Contacts of the strand formed by residues 389 - 397 (chain A) in PDB entry 5VLR
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 ARG 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A LEU* 3.7 3.6 - - - -
348A PHE* 2.9 55.4 + - + +
349A HIS 4.7 0.2 - - - +
350A GLY* 4.7 11.1 - - - +
387A MET 4.1 5.8 + - - +
388A ALA* 1.3 74.3 - - - +
390A LEU* 1.3 61.0 + - - +
391A CYS* 3.7 13.9 + - - -
422A ASN* 3.9 5.0 - - + +
423A LEU 3.2 12.1 - - - +
424A MET* 4.1 16.4 - - - -
425A LEU* 4.7 2.5 - - - -
455A PRO 2.8 35.1 + - - -
456A THR 4.4 1.0 + - - -
457A GLY 2.8 24.0 + - - -
458A THR* 5.6 0.2 - - - +
459A VAL* 3.4 34.8 - - + +
588A PRO* 6.2 1.8 - - - +
621A TYR 4.8 9.5 + - - -
622A GLU 4.8 1.6 + - - -
623A SER* 4.7 9.1 - - - +
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Residues in contact with LEU 390 (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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323A PHE* 3.7 34.8 - - + -
325A ILE* 3.7 23.1 - - + -
345A ALA* 4.2 8.3 - - + -
346A GLY 3.7 12.1 - - - +
347A LEU* 4.7 6.1 - - + +
377A PHE* 4.5 7.2 - - + -
389A ARG* 1.3 70.1 - - - +
391A CYS* 1.3 66.9 + - - +
392A PHE* 3.5 37.3 - - + -
421A ALA 4.1 0.9 - - - +
422A ASN* 3.3 1.7 - - - -
423A LEU* 2.7 56.2 + - + +
425A LEU* 4.3 11.3 - - + +
475A LEU* 5.4 0.7 - - + -
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Residues in contact with CYS 391 (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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345A ALA* 3.3 5.5 - - - -
346A GLY 3.0 35.4 + - - +
348A PHE* 3.5 31.0 - - + -
389A ARG* 3.8 15.0 - - - -
390A LEU* 1.3 79.6 - - - +
392A PHE* 1.3 60.1 + - - +
422A ASN* 3.2 26.0 - - - +
453A LEU* 3.4 18.1 - - + +
454A ASN 5.1 0.2 - - - +
455A PRO* 3.8 17.5 - - + -
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Residues in contact with PHE 392 (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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325A ILE* 4.6 9.6 - - + -
327A LEU* 5.8 5.2 - - + -
343A VAL* 5.7 8.3 - - + -
344A GLN 3.5 4.7 - - - -
345A ALA* 3.9 20.2 - - + -
375A LEU* 5.4 3.1 - - + -
390A LEU* 3.5 45.1 - - + -
391A CYS* 1.3 73.8 - - - +
393A ALA* 1.3 61.4 + - - +
420A TRP* 3.1 7.6 - - - +
421A ALA* 2.8 47.1 + - + +
422A ASN* 4.7 0.9 - - - +
423A LEU* 4.8 3.1 - - + -
439A LEU* 3.5 33.7 - - + -
441A MET* 5.6 5.8 - - - -
453A LEU* 3.7 3.4 - - - +
454A ASN 5.6 0.9 + - - -
471A LEU* 5.8 11.4 - - + -
473A ILE* 3.7 31.4 - - + -
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Residues in contact with ALA 393 (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 VAL 4.0 0.2 - - - +
343A VAL* 3.4 4.5 - - - +
344A GLN* 2.9 34.7 + - + +
392A PHE* 1.3 75.3 - - - +
394A LEU* 1.3 59.9 + - - +
395A TYR* 3.8 14.7 + - + -
417A PRO* 6.5 0.2 - - + -
419A ALA 3.3 9.9 - - - +
420A TRP* 4.7 4.7 - - + -
441A MET* 5.8 0.7 - - - -
444A SER* 5.3 3.1 - - - +
452A LEU 3.3 26.7 - - - +
453A LEU* 3.8 11.4 - - + -
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Residues in contact with LEU 394 (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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333A VAL* 5.1 11.7 - - + -
341A LEU* 4.9 12.6 - - + -
342A VAL 3.5 9.4 - - - +
343A VAL* 4.5 5.2 - - + +
371A TRP* 5.1 11.0 - - + -
393A ALA* 1.3 72.4 - - - +
395A TYR* 1.3 60.4 + - - +
417A PRO* 3.9 0.9 - - - +
418A ILE* 2.8 50.7 + - + +
419A ALA 2.8 13.5 + - - +
441A MET* 4.3 25.3 - - + -
444A SER* 5.1 0.2 + - - -
471A LEU* 5.8 2.0 - - + -
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Residues in contact with TYR 395 (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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341A LEU* 3.4 5.9 - - - +
342A VAL* 2.8 40.4 + - + +
344A GLN* 4.6 11.2 - - + -
393A ALA* 3.8 17.5 - - + -
394A LEU* 1.3 79.1 - - - +
396A ALA* 1.3 57.1 + - - +
397A VAL* 3.7 15.6 + - + -
415A ASP* 3.7 27.4 - - + -
416A CYS 3.1 22.2 - - - -
417A PRO* 3.6 25.0 - - + +
418A ILE* 3.9 4.5 - - - -
450A GLY 4.2 3.6 + - - -
451A GLU 3.3 8.3 + - - -
452A LEU* 3.1 47.3 + - + -
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Residues in contact with ALA 396 (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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335A ALA* 4.3 17.0 - - + -
336A ASP* 5.6 1.1 - - + +
339A MET* 3.7 23.2 - - + +
340A LYS 3.5 6.5 - - - -
341A LEU* 4.7 3.6 - - + +
395A TYR* 1.3 69.7 - - - +
397A VAL* 1.3 61.0 + - - +
398A ILE* 4.1 3.8 + - - +
415A ASP* 4.4 0.9 - - - -
416A CYS* 2.9 46.6 + - + +
418A ILE* 3.7 12.5 - - + +
564B ASN 5.5 0.9 - - - +
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Residues in contact with VAL 397 (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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339A MET* 3.4 2.6 - - - +
340A LYS* 2.8 39.9 + - + +
342A VAL* 3.8 27.6 - - + -
362A GLU* 3.7 21.5 - - + +
395A TYR* 4.1 11.9 - - + -
396A ALA* 1.3 72.8 - - - +
398A ILE* 1.3 75.2 + - - +
399A GLU 3.3 1.6 + - - -
400A LYS* 5.6 0.9 - - + +
415A ASP* 3.4 28.7 - - - +
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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