Contacts of the helix formed by residues 1617 - 1621 (chain B) in PDB entry 3SE2
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 ASN1617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B SCN 3.5 23.7 - - - -
1610B HIS* 2.8 29.0 + - - -
1614B ASN* 3.6 27.2 - - - +
1615B GLY 3.2 0.4 + - - -
1616B PHE* 1.3 78.5 - - - +
1618B ARG* 1.3 66.1 + - - +
1619B SER* 3.4 18.7 + - - +
1620B TYR* 3.1 15.9 + - - +
1621B ALA* 3.6 4.0 + - - +
1632B THR* 4.4 2.4 + - - -
1706B TYR 5.8 0.2 - - - -
1707B ASP* 3.1 23.8 - - + +
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Residues in contact with ARG1618 (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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1617B ASN* 1.3 75.8 - - - +
1619B SER* 1.3 61.9 + - - +
1621B ALA* 3.2 24.2 + - - +
1705B PHE 3.9 22.5 + - - +
1706B TYR* 5.3 2.2 - - - +
1707B ASP* 2.8 34.4 + - - +
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Residues in contact with SER1619 (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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1610B HIS* 3.9 11.0 - - - -
1617B ASN* 3.4 21.5 + - - +
1618B ARG* 1.3 76.2 - - - +
1620B TYR* 1.3 59.8 + - - +
1621B ALA* 3.5 5.6 + - - +
1652D ASN* 4.2 20.3 + - - +
1654D ARG* 4.8 9.4 + - - -
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Residues in contact with TYR1620 (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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2B LDR 4.9 5.6 - + - -
1601B HIS* 2.8 35.1 + + - -
1603B THR* 2.6 27.4 + - - +
1607B SER* 3.7 26.5 - - - -
1610B HIS* 4.0 22.2 + + + +
1611B VAL* 3.9 10.8 - - + -
1616B PHE* 3.8 16.2 - + + -
1617B ASN* 3.1 28.2 + - - +
1619B SER* 1.3 78.3 + - - +
1621B ALA* 1.3 66.4 + - - +
1622B GLY* 2.8 12.7 + - - -
1632B THR* 3.6 17.9 - - + -
1652D ASN* 6.2 0.7 - - - +
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Residues in contact with ALA1621 (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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1617B ASN 3.6 4.0 + - - +
1618B ARG* 3.2 20.0 + - - +
1619B SER 4.1 5.2 - - - +
1620B TYR* 1.3 74.6 - - - +
1622B GLY* 1.3 57.6 + - - +
1630B LYS* 4.6 7.0 - - + +
1631B GLY* 4.2 30.7 - - - +
1632B THR* 4.4 3.3 + - - -
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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