Contacts of the helix formed by residues 430 - 441 (chain R) in PDB entry 6VMS
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 ASN 430 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A LYS 3.9 20.3 + - - +
350A ASP* 4.2 10.9 + - - +
352A GLY* 4.4 15.5 - - - -
354A PHE* 5.0 4.7 - - - -
65R LEU* 4.9 3.6 - - - +
70R ASN* 4.9 2.6 + - - +
426R TYR 5.2 3.6 - - - +
427R THR 3.3 3.5 + - - +
429R PHE* 1.3 77.7 - - - +
431R ILE* 1.3 60.2 + - - +
432R GLU* 2.9 26.8 + - - +
433R PHE* 2.8 54.8 + - + +
434R ARG* 3.2 12.4 + - - +
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Residues in contact with ILE 431 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A PHE* 5.6 0.8 + - - -
370R LYS* 5.8 0.4 - - - +
429R PHE 3.8 3.6 + - - -
430R ASN* 1.3 75.0 + - - +
432R GLU* 1.3 70.9 + - + +
434R ARG* 3.4 24.1 + - + +
435R LYS* 3.3 53.1 + - + +
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Residues in contact with GLU 432 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62R GLU* 4.6 11.4 - - + +
64R ALA* 3.5 29.4 - - + +
65R LEU* 3.2 37.9 - - + -
430R ASN* 2.9 15.4 + - - +
431R ILE* 1.3 87.2 - - + +
433R PHE* 1.3 59.1 + - - +
435R LYS* 4.1 10.5 - - - +
436R ALA* 3.1 26.6 + - - +
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Residues in contact with PHE 433 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R VAL* 4.8 12.3 - - + -
58R ALA* 4.1 18.6 - - + -
59R VAL* 4.3 14.1 - - + -
65R LEU* 3.5 24.5 - - + -
70R ASN* 3.5 37.2 - - + -
73R ILE* 4.9 4.0 - - + -
426R TYR 4.0 12.3 - - - -
427R THR* 3.0 52.3 - - + +
428R THR* 5.9 0.4 - - - -
430R ASN* 2.8 31.2 + - + -
432R GLU* 1.3 71.1 - - - +
434R ARG* 1.3 63.8 + - - +
436R ALA* 4.1 1.6 - - - -
437R PHE* 2.9 32.8 + + - -
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Residues in contact with ARG 434 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370R LYS* 6.1 1.6 - - - +
428R THR* 2.6 37.3 + - + +
429R PHE* 4.4 20.1 - - - +
430R ASN 3.2 9.0 + - - +
431R ILE* 3.4 27.0 + - + +
433R PHE* 1.3 78.5 - - - +
435R LYS* 1.3 62.1 + - + +
437R PHE* 3.4 12.3 + - - +
438R LEU* 3.5 20.7 + - + +
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Residues in contact with LYS 435 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431R ILE* 3.3 42.9 + - + +
432R GLU* 4.1 11.4 - - - +
434R ARG* 1.3 74.7 - - + +
436R ALA* 1.3 65.9 + - - +
437R PHE 3.3 0.3 + - - -
438R LEU* 3.3 19.0 + - + +
439R LYS* 3.3 22.1 + - + +
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Residues in contact with ALA 436 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58R ALA* 3.9 20.9 - - + -
62R GLU* 3.9 33.8 - - + +
65R LEU* 4.4 2.7 - - + -
432R GLU 3.1 19.0 + - - +
433R PHE* 3.2 7.6 + - - +
435R LYS* 1.3 77.2 - - - +
437R PHE* 1.3 62.2 + - - +
439R LYS* 3.4 3.0 + - - +
440R ILE* 3.0 33.2 + - + +
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Residues in contact with PHE 437 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R PHE* 5.2 12.6 - + - -
51R GLY* 5.1 4.7 - - - -
54R LEU* 4.2 37.7 - - + -
55R VAL* 4.6 9.4 - - + -
58R ALA* 4.8 10.1 - - + -
423R PRO 5.4 0.9 - - - -
424R ILE* 6.5 2.0 - - + -
427R THR* 3.3 34.3 - - + -
428R THR* 5.4 9.4 - - + -
433R PHE* 2.9 34.9 + + + +
434R ARG* 3.7 7.6 - - - +
435R LYS 3.2 0.4 - - - -
436R ALA* 1.3 79.9 - - + +
438R LEU* 1.3 65.4 + - + +
440R ILE* 3.2 8.2 + - + +
441R LEU* 3.0 39.8 + - + +
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Residues in contact with LEU 438 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434R ARG* 3.5 15.5 + - + +
435R LYS* 3.3 11.0 + - + +
437R PHE* 1.3 78.8 - - + +
439R LYS* 1.3 63.2 + - + +
441R LEU* 3.4 7.9 + - + -
442R HIS* 3.3 2.9 + - - -
443R CYS* 3.3 54.7 + - + +
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Residues in contact with LYS 439 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R ARG* 4.1 14.1 + - - +
62R GLU* 3.9 25.9 + - - +
435R LYS* 3.3 16.6 + - + +
436R ALA* 4.0 6.3 - - - +
437R PHE 3.3 0.4 - - - -
438R LEU* 1.3 76.0 - - + +
440R ILE* 1.3 67.7 + - + +
442R HIS* 3.2 20.6 + - - +
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Residues in contact with ILE 440 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R LEU* 4.0 32.5 - - + +
57R MET* 4.9 4.7 - - + -
58R ALA* 3.5 43.3 - - + +
61R ARG* 3.4 34.5 + - + +
62R GLU* 6.0 1.6 - - + +
436R ALA* 3.0 30.9 + - + +
437R PHE* 3.2 9.8 + - + +
439R LYS* 1.3 76.4 - - + +
441R LEU* 1.3 65.3 + - + +
442R HIS* 3.4 14.4 + - - -
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Residues in contact with LEU 441 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R PHE* 4.8 17.0 - - + -
54R LEU* 4.3 28.3 - - + -
437R PHE* 3.0 31.4 + - + +
438R LEU* 4.0 11.2 - - + +
439R LYS 3.2 0.2 - - - -
440R ILE* 1.3 78.4 - - + +
442R HIS* 1.3 71.8 + - - +
443R CYS* 3.1 7.0 + - + +
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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