Contacts of the helix formed by residues 1637 - 1643 (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 ASN1637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1557A GLN* 5.7 2.9 - - - +
1558A THR* 3.8 20.1 - - - +
1600A PHE* 3.9 2.9 - - - -
1635A ALA* 3.1 20.5 - - - +
1636A VAL* 1.3 96.9 - - - +
1638A ALA* 1.3 65.6 + - - +
1639A ASN* 3.3 18.3 + - - +
1640A TYR* 3.4 10.2 + - + +
1700A SER* 4.5 4.4 + - - +
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Residues in contact with ALA1638 (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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1554A LYS 4.9 0.6 + - - +
1555A PHE* 3.7 29.6 - - + +
1558A THR* 3.1 8.7 + - - +
1559A CYS* 3.5 16.6 - - - -
1600A PHE* 3.7 33.5 - - + -
1637A ASN* 1.3 71.1 - - - +
1639A ASN* 1.3 61.4 + - - +
1641A SER* 3.0 7.0 + - - -
1642A ALA* 2.8 25.6 + - - +
1657A VAL* 5.0 1.7 - - + +
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Residues in contact with ASN1639 (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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1558A THR* 3.2 34.6 + - - +
1559A CYS* 3.3 10.9 - - - -
1561A HIS* 5.1 5.6 - - + +
1562A PHE* 6.0 0.2 - - + -
1637A ASN* 3.4 20.8 + - - +
1638A ALA* 1.3 75.0 - - - +
1640A TYR* 1.3 74.0 + - - +
1642A ALA* 3.1 12.3 + - - +
1643A ASN* 3.4 8.7 + - - +
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Residues in contact with TYR1640 (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 3.2 36.3 - + - -
1628A TYR* 5.5 2.8 - - - -
1635A ALA* 3.7 7.9 - - + -
1637A ASN* 3.4 15.0 + - + +
1638A ALA 3.2 0.2 - - - -
1639A ASN* 1.3 89.7 + - - +
1641A SER* 1.3 62.2 + - - +
1642A ALA 3.3 0.2 + - - -
1643A ASN* 3.4 18.5 + - - +
1646A TYR* 3.5 20.8 - + - -
1700A SER* 3.8 33.4 + - - -
1701A LEU* 3.8 17.6 - - + +
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Residues in contact with SER1641 (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 2.7 29.4 + - - -
1600A PHE* 3.5 21.7 - - - +
1602A GLY* 3.6 10.8 - - - -
1635A ALA* 3.4 18.7 - - - +
1638A ALA 3.0 9.4 + - - -
1640A TYR* 1.3 79.1 - - - +
1642A ALA* 1.3 56.8 + - - +
1643A ASN 3.1 2.9 + - - +
1646A TYR* 3.7 4.3 - - - +
1647A SER* 2.9 26.2 + - - -
1657A VAL* 4.2 8.5 - - - -
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Residues in contact with ALA1642 (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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1559A CYS* 3.9 10.5 - - - -
1562A PHE* 3.6 33.3 - - + -
1638A ALA 2.8 16.6 + - - +
1639A ASN* 3.1 8.6 + - - +
1641A SER* 1.3 69.4 - - - +
1643A ASN* 1.3 57.6 + - - +
1644A ASP* 3.4 0.9 + - - +
1647A SER* 3.1 9.2 - - - -
1655A LYS* 2.5 32.7 + - - +
1657A VAL* 4.5 0.9 - - + +
1718A PHE* 4.3 12.1 - - + -
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Residues in contact with ASN1643 (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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1639A ASN 3.4 5.3 + - - +
1640A TYR 3.4 17.1 + - - +
1641A SER 3.1 0.6 - - - -
1642A ALA* 1.3 75.3 - - - +
1644A ASP* 1.3 75.5 + - - +
1645A THR* 2.7 31.9 + - - +
1646A TYR* 2.9 21.0 + - + +
1647A SER* 2.8 27.5 + - - -
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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