Contacts of the strand formed by residues 437 - 447 (chain B) in PDB entry 3VOQ
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 LEU 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404B ILE* 5.9 0.2 - - + -
409B VAL* 3.7 32.5 - - + -
432B ILE* 3.9 19.7 - - + -
433B ASP 4.2 0.7 - - - +
434B SER* 3.1 32.6 + - - +
435B ASP 4.3 0.7 - - - +
436B LEU* 1.4 82.0 - - - +
438B CYS* 1.3 61.7 + - - +
439B ALA 5.1 0.7 - - - +
455B LEU* 4.2 21.8 - - + -
456B THR 4.0 0.9 - - - -
457B TYR* 4.0 9.4 - - + -
482B VAL* 4.5 18.2 - - + -
485B ILE* 5.1 10.8 - - + -
486B LEU* 3.9 11.8 - - + +
489B ARG* 2.9 28.6 + - - +
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Residues in contact with CYS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B LEU 3.7 11.0 - - - -
437B LEU* 1.3 80.0 - - - +
439B ALA* 1.3 61.7 + - + +
456B THR* 2.8 26.4 + - + +
457B TYR* 4.0 6.7 - - - -
458B LEU* 4.0 11.2 - - - -
463B TYR* 3.8 31.4 - - + -
486B LEU* 3.9 13.6 - - - +
489B ARG* 5.1 1.2 + - - +
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LEU* 5.1 0.8 - - - +
438B CYS* 1.3 82.8 - - + +
440B CYS* 1.3 63.9 + - - +
441B ASP* 4.0 14.8 - - - +
454B LYS 4.5 0.7 - - - -
455B LEU* 3.6 5.7 - - - +
456B THR* 2.9 39.9 + - + +
482B VAL* 5.0 0.4 - - - -
483B ASN* 5.4 0.4 - - - -
486B LEU* 3.8 12.2 - - - +
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Residues in contact with CYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B ALA* 1.3 79.5 - - - +
441B ASP* 1.3 68.1 + - - +
453B PHE* 3.7 33.7 - - - -
454B LYS 3.3 6.5 - - - -
455B LEU* 4.0 6.1 - - + -
479B VAL* 3.7 23.8 - - - +
482B VAL* 3.4 35.9 - - + -
483B ASN* 2.8 31.8 + - - +
486B LEU* 4.2 3.8 - - - +
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Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A PHE* 3.0 29.2 - - - +
424A TRP 5.0 0.6 - - - -
425A ILE* 3.6 31.7 - - + +
439B ALA* 4.0 16.6 - - - +
440B CYS* 1.3 82.4 - - - +
442B LEU* 1.3 59.6 + - - +
443B ALA 3.7 0.2 + - - -
453B PHE* 3.2 6.7 - - - +
454B LYS* 2.8 38.0 + - + +
479B VAL* 4.3 2.5 - - - -
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A THR* 4.2 21.5 - - + +
423A PHE* 2.8 15.7 + - + +
424A TRP* 3.5 25.8 - - + -
425A ILE* 2.9 26.5 + - - +
441B ASP* 1.3 71.2 - - - +
443B ALA* 1.3 60.5 + - - +
444B GLU 4.0 13.9 - - - +
445B GLU* 4.5 20.4 - - + +
451B ALA* 4.1 7.6 - - + -
452B ILE 3.5 17.3 - - - +
453B PHE* 4.2 2.5 - - - -
475B VAL* 3.7 23.8 - - + -
476B ASN* 6.2 2.0 - - - +
479B VAL* 4.3 11.2 - - + +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PHE* 3.7 35.0 - - + -
398A THR* 4.6 4.3 - - - +
424A TRP* 3.8 14.4 + - - -
425A ILE* 4.0 25.0 - - + +
427A GLN* 4.6 5.2 + - - -
441B ASP 3.7 0.6 + - - -
442B LEU* 1.3 75.9 - - - +
444B GLU* 1.3 65.0 + - - +
452B ILE* 2.8 22.2 + - + +
453B PHE* 4.5 6.5 - - - -
454B LYS* 4.8 2.7 - - + +
467B TYR* 5.4 0.4 - - + -
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PHE* 4.1 6.1 - - + -
397A THR 3.3 22.5 - - - +
398A THR* 3.3 28.4 - - + +
399A ASP* 4.9 4.4 + - - +
424A TRP* 4.5 10.9 + - - +
442B LEU* 3.7 3.7 - - - +
443B ALA* 1.3 79.7 - - - +
445B GLU* 1.3 69.1 + - - +
446B LYS* 3.3 32.3 + - + +
451B ALA* 3.2 3.3 - - - +
452B ILE* 2.8 49.2 + - + +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TRP* 4.7 4.2 - - - +
442B LEU* 4.5 22.1 - - + +
444B GLU* 1.3 82.4 + - - +
446B LYS* 1.3 62.7 + - - +
447B SER* 4.0 17.2 - - - +
448B PRO* 4.4 4.0 - - - +
450B HIS 3.9 0.9 - - - -
451B ALA* 3.7 19.2 - - + +
472B ALA* 3.8 20.8 - - + +
476B ASN* 6.1 0.9 - - - +
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Residues in contact with LYS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A THR* 3.0 45.0 + - - +
398A THR* 5.2 0.7 - - - +
399A ASP* 6.0 3.6 - - - -
444B GLU* 3.3 19.5 + - + +
445B GLU* 1.3 74.0 - - - +
447B SER* 1.3 62.2 + - - +
450B HIS* 2.8 46.8 + - + +
452B ILE* 3.7 23.2 - - + +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLU* 4.0 8.2 - - - +
446B LYS* 1.3 80.2 - - - +
448B PRO* 1.3 76.5 - - - +
449B SER* 3.2 21.9 + - - -
450B HIS* 3.0 26.2 + - - +
472B ALA* 3.7 7.1 - - - +
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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