Contacts of the helix formed by residues 441 - 454 (chain B) in PDB entry 2VGL
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 GLU 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ARG* 2.8 47.2 + - - -
404B ASN* 4.8 1.1 - - - +
405B TYR* 4.6 2.1 - - - -
408B GLN* 2.9 40.1 + - - +
409B GLU* 4.3 1.8 - - - +
439B LEU 3.4 1.2 - - - +
440B ASP* 1.3 81.5 + - - +
442B PRO* 1.3 72.3 - - + +
443B ASP* 3.5 5.5 + - + +
444B ALA* 3.8 2.9 + - + +
445B ARG* 3.0 24.4 + - - +
314M SER* 4.6 12.7 - - - +
316M LEU* 5.5 1.6 - - - -
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Residues in contact with PRO 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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440B ASP 3.6 2.2 - - - +
441B GLU* 1.3 86.7 - - + +
443B ASP* 1.3 73.2 + - + +
445B ARG* 3.4 12.6 + - + +
446B ALA* 3.3 21.7 + - - +
477B SER* 3.5 34.3 - - - +
480B VAL* 4.1 6.1 - - + +
313M PRO 5.8 0.9 - - - +
314M SER* 4.2 23.6 - - - +
316M LEU* 5.3 11.7 - - + -
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Residues in contact with ASP 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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375B ARG* 5.8 1.7 + - - -
412B VAL* 3.8 19.9 - - + +
415B ARG* 4.7 3.0 + - - +
441B GLU* 3.5 2.9 - - + -
442B PRO* 1.3 79.5 - - + +
444B ALA* 1.3 68.5 + - - +
445B ARG 3.1 2.0 + - - -
446B ALA* 3.3 7.0 + - - +
447B ALA* 2.9 23.0 + - - +
479B GLN* 5.9 4.2 + - - +
314M SER* 6.0 2.8 - - - -
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Residues in contact with ALA 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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408B GLN* 3.2 46.0 - - + +
411B ILE* 3.5 25.3 - - + +
412B VAL* 3.9 3.7 - - - +
439B LEU* 3.6 14.8 - - + +
441B GLU* 3.8 4.9 + - + +
443B ASP* 1.3 78.6 - - - +
445B ARG* 1.3 62.5 + - - +
447B ALA* 3.2 4.7 - - - +
448B MET 3.1 17.3 + - - -
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Residues in contact with ARG 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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436B LEU 5.9 1.4 + - - -
439B LEU* 3.3 30.9 + - + +
440B ASP* 4.4 6.5 + - - -
441B GLU 3.0 18.8 - - - +
442B PRO* 3.6 10.8 - - - +
443B ASP 3.1 0.6 - - - -
444B ALA* 1.3 75.4 - - - +
446B ALA* 1.3 60.8 + - - +
448B MET* 2.9 7.6 + - - +
449B ILE* 2.8 36.7 + - + +
469B PHE* 4.6 33.1 - - + +
476B GLU* 2.7 41.9 + - - -
480B VAL* 3.8 11.0 - - + -
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Residues in contact with ALA 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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415B ARG* 3.9 10.6 + - - +
442B PRO 3.3 12.8 + - - +
443B ASP* 3.3 6.6 + - - +
445B ARG* 1.3 78.9 - - - +
447B ALA* 1.3 59.6 + - - +
449B ILE* 4.0 1.3 - - - -
450B TRP* 3.3 21.7 + - - +
479B GLN* 4.2 10.8 - - + +
480B VAL* 4.0 8.4 - - + +
483B THR* 3.4 37.2 + - + +
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Residues in contact with ALA 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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411B ILE* 3.7 21.3 - - + +
412B VAL* 4.0 18.8 - - + -
415B ARG* 3.8 20.0 - - + +
443B ASP 2.9 12.9 + - - +
444B ALA 3.2 11.4 - - - +
446B ALA* 1.3 75.9 - - - +
448B MET* 1.3 63.8 + - - +
450B TRP* 4.0 3.5 - - - +
451B ILE* 3.1 29.4 + - - +
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Residues in contact with MET 448 (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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411B ILE* 2.6 41.2 - - + +
