4 + - + +
396A VAL* 4.4 11.4 - - + -
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Residues in contact with GLN 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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360A TYR 3.6 0.6 - - - +
361A ILE* 3.3 5.7 - - - -
362A SER* 2.7 53.9 + - - +
363A GLU* 3.8 29.9 - - - +
386A ARG* 4.0 3.5 - - - +
387A PHE* 1.3 78.0 - - - +
389A PHE* 1.3 59.4 + - - +
390A HIS 3.5 8.4 + - - +
391A ASN* 3.4 36.8 + - - +
392A THR 3.4 12.1 - - - +
393A SER* 4.3 9.8 - - - +
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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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65A GOL 4.1 0.7 - - - -
265A PHE* 3.6 50.7 - + + -
267A PHE* 4.3 11.9 - + - -
296A VAL* 4.3 13.9 - - + -
357A HIS* 3.9 32.1 - + + -
360A TYR* 3.5 8.7 - - + -
361A ILE* 3.8 15.0 - - + -
387A PHE* 4.0 8.0 + + + -
388A GLN* 1.3 71.7 - - - +
390A HIS* 1.3 88.5 + + - +
392A THR 2.8 21.7 + - - +
394A ILE* 4.0 16.6 - - + -
560A VAL* 3.2 26.5 - - + +
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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