Contacts of the helix formed by residues 1572 - 1588 (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 ASN1572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1534B GLN* 2.8 27.2 + - - -
1535B ASN 3.3 13.6 + - - +
1536B PHE* 3.8 7.4 - - + +
1570B ILE* 4.7 2.5 - - + -
1571B GLN* 1.3 74.5 - - - +
1573B PRO* 1.3 61.2 - - - +
1574B ASP 3.4 3.8 + - - -
1575B LEU* 3.0 26.7 + - + +
1576B TRP* 2.8 30.6 + - - +
1612B ASN 3.1 23.4 + - - +
1613B ARG* 3.1 13.9 + - - +
1711B TYR* 2.9 18.2 + - + +
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Residues in contact with PRO1573 (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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1535B ASN 3.8 11.2 - - - +
1536B PHE* 5.2 0.2 - - - -
1571B GLN* 3.8 9.0 - - + +
1572B ASN* 1.3 86.6 - - - +
1574B ASP* 1.3 69.6 + - - +
1576B TRP* 3.4 6.5 + - + +
1577B ASN* 2.9 37.2 + - - +
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Residues in contact with ASP1574 (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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1532B LYS* 2.9 29.6 + - - +
1533B GLN* 3.4 3.8 + - - +
1534B GLN* 3.1 37.4 + - + -
1535B ASN 4.7 1.0 + - - -
1572B ASN* 3.3 2.0 + - - -
1573B PRO* 1.3 84.4 - - - +
1575B LEU* 1.3 58.2 + - - +
1577B ASN* 3.3 9.1 + - - +
1578B SER* 3.0 33.6 + - - +
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Residues in contact with LEU1575 (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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1534B GLN* 4.0 13.8 - - - +
1572B ASN* 3.0 28.6 + - + +
1574B ASP* 1.3 79.1 - - - +
1576B TRP* 1.3 55.5 + - - +
1578B SER* 3.6 2.7 + - - -
1579B TYR* 3.0 28.1 + - + +
1612B ASN 4.3 5.4 - - - +
1613B ARG 4.0 7.9 - - - +
1614B ASN 4.0 11.4 - - - +
1615B GLY* 3.5 27.4 - - - +
1708B TYR* 3.6 35.7 - - + -
1710B ALA 5.2 4.3 - - - +
1711B TYR* 3.9 11.9 - - + -
1712B PRO* 3.9 19.5 - - + -
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Residues in contact with TRP1576 (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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1572B ASN 2.8 18.4 + - - +
1573B PRO* 3.7 8.1 - - + +
1575B LEU* 1.3 75.1 - - - +
1577B ASN* 1.3 71.4 + - - +
1579B TYR* 3.2 6.2 + + - +
1580B GLN* 2.8 71.2 + - + +
1661B ARG* 3.8 33.7 - - - -
1711B TYR* 3.5 45.4 - + + +
1713B GLU* 4.8 8.5 - - + -
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Residues in contact with ASN1577 (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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1573B PRO* 2.9 32.5 + - - +
1574B ASP* 3.8 8.1 + - - +
1576B TRP* 1.3 85.5 - - - +
1578B SER* 1.3 58.1 + - - +
1580B GLN* 3.4 6.4 + - - +
1581B ALA* 2.8 30.1 + - - +
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Residues in contact with SER1578 (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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1534B GLN* 5.1 1.4 + - - -
1574B ASP* 3.0 18.0 + - - +
1575B LEU 3.9 0.9 - - - -
1577B ASN* 1.3 75.5 - - - +
1579B TYR* 1.3 62.9 + - - +
1581B ALA* 3.3 7.4 + - - +
1582B LYS* 3.2 23.2 + - - +
1708B TYR* 3.4 44.8 + - - +
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Residues in contact with TYR1579 (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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1575B LEU* 3.0 20.5 + - + +
1576B TRP* 3.5 9.2 - + - +
1578B SER* 1.3 76.8 - - - +
1580B GLN* 1.3 82.8 + - + +
1582B LYS* 3.3 5.7 - - - +
1583B LYS* 2.9 26.4 + - + +
1596B GLU* 2.6 36.5 + - - +
1661B ARG* 3.3 30.9 - - + +
1662B VAL 3.9 0.2 + - - -
1663B LEU* 3.5 31.9 - - + +
1708B TYR* 3.5 25.7 - - - +
1709B GLN 3.6 9.6 - - - -
1710B ALA 3.9 12.8 - - - +
1711B TYR* 3.9 16.6 - - + -