432B LEU* 3.8 43.5 - - + +
433B CYS* 4.6 11.4 - - - -
435B ASN 5.1 1.1 - - - +
436B LEU* 4.8 18.8 - - + -
439B LEU* 3.4 28.3 - - + -
444B ALA 3.1 5.4 + - - +
445B ARG* 2.9 9.2 + - - +
447B ALA* 1.3 72.6 - - - +
449B ILE* 1.3 55.8 + - + +
451B ILE* 2.6 51.5 + - + +
452B VAL* 2.7 24.2 + - + +
469B PHE* 5.2 5.2 - - + -
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Residues in contact with ILE 449 (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 ARG* 2.8 21.1 + - + +
448B MET* 1.3 72.7 - - - +
450B TRP* 1.3 56.5 + - - +
452B VAL* 3.2 10.8 + - - +
453B GLY* 2.7 24.4 + - - -
466B LEU* 5.2 8.6 - - + +
469B PHE* 3.6 38.1 - - + -
476B GLU* 5.9 0.2 - - - +
480B VAL* 4.1 31.6 - - + +
483B THR* 3.2 36.8 - - + +
484B LEU* 3.7 19.3 - - + -
487B ALA* 3.6 8.9 - - + +
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Residues in contact with TRP 450 (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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574A VAL* 4.2 23.4 - - + +
577A GLN* 5.4 5.3 + - - -
578A GLN* 5.7 3.7 + - - -
415B ARG* 3.5 33.4 - - + +
418B PHE* 4.0 22.4 - + + -
419B ARG* 3.2 38.9 - - + +
446B ALA 3.3 17.9 + - - +
447B ALA 4.0 1.3 - - - +
448B MET 3.2 0.6 - - - -
449B ILE* 1.3 79.7 - - - +
451B ILE* 1.3 69.9 + - + +
453B GLY* 2.9 14.1 + - - +
454B GLU* 2.9 46.9 + - + +
455B TYR* 5.0 2.7 - + - -
483B THR* 3.8 7.8 - - + +
486B THR* 5.7 5.8 - - + -
487B ALA* 4.7 3.8 - - + -
490B LYS* 3.5 22.3 - - + +
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 4.4 7.0 - - + -
414B ILE* 4.6 10.5 - - + -
415B ARG* 4.9 7.2 - - + -
418B PHE* 4.3 14.6 - - + -
429B ILE* 4.2 32.3 - - + -
432B LEU* 4.6 12.6 - - + -
433B CYS* 5.6 1.3 - - - -
447B ALA 3.1 22.6 + - - +
448B MET* 2.6 46.1 + - + +
450B TRP* 1.3 82.3 - - + +
452B VAL* 1.3 54.9 + - + +
453B GLY 2.9 3.8 - - - -
454B GLU* 2.5 29.6 - - - +
455B TYR* 3.8 10.5 - - + +
459B ILE* 5.5 0.3 - - - +
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Residues in contact with VAL 452 (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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433B CYS* 5.2 9.9 - - - -
436B LEU* 5.5 4.9 - - + -
448B MET* 2.7 27.9 + - + +
449B ILE* 3.5 6.1 - - - +
451B ILE* 1.3 75.5 - - + +
453B GLY* 1.3 58.2 + - - +
454B GLU 3.1 8.2 - - - +
455B TYR 4.9 3.6 - - - -
456B ALA* 3.5 14.6 - - - +
459B ILE* 4.9 7.9 - - + -
462B ALA* 3.9 29.8 - - + +
465B LEU* 4.3 20.4 - - + -
466B LEU* 3.7 31.4 - - + +
469B PHE* 6.5 1.1 - - + -
487B ALA* 4.9 2.8 - - - +
491B LEU* 5.9 1.2 - - - +
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Residues in contact with GLY 453 (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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449B ILE 2.7 13.7 + - - -
450B TRP* 3.1 7.0 - - - -
451B ILE 2.9 2.6 - - - -
452B VAL* 1.3 78.6 - - - +
454B GLU* 1.3 61.7 + - - +
456B ALA* 3.6 11.6 - - - +
487B ALA* 3.9 22.0 - - - -
490B LYS* 3.7 25.8 - - - +
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Residues in contact with GLU 454 (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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450B TRP* 2.9 49.6 + - + +
451B ILE 2.5 22.3 - - - +
452B VAL 3.1 1.6 - - - -
453B GLY* 1.3 74.5 - - - -
455B TYR* 1.3 88.7 + - + +
456B ALA 2.8 2.5 + - - -
490B LYS* 2.6 32.9 + - - +
542B LEU* 5.8 0.7 - - - +
545B LYS* 5.5 6.9 - - - +
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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