Contacts of the helix formed by residues 1545 - 1560 (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 ASP1545 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1541A LEU* 4.4 15.2 - - + +
1542A LEU* 2.9 24.1 + - + +
1544A SER* 1.3 78.7 + - - +
1546A PRO* 1.4 79.0 - - - +
1547A GLU* 3.1 23.7 + - - +
1548A TYR* 2.9 23.3 + - + +
1549A ASN* 3.2 7.9 + - - -
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Residues in contact with PRO1546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A SER 3.5 8.5 - - - +
1545A ASP* 1.4 89.5 - - - +
1547A GLU* 1.3 56.4 + - - +
1549A ASN* 3.2 14.2 + - + +
1550A THR* 2.9 32.4 + - - +
1582D LYS* 5.0 3.1 - - - +
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Residues in contact with GLU1547 (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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1541A LEU* 4.0 14.2 - - + +
1545A ASP* 3.1 16.1 + - - +
1546A PRO* 1.3 74.9 - - - +
1548A TYR* 1.3 67.4 + - - +
1550A THR* 3.4 6.5 + - - -
1551A VAL* 3.1 29.8 + - + +
1569A ARG* 2.6 36.7 + - - -
1714A TYR* 2.5 34.9 + - + +
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Residues in contact with TYR1548 (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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1541A LEU* 3.6 32.7 - - + +
1542A LEU 3.2 22.0 - - - +
1543A PRO* 3.7 17.5 - - + -
1545A ASP* 2.9 7.3 + - + +
1547A GLU* 1.3 80.8 - - - +
1549A ASN* 1.3 73.3 + - - +
1551A VAL 3.3 0.2 + - - -
1552A ALA* 2.8 44.7 + - + +
1564A ILE* 3.3 15.3 - - + +
1567A ILE* 3.4 39.1 - - + +
1721A GOL 4.3 7.0 - - - -
1618D ARG* 2.5 50.3 + - + +
1707D ASP* 5.4 1.1 - - - -
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Residues in contact with ASN1549 (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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1543A PRO 3.6 13.5 + - - +
1544A SER 4.8 3.0 + - - -
1545A ASP 3.2 12.1 + - - -
1546A PRO* 3.2 15.3 + - + +
1548A TYR* 1.3 88.0 - - - +
1550A THR* 1.3 56.3 + - - +
1553A SER* 2.9 27.5 + - - -
1721A GOL 3.0 35.8 + - - +
1582D LYS* 5.3 4.8 - - - +
1676D VAL* 4.5 0.4 - - - +
1706D TYR* 3.5 35.5 - - + +
1707D ASP 5.3 0.3 + - - -
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Residues in contact with THR1550 (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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1546A PRO* 2.9 17.6 + - - +
1547A GLU* 3.8 8.1 - - - -
1549A ASN* 1.3 75.5 - - - +
1551A VAL* 1.3 64.2 + - + +
1553A SER* 2.4 26.2 + - - +
1554A LYS* 3.1 32.4 + - + +
1659A TYR* 6.4 0.4 - - + -
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Residues in contact with VAL1551 (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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1541A LEU* 4.8 0.2 - - + -
1547A GLU* 3.1 18.2 + - + +
1548A TYR 3.9 2.0 - - - +
1550A THR* 1.3 77.6 - - + +
1552A ALA* 1.3 63.0 + - - +
1554A LYS* 3.0 18.8 + - - +
1555A PHE* 3.2 12.5 + - - +
1567A ILE* 4.0 25.6 - - + -
1600A PHE* 5.5 0.2 - - - -
1659A TYR* 4.1 16.8 - - + -
1714A TYR* 3.7 52.9 - - + +
1716A ILE* 4.1 13.2 - - + +
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Residues in contact with ALA1552 (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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1548A TYR* 2.8 33.4 + - + +
1551A VAL* 1.3 72.4 - - - +
1553A SER* 1.3 56.5 + - - +
1555A PHE* 3.5 4.1 + - - +
1556A ASN* 2.9 33.8 + - - +
1564A ILE* 3.8 19.7 - - + -
1567A ILE* 3.5 17.1 - - + +
1721A GOL 3.5 22.2 - - - -
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Residues in contact with SER1553 (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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1549A ASN 2.9 17.3 + - - -