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Residues in contact with GLN1580 (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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1576B TRP* 2.8 73.2 + - + +
1577B ASN* 3.8 6.5 - - - +
1579B TYR* 1.3 91.7 - - - +
1581B ALA* 1.3 59.5 + - - +
1583B LYS* 3.5 21.7 - - - +
1584B LYS* 2.9 30.1 + - - +
1596B GLU* 4.8 2.2 + - - -
1661B ARG* 5.3 1.2 - - - +
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Residues in contact with ALA1581 (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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1577B ASN 2.8 20.8 + - - +
1578B SER* 3.7 7.4 - - - +
1580B GLN* 1.3 73.5 - - - +
1582B LYS* 1.3 61.2 + - - +
1584B LYS* 3.6 9.1 - - - +
1585B THR* 3.2 30.6 + - + +
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Residues in contact with LYS1582 (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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1578B SER 3.2 8.0 + - - +
1579B TYR 3.3 10.1 - - - +
1581B ALA* 1.3 77.3 - - - +
1583B LYS* 1.3 65.1 + - - +
1585B THR* 3.1 11.1 + - - +
1586B MET* 3.0 29.9 + - + +
1663B LEU* 3.7 13.7 - - + -
1706B TYR* 5.4 7.3 - - + +
1707B ASP 4.0 13.1 + - - +
1708B TYR* 3.8 37.4 - - + +
1709B GLN* 4.9 4.0 - - + +
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Residues in contact with LYS1583 (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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1579B TYR* 2.9 17.1 + - + +
1580B GLN* 3.2 27.8 + - - +
1582B LYS* 1.3 75.5 - - - +
1584B LYS* 1.3 54.6 + - - +
1586B MET* 3.0 4.2 + - - +
1587B ASP* 2.7 66.2 + - - +
1596B GLU* 3.6 43.7 - - - +
1663B LEU* 3.7 22.6 - - + +
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Residues in contact with LYS1584 (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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1580B GLN 2.9 16.2 + - - +
1581B ALA* 3.6 9.6 - - - +
1583B LYS* 1.3 76.0 - - - +
1585B THR* 1.3 65.4 + - + +
1587B ASP* 3.3 7.2 + - - +
1588B ALA* 3.1 23.3 + - - +
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Residues in contact with THR1585 (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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1581B ALA 3.2 14.0 + - - +
1582B LYS* 3.1 18.7 + - - +
1584B LYS* 1.3 79.4 - - + +
1586B MET* 1.3 60.5 + - - +
1588B ALA* 3.4 15.2 + - - +
1589B LYS* 3.4 15.0 + - - +
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Residues in contact with MET1586 (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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1582B LYS* 3.0 19.2 + - + +
1583B LYS* 3.0 6.9 + - - +
1585B THR* 1.3 74.3 + - - +
1587B ASP* 1.3 61.4 + - - +
1589B LYS* 3.1 10.2 + - - +
1590B ASN* 3.0 41.1 + - - +
1595B ASN* 3.3 18.5 + - + +
1663B LEU* 3.6 37.7 - - + +
1665B GLY* 3.6 29.8 - - - -
1690B ASP* 4.0 19.7 - - + +
1709B GLN* 4.5 6.1 - - - +
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Residues in contact with ASP1587 (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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1583B LYS* 2.7 56.1 + - - +
1584B LYS* 3.7 7.0 + - - +
1586B MET* 1.3 72.7 - - - +
1588B ALA* 1.3 59.8 + - - +
1589B LYS 3.2 1.0 + - - -
1590B ASN 4.0 4.5 + - - -
1591B GLY* 4.2 14.0 + - - +
1593B THR 5.0 0.5 - - - +
1595B ASN* 2.6 39.8 + - - +
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Residues in contact with ALA1588 (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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1584B LYS* 3.1 15.6 + - + +
1585B THR* 3.6 9.0 - - - +
1586B MET 3.2 0.6 - - - -
1587B ASP* 1.3 75.2 - - - +
1589B LYS* 1.3 57.2 + - - +
1591B GLY 5.2 0.6 + - - -
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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