Contacts of the helix formed by residues 423 - 437 (chain B) in PDB entry 5VOT
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 423 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404B PRO 3.4 7.2 - - - -
405B TYR 3.1 12.3 - - - -
407B MET* 4.4 1.1 - - - -
422B GLU* 1.3 78.6 - - - +
424B TYR* 1.3 68.0 + - - +
425B CYS 3.4 0.2 - - - -
426B VAL* 3.3 11.3 + - - +
427B ASP* 3.3 9.0 + - - +
766B TRP* 3.3 33.4 + - - -
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Residues in contact with TYR 424 (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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404B PRO 2.7 20.7 + - - +
405B TYR* 2.8 16.8 + + + -
423B GLY* 1.3 70.8 - - - -
425B CYS* 1.3 67.2 + - - +
427B ASP* 3.0 7.7 + - + +
428B LEU* 2.9 26.8 + - + +
495B PHE* 4.5 15.9 - + - -
496B MET* 3.7 28.2 - - + +
759B LEU* 3.3 35.7 + - + +
762B LEU* 3.4 35.3 - - + +
763B LYS 3.6 2.2 - - - -
766B TRP* 3.5 30.9 - + + +
767B TRP* 3.5 24.2 - + + -
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Residues in contact with CYS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 2.8 49.8 + - - +
406B VAL* 3.8 12.1 - - + -
424B TYR* 1.3 78.8 - - - +
426B VAL* 1.3 56.8 + - - +
428B LEU* 3.3 16.8 - - - +
429B ALA* 2.9 28.4 + - - +
476B ILE* 4.0 15.3 - - + +
477B ALA* 3.9 10.3 - - - -
478B PRO* 3.6 17.0 - - - -
495B PHE* 6.1 3.1 - - - -
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 4.4 11.9 - - + -
418B ASN 5.1 3.1 - - - +
421B TYR* 4.2 15.9 - - + +
422B GLU* 3.4 38.6 - - - +
423B GLY* 3.3 11.2 - - - +
424B TYR 3.1 1.0 - - - -
425B CYS* 1.3 74.3 - - - +
427B ASP* 1.3 66.4 + - - +
429B ALA* 3.1 8.1 + - + +
430B ALA* 2.9 28.3 + - + +
440B TYR* 5.5 2.2 + - - +
442B LEU* 4.8 18.6 - - + -
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 3.3 5.0 + - - +
424B TYR* 3.0 8.3 + - + +
426B VAL* 1.3 81.4 - - - +
428B LEU* 1.3 62.0 + - - +
430B ALA* 3.3 8.5 + - - +
431B GLU* 2.9 31.2 + - + +
762B LEU* 4.3 27.0 - - + +
765B LYS* 3.8 12.7 + - - -
766B TRP* 2.9 33.0 + - - +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 2.9 22.5 + - + +
425B CYS* 3.3 18.2 - - - +
427B ASP* 1.3 76.7 - - - +
429B ALA* 1.3 58.1 + - - +
431B GLU* 3.2 4.7 + - - +
432B ILE* 2.9 54.7 + - + +
476B ILE* 3.6 24.0 - - + -
477B ALA 5.5 0.4 - - - +
495B PHE* 4.6 23.8 - - + -
734B ILE* 3.8 17.0 - - + -
750B VAL* 5.7 3.8 - - + -
753B LEU* 5.1 3.8 - - + -
759B LEU* 4.5 22.7 - - + -
762B LEU* 5.4 2.8 - - - +
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 5.2 2.9 - - + -
425B CYS 2.9 16.5 + - - +
426B VAL* 3.1 9.8 + - - +
428B LEU* 1.3 73.3 - - - +
430B ALA* 1.3 57.5 + - - +
432B ILE* 4.1 1.7 - - - +
433B ALA* 2.9 34.0 + - - +
440B TYR* 4.8 20.6 - - + +
442B LEU* 4.9 10.5 - - + -
476B ILE* 4.2 28.4 - - + +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B VAL* 2.9 14.7 + - + +
427B ASP* 3.6 13.5 - - - +
428B LEU 3.2 0.2 - - - -
429B ALA* 1.3 77.4 - - - +
431B GLU* 1.3 59.5 + - + +
433B ALA* 4.0 2.9 - - - +
434B LYS* 2.9 30.7 + - - +
440B TYR* 4.6 13.1 + - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ASP* 2.9 23.0 + - + +
428B LEU* 3.6 6.1 - - + +
430B ALA* 1.3 77.9 - - + +
432B ILE* 1.3 57.5 + - - +
434B LYS* 3.1 8.6 + - - +
435B HIS* 2.9 55.7 + - - -
753B LEU* 3.8 25.9 - - + +
758B LEU* 4.1 22.5 - - + +
759B LEU* 5.8 1.3 - - + -
762B LEU* 5.0 13.4 - - + +
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Residues in contact with ILE 432 (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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428B LEU* 2.9 37.1 + - + +
429B ALA* 4.1 5.2 - - - +
431B GLU* 1.3 75.3 - - - +
433B ALA* 1.3 58.2 + - - +
435B HIS* 3.3 3.1 + - - -
436B CYS* 2.9 35.3 + - - +
438B PHE* 4.1 9.4 - - + -
474B ILE* 5.5 1.3 - - + -
476B ILE* 5.1 12.3 - - + -
734B ILE* 5.7 4.3 - - + -
746B VAL* 3.9 31.0 - - + -
749B ALA* 4.6 4.9 - - + -
750B VAL* 3.8 32.1 - - + +
753B LEU* 4.1 21.1 - - + -
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Residues in contact with ALA 433 (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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429B ALA 2.9 19.2 + - - +
430B ALA 4.1 2.2 - - - +
432B ILE* 1.3 76.4 - - - +
434B LYS* 1.3 54.9 + - - +
437B GLY* 2.7 32.2 + - - -
438B PHE* 3.4 33.0 + - + +
440B TYR* 3.7 31.4 - - + -
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Residues in contact with LYS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ALA 2.9 21.2 + - - +
431B GLU* 3.1 10.7 + - - +
433B ALA* 1.3 79.9 - - - +
435B HIS* 1.3 91.2 + - + +
436B CYS 3.4 0.2 + - - -
437B GLY* 3.5 7.1 + - - -
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Residues in contact with HIS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU* 2.9 45.1 + - - +
432B ILE 4.1 0.9 - - - +
434B LYS* 1.3 99.0 + - + +
436B CYS* 1.3 61.5 + - - +
749B ALA* 3.8 24.7 - - + -
752B LYS* 4.5 21.5 + - + +
753B LEU* 3.4 35.4 - - + +
756B GLN* 4.4 10.5 - - - -
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Residues in contact with CYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ILE* 2.9 20.3 + - - +
435B HIS* 1.3 79.7 - - - +
437B GLY* 1.3 66.7 + - - +
438B PHE* 3.4 18.6 - - + +
742B LEU* 6.2 3.8 - - + -
745B ALA* 4.2 16.8 - - + -
746B VAL* 4.1 36.6 - - + -
749B ALA* 4.3 9.2 - - - -
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Residues in contact with GLY 437 (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 ALA 2.7 18.8 + - - -
434B LYS 3.5 5.7 + - - -
435B HIS 3.5 2.8 - - - -
436B CYS* 1.3 77.2 - - - +
438B PHE* 1.3 58.5 + - - +
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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