Contacts of the helix formed by residues 1619 - 1624 (chain A) 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 SER1619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1610A HIS* 4.1 9.5 + - - -
1617A ASN* 3.5 20.7 + - - +
1618A ARG* 1.3 76.4 - - - +
1620A TYR* 1.3 65.2 + - - +
1621A ALA 3.2 0.9 + - - -
1622A GLY* 3.5 10.2 + - - -
1623A LYS* 5.5 0.2 - - - +
1652C ASN* 5.0 8.5 - - - +
1654C ARG* 5.3 6.0 + - - -
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Residues in contact with TYR1620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LDR 4.9 1.7 - - - -
1601A HIS* 2.6 35.6 + + - -
1602A GLY 4.6 0.2 + - - -
1603A THR* 2.7 22.0 + - - +
1607A SER* 3.9 16.6 - - - -
1610A HIS* 4.4 18.3 + + + -
1611A VAL* 4.0 17.9 - - + -
1616A PHE* 3.9 13.9 - + - -
1617A ASN* 3.4 23.6 + - + +
1618A ARG 3.4 0.4 - - - -
1619A SER* 1.3 79.3 + - - +
1621A ALA* 1.3 63.5 + - - +
1623A LYS* 2.9 59.4 + - + +
1624A ASN* 3.7 14.8 - - - -
1632A THR* 3.7 16.2 - - + -
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Residues in contact with ALA1621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617A ASN 3.3 8.1 + - - +
1618A ARG* 3.3 17.9 - - - +
1619A SER 3.2 2.0 - - - -
1620A TYR* 1.3 76.4 - - - +
1622A GLY* 1.3 58.9 + - - +
1623A LYS 3.1 2.3 + - - -
1624A ASN* 3.2 28.2 + - - +
1630A LYS* 4.5 8.1 - - + +
1631A GLY* 3.7 31.1 + - - +
1632A THR* 4.0 4.9 - - - +
1705A PHE 6.2 0.2 - - - +
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Residues in contact with GLY1622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1618A ARG 4.6 0.8 + - - -
1619A SER 3.5 9.4 + - - -
1620A TYR 2.9 4.8 + - - -
1621A ALA* 1.3 73.7 - - - +
1623A LYS* 1.3 59.9 + - - +
1624A ASN 3.2 5.2 + - - +
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Residues in contact with LYS1623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LDR 3.6 15.1 - - + -
1603A THR* 4.6 1.3 - - - +
1604A ASP* 4.1 12.2 + - - +
1607A SER* 3.3 26.5 + - - +
1619A SER 5.5 0.4 - - - +
1620A TYR* 2.9 48.5 + - + +
1622A GLY* 1.3 76.9 - - - +
1624A ASN* 1.3 69.9 + - - +
1650C ASP* 6.1 1.4 - - - +
1651C ALA* 4.0 25.4 - - - +
1652C ASN* 4.1 19.3 - - - +
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Residues in contact with ASN1624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LDR 3.1 17.6 - - + -
1601A HIS* 3.5 16.1 - - - -
1620A TYR* 3.7 28.7 + - - -
1621A ALA* 3.2 14.4 + - - +
1622A GLY 4.2 4.5 - - - +
1623A LYS* 1.3 83.6 - - - +
1625A ALA* 1.3 65.8 + - - +
1626A VAL* 4.3 7.3 - - - +
1631A GLY 3.1 28.8 + - - +
1632A THR* 3.7 7.7 - - - +
1633A TYR* 2.9 28.7 + - + -
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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