Contacts of the helix formed by residues 423 - 437 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C PRO 3.4 9.4 - - - -
405C TYR 3.2 10.3 - - - -
407C MET* 4.5 0.9 - - - -
422C GLU* 1.3 77.6 - - - +
424C TYR* 1.3 68.2 + - - +
425C CYS 3.5 0.2 - - - -
426C VAL* 3.3 16.7 - - - +
427C ASP* 3.3 5.2 + - - +
766C TRP* 3.2 33.1 - - - -
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Residues in contact with TYR 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C PRO 3.0 17.5 + - - +
405C TYR* 3.0 11.2 + + - -
423C GLY* 1.3 69.9 - - - -
425C CYS* 1.3 75.8 + - - +
427C ASP* 2.9 16.5 + - + +
428C LEU* 2.9 27.1 + - + +
495C PHE* 4.0 32.5 - + - -
496C MET* 4.5 7.5 - - + +
759C LEU* 4.0 25.7 + - + +
762C LEU* 3.6 28.5 - - + -
763C LYS* 3.8 9.8 - - - +
766C TRP* 3.4 34.4 - + + +
767C TRP* 3.7 28.7 - + + -
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Residues in contact with CYS 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C THR* 5.7 0.2 - - - -
405C TYR* 3.1 45.4 + - - +
406C VAL* 4.0 10.5 - - + -
424C TYR* 1.3 83.2 - - - +
426C VAL* 1.3 57.2 + - - +
428C LEU* 3.9 9.6 - - - +
429C ALA* 2.9 32.1 + - - +
442C LEU* 5.7 0.8 - - - +
476C ILE* 3.8 20.0 - - + +
477C ALA* 3.9 26.0 - - - -
478C PRO* 4.0 0.7 - - - -
495C PHE* 6.0 3.6 - - - -
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Residues in contact with VAL 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C TYR 4.6 2.0 - - - +
406C VAL* 4.9 8.3 - - + -
418C ASN 5.6 0.7 - - - +
421C TYR* 4.2 20.4 - - + +
422C GLU* 3.4 34.3 - - - +
423C GLY* 3.3 11.4 - - - +
424C TYR 3.0 0.4 + - - -
425C CYS* 1.3 77.8 - - - +
427C ASP* 1.3 65.6 + - - +
429C ALA* 3.8 3.6 - - - +
430C ALA* 2.9 30.8 + - + +
440C TYR* 5.6 0.2 + - - -
442C LEU* 4.4 20.6 - - + -
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Residues in contact with ASP 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLY 3.3 5.3 + - - +
424C TYR 2.9 6.9 + - - +
426C VAL* 1.3 82.7 - - - +
428C LEU* 1.3 63.6 + - - +
430C ALA* 3.2 8.2 + - - +
431C GLU* 2.9 29.3 + - + +
762C LEU* 4.7 19.1 - - + +
765C LYS* 4.0 17.0 + - - +
766C TRP* 2.9 36.9 + - - +
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Residues in contact with LEU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR* 2.9 36.3 + - + +
425C CYS* 3.9 7.0 - - - +
427C ASP* 1.3 76.1 - - - +
429C ALA* 1.3 64.4 + - - +
431C GLU* 2.9 9.2 + - - +
432C ILE* 2.9 38.0 + - + +
476C ILE* 4.0 19.1 - - + -
495C PHE* 4.7 18.2 - - + -
734C ILE* 4.3 13.9 - - + -
750C VAL* 5.9 5.4 - - + -
753C LEU* 4.3 21.5 - - + -
759C LEU* 4.6 14.8 - - + -
762C LEU* 5.0 9.2 - - + +
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C VAL* 4.8 12.3 - - + -
425C CYS 2.9 23.1 + - - +
426C VAL* 3.8 4.3 - - - +
428C LEU* 1.3 74.0 - - - +
430C ALA* 1.3 57.0 + - - +
432C ILE* 3.1 3.3 + - - +
433C ALA* 2.9 30.2 + - - +
438C PHE* 5.5 0.2 - - - -
440C TYR* 5.2 7.9 - - + -
442C LEU* 5.0 9.0 - - + -
476C ILE* 3.6 33.7 - - + +
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Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C VAL* 2.9 16.7 + - + +
427C ASP* 3.2 13.0 + - - +
429C ALA* 1.3 76.8 - - - +
431C GLU* 1.3 59.9 + - + +
433C ALA* 3.4 5.4 + - - +
434C LYS* 2.9 27.4 + - - +
440C TYR* 4.4 19.4 + - - +
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Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ASP* 2.9 20.0 + - + +
428C LEU* 3.4 8.7 - - - +
430C ALA* 1.3 77.3 - - + +
432C ILE* 1.3 59.2 + - - +
434C LYS* 3.1 13.2 + - - +
435C HIS* 2.9 52.0 + - + -
753C LEU* 3.9 27.6 - - + +
758C LEU* 4.6 18.8 - - + +
762C LEU* 5.4 4.7 - - + -
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Residues in contact with ILE 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C LEU* 2.9 33.8 + - + +
429C ALA* 3.1 10.7 + - - +
431C GLU* 1.3 79.4 - - - +
433C ALA* 1.3 57.7 + - - +
435C HIS* 3.3 3.4 + - - -
436C CYS* 2.9 43.5 + - + +
438C PHE* 5.1 6.3 - - + -
474C ILE* 5.6 2.5 - - + -
476C ILE* 4.7 13.9 - - + -
734C ILE* 5.8 2.9 - - + -
746C VAL* 3.9 27.1 - - + +
749C ALA* 4.1 22.0 - - + -
750C VAL* 4.4 20.2 - - + +
753C LEU* 4.9 5.4 - - + -
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C ALA 2.9 14.2 + - - +
430C ALA 3.8 3.6 - - - +
432C ILE* 1.3 76.2 - - - +
434C LYS* 1.3 55.3 + - - +
437C GLY* 2.5 34.5 + - - -
438C PHE* 3.4 30.2 + - + +
440C TYR* 3.6 37.2 - - + -
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Residues in contact with LYS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C ALA 2.9 14.3 + - - +
431C GLU* 3.1 19.9 + - - +
433C ALA* 1.3 78.2 - - - +
435C HIS* 1.3 93.4 + - + +
436C CYS 3.3 0.9 + - - -
437C GLY* 3.6 7.2 + - - -
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Residues in contact with HIS 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C GLU* 2.9 48.2 + - + +
432C ILE* 4.1 1.6 - - - +
434C LYS* 1.3 102.3 + - + +
436C CYS* 1.3 62.0 + - - +
749C ALA* 4.0 28.7 - - + -
752C LYS* 3.5 41.0 + - + +
753C LEU* 4.4 17.6 - - + +
756C GLN* 4.8 6.3 + - - -
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Residues in contact with CYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 2.9 24.5 + - - +
435C HIS* 1.3 88.1 - - - +
437C GLY* 1.3 65.7 + - - +
438C PHE* 3.3 21.4 - - + +
742C LEU* 5.3 10.5 - - + +
745C ALA* 4.8 9.9 - - - -
746C VAL* 4.0 36.3 - - - -
749C ALA* 5.1 2.0 - - - -
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Residues in contact with GLY 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C ALA 2.5 19.1 + - - -
434C LYS 3.6 6.9 + - - -
436C CYS* 1.3 76.2 - - - +
438C PHE* 1.3 58.2 + - - +
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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