Contacts of the helix formed by residues 1978 - 1983 (chain G) in PDB entry 2VKZ
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 SER1978 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.0 27.5 - - - +
25A PRO* 6.0 0.9 - - - -
1885G LEU* 4.7 5.6 - - - +
1887G GLU* 3.6 21.1 - - - -
1889G VAL* 4.4 9.6 - - - -
1901G ALA* 5.1 3.1 - - - -
1975G PRO* 2.5 26.5 + - - +
1976G PHE 3.1 0.6 - - - -
1977G HIS* 1.3 78.9 + - - +
1979G THR* 1.3 62.6 + - - +
1980G TYR* 3.0 23.7 + - - +
1981G LEU 3.9 3.6 + - - -
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Residues in contact with THR1979 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.6 5.2 - - - -
1885G LEU* 5.0 4.0 - - - +
1887G GLU* 3.1 29.7 + - - +
1978G SER* 1.3 75.3 - - - +
1980G TYR* 1.3 66.9 + - - +
1981G LEU 3.3 0.7 - - - -
1982G MET* 3.1 27.8 + - - +
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Residues in contact with TYR1980 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841G ALA* 3.6 18.9 + - + -
1842G VAL* 3.7 12.5 - - + +
1843G PRO* 3.7 25.1 - - - +
1852G TYR* 3.2 34.8 + + - -
1885G LEU* 4.1 21.0 - - + +
1975G PRO* 3.6 15.7 - - + -
1978G SER* 3.0 16.9 + - - +
1979G THR* 1.3 82.2 + - - +
1981G LEU* 1.5 75.9 + - + +
1982G MET 3.2 4.3 + - - -
1983G ASN* 3.6 17.3 + - - -
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Residues in contact with LEU1981 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.8 41.3 - - + +
23A ALA* 4.6 3.0 - - - +
1838G MET* 5.2 1.8 - - + -
1841G ALA* 5.0 11.4 - - + -
1974G VAL* 4.1 14.8 - - + -
1975G PRO 3.8 18.2 - - - +
1976G PHE* 2.9 37.7 - - + +
1978G SER* 3.9 4.5 + - - +
1979G THR 3.3 1.4 + - - -
1980G TYR* 1.5 94.6 - - + +
1982G MET* 1.3 63.6 + - - +
1983G ASN 3.3 3.5 + - - +
1984G GLY* 3.6 13.0 + - - +
1985G VAL* 3.8 14.0 + - - +
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Residues in contact with MET1982 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.5 35.9 - - + +
23A ALA* 3.2 28.7 - - + -
1979G THR* 3.1 21.0 + - - +
1980G TYR 3.2 2.4 - - - +
1981G LEU* 1.3 78.7 - - - +
1983G ASN* 1.4 64.6 + - - +
1985G VAL* 3.6 22.4 - - - +
1986G LYS* 5.2 1.4 + - - +
2032G LEU 5.4 1.3 - - - +
2033G THR* 3.7 19.3 - - - +
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Residues in contact with ASN1983 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1739G GLU 3.7 0.9 - - - +
1740G THR* 3.5 27.8 - - + +
1741G ILE* 3.2 42.9 + - - +
1742G VAL* 4.4 11.3 - - - +
1980G TYR 3.6 17.4 + - - -
1981G LEU 3.3 0.8 - - - -
1982G MET* 1.4 77.6 - - - +
1984G GLY* 1.3 58.6 + - - +
1985G VAL 3.1 8.9 + - - -
1986G LYS 4.4 1.6 + - - -
1987G PRO* 3.9 4.9 - - - +
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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