1550A THR* 2.4 28.9 + - - +
1552A ALA* 1.3 77.6 - - - +
1554A LYS* 1.3 69.5 + - - +
1556A ASN 3.4 0.2 + - - -
1557A GLN* 3.2 12.1 + - - +
1721A GOL 3.3 10.3 - - - -
1675D ILE* 3.1 22.3 - - - +
1676D VAL* 3.2 33.1 - - - +
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Residues in contact with LYS1554 (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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1550A THR* 3.1 32.3 + - + +
1551A VAL 3.0 5.5 + - - +
1553A SER* 1.3 79.8 + - - +
1555A PHE* 1.3 66.9 + - - +
1557A GLN* 3.6 15.9 + - - +
1558A THR* 4.7 1.0 + - - -
1598A GLN* 5.9 1.1 - - - -
1600A PHE* 3.6 17.2 - - + -
1638A ALA* 4.9 0.9 + - - +
1659A TYR* 3.3 45.1 - - + +
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Residues in contact with PHE1555 (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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1551A VAL 3.2 8.2 + - - +
1552A ALA* 3.6 8.3 - - - +
1554A LYS* 1.3 80.0 - - - +
1556A ASN* 1.3 69.1 + - - +
1557A GLN 3.1 1.4 + - - -
1558A THR 3.4 2.9 + - - -
1559A CYS* 3.0 63.3 + - + +
1562A PHE* 4.3 7.2 - + + -
1564A ILE* 4.1 22.0 - - + -
1600A PHE* 3.7 11.0 - + + -
1638A ALA* 3.7 19.1 - - + +
1657A VAL* 4.3 12.3 - - + -
1716A ILE* 3.8 28.7 - - + -
1718A PHE* 3.8 46.2 - + - -
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Residues in contact with ASN1556 (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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1552A ALA 2.9 18.6 + - - +
1553A SER 3.8 1.1 - - - +
1554A LYS 3.4 0.4 - - - -
1555A PHE* 1.3 84.5 - - - +
1557A GLN* 1.3 66.2 + - - +
1558A THR* 3.0 4.5 + - - -
1559A CYS 3.6 1.5 - - - +
1560A SER* 3.4 34.1 + - - +
1562A PHE 5.0 2.6 - - - +
1564A ILE* 3.8 13.8 - - - +
1721A GOL 2.9 35.8 + - - +
1630D LYS* 5.2 0.2 - - - -
1675D ILE* 3.4 33.8 - - + +
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Residues in contact with GLN1557 (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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1553A SER 3.2 9.1 + - - +
1554A LYS* 3.6 15.7 - - - +
1555A PHE 3.1 1.4 - - - -
1556A ASN* 1.3 76.0 - - - +
1558A THR* 1.3 68.2 + - + +
1637A ASN* 5.7 2.5 - - - +
1630D LYS* 4.9 10.6 - - - -
1673D SER* 3.1 34.5 + - - +
1674D LEU* 5.6 0.2 - - - -
1675D ILE* 3.6 22.0 + - - +
1676D VAL* 5.8 0.5 - - - +
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Residues in contact with THR1558 (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 4.7 1.1 + - - -
1555A PHE 3.4 1.5 + - - -
1557A GLN* 1.3 91.3 - - + +
1559A CYS* 1.3 57.8 + - - +
1560A SER* 3.7 2.2 - - - -
1561A HIS* 3.3 16.7 + - - -
1637A ASN* 3.8 28.2 - - + +
1638A ALA* 3.1 28.8 + - - +
1639A ASN* 3.2 27.5 + - - +
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Residues in contact with CYS1559 (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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1555A PHE* 3.0 38.4 + - + +
1556A ASN* 3.9 5.3 - - - +
1558A THR* 1.3 76.5 - - - +
1560A SER* 1.3 61.8 + - - +
1561A HIS* 3.1 9.2 - - - -
1562A PHE* 3.1 25.6 + - + +
1638A ALA* 3.5 15.5 - - - -
1639A ASN* 3.3 39.3 - - - -
1642A ALA* 3.9 14.1 - - - -
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Residues in contact with SER1560 (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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1556A ASN* 3.4 32.1 + - - -
1558A THR 3.7 1.7 - - - -
1559A CYS* 1.3 76.4 - - - +
1561A HIS* 1.3 63.4 + - - +
1562A PHE 3.2 8.9 - - - +
1563A ARG* 6.0 0.2 - - - -
1630D LYS* 3.2 28.8 - - - +
1675D ILE* 3.8 13.7 - - - -
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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