Contacts of the helix formed by residues 1987 - 1994 (chain H) 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 PRO1987 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1738H PHE* 5.4 3.1 - - + -
1739H GLU* 3.0 71.6 - - + +
1740H THR 4.8 0.4 - - - +
1741H ILE* 5.2 0.2 - - + -
1746H LEU* 5.1 3.4 - - + -
1833H TYR* 4.3 13.3 + - - +
1983H ASN 4.0 4.7 - - - +
1984H GLY* 3.4 15.5 - - - +
1985H VAL 3.3 1.1 - - - +
1986H LYS* 1.3 92.5 - - + +
1988H PHE* 1.3 61.3 + - - +
1990H SER* 3.3 8.2 + - - +
1991H PHE* 3.3 21.1 + - - +
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Residues in contact with PHE1988 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 4.5 2.0 - - - -
19B ALA* 4.3 8.3 - - - -
22B PHE* 3.9 27.6 - + + -
1812H TYR* 3.4 20.6 - - - -
1830H VAL* 4.4 7.2 - - + -
1833H TYR* 3.8 26.2 - + + -
1834H ARG* 3.6 47.1 - - + -
1837H THR* 4.6 3.4 - - + -
1984H GLY 3.8 12.3 - - - +
1985H VAL* 3.0 8.4 + - - +
1987H PRO* 1.3 75.4 - - - +
1989H LYS* 1.3 54.9 + - - +
1990H SER 3.0 4.5 - - - -
1991H PHE* 2.9 7.9 + + + +
1992H LEU* 2.7 67.3 + - + +
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Residues in contact with LYS1989 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 4.2 12.1 - - - +
16B GLU* 3.2 34.3 + - - +
19B ALA* 4.0 22.6 - - + +
20B TYR* 5.2 2.0 + - - -
1985H VAL* 2.7 20.9 + - + +
1986H LYS* 3.8 18.6 - - + +
1987H PRO 3.4 0.2 - - - -
1988H PHE* 1.3 76.9 - - - +
1990H SER* 1.3 55.7 + - - +
1992H LEU* 4.2 4.3 - - - +
1993H LYS* 3.0 41.3 + - + +
2035H SER* 3.9 4.9 + - - -
2037H PRO* 3.4 29.8 - - - +
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Residues in contact with SER1990 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1739H GLU* 5.2 3.5 + - - -
1986H LYS 3.4 13.8 + - - -
1987H PRO* 3.3 9.9 + - - +
1988H PHE 3.0 0.8 - - - -
1989H LYS* 1.3 77.7 - - - +
1991H PHE* 1.3 67.5 + - - +
1992H LEU 3.2 1.6 - - - -
1993H LYS* 3.1 7.0 + - - +
1994H LYS* 2.9 48.2 + - - +
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Residues in contact with PHE1991 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1736H MET* 5.0 6.5 - - + -
1829H GLU* 4.3 16.6 - - + -
1830H VAL* 3.6 31.9 - - + -
1833H TYR* 3.6 53.6 - + + -
1987H PRO 3.3 12.0 + - - +
1988H PHE* 2.9 17.9 + + + +
1990H SER* 1.3 82.5 + - - +
1992H LEU* 1.3 62.6 + - + +
1994H LYS* 3.2 19.2 + - + +
1995H ASN* 3.3 38.1 + - - +
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Residues in contact with LEU1992 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 4.1 13.7 - - - +
18B LEU* 3.7 17.7 - - + -
19B ALA* 3.6 33.7 - - + +
1812H TYR* 4.3 5.8 - - + +
1830H VAL* 3.5 36.1 - - + -
1988H PHE* 2.7 45.8 + - + +
1989H LYS* 4.6 3.1 - - - +
1991H PHE* 1.3 73.4 - - + +
1993H LYS* 1.3 55.1 + - - +
1995H ASN* 3.0 4.0 + - - -
1996H ILE* 2.7 48.8 + - + +
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Residues in contact with LYS1993 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B HIS* 4.5 19.1 + - - +
12B ILE* 4.9 12.0 - - - +
15B THR* 3.8 20.2 - - + +
1989H LYS* 3.0 39.9 + - - +
1990H SER* 3.1 8.8 + - - +
1992H LEU* 1.3 76.2 - - - +
1994H LYS* 1.3 61.1 + - + +
1995H ASN 3.2 0.6 + - - -
1996H ILE* 3.8 16.2 - - - +
1997H ILE* 4.9 2.9 + - - +
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Residues in contact with LYS1994 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1990H SER* 2.9 37.7 + - - +
1991H PHE* 3.6 12.3 - - + +
1992H LEU 3.1 0.4 - - - -
1993H LYS* 1.3 76.7 - - + +
1995H ASN* 1.3 66.8 + - - +
1997H ILE* 5.3 5.4 - - - +
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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