Contacts of the helix formed by residues 1572 - 1590 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D GOL 3.8 2.3 - - - -
1534D GLN* 3.0 22.1 + - - -
1535D ASN 3.4 13.6 + - - +
1536D PHE* 3.8 7.9 - - + +
1570D ILE* 4.7 2.5 - - + -
1571D GLN* 1.3 74.7 - - - +
1573D PRO* 1.3 59.5 - - - +
1574D ASP 3.5 1.0 + - - -
1575D LEU* 3.0 26.1 + - + +
1576D TRP* 2.8 29.3 + - - +
1612D ASN 3.0 19.5 + - - +
1613D ARG 2.9 28.3 + - - -
1711D TYR* 2.8 16.5 + - + +
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Residues in contact with PRO1573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GOL 3.6 18.6 - - - +
1535D ASN 3.8 12.3 - - - +
1536D PHE* 5.0 0.2 - - - -
1537D CYS* 6.5 0.4 - - - -
1571D GLN* 3.6 8.7 - - + +
1572D ASN* 1.3 85.8 - - - +
1574D ASP* 1.3 60.4 + - - +
1576D TRP* 3.6 2.8 - - + +
1577D ASN* 2.8 41.6 + - - +
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Residues in contact with ASP1574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532D LYS* 3.3 15.1 + - - +
1533D GLN* 3.1 15.8 + - - +
1534D GLN* 3.0 42.4 + - + +
1535D ASN 4.9 0.6 + - - -
1572D ASN* 3.3 1.6 + - - -
1573D PRO* 1.3 81.7 - - - +
1575D LEU* 1.3 65.9 + - - +
1577D ASN* 3.2 11.3 + - - +
1578D SER* 3.0 27.5 + - - +
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Residues in contact with LEU1575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534D GLN* 4.0 12.2 - - - +
1572D ASN* 3.0 28.9 + - + +
1574D ASP* 1.3 76.4 - - - +
1576D TRP* 1.3 57.6 + - - +
1578D SER* 3.4 2.5 + - - -
1579D TYR* 2.9 28.7 + - + +
1611D VAL 4.3 3.8 - - - +
1612D ASN 4.5 1.6 - - - +
1613D ARG 4.1 8.1 - - - +
1614D ASN 3.9 14.1 - - - +
1615D GLY* 3.6 22.0 - - - +
1707D ASP 5.1 1.8 - - - +
1708D TYR* 3.7 30.3 - - + -
1710D ALA 5.2 5.2 - - - +
1711D TYR* 3.9 11.4 - - + -
1712D PRO* 3.9 25.1 - - + -
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Residues in contact with TRP1576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GOL 3.7 35.3 - - - +
1572D ASN 2.8 17.3 + - - +
1573D PRO* 3.6 7.4 - - + +
1575D LEU* 1.3 75.8 - - - +
1577D ASN* 1.3 69.6 + - - +
1579D TYR* 3.4 9.0 + + - +
1580D GLN* 2.9 72.7 + - + +
1661D ARG* 4.3 26.0 - - - -
1711D TYR* 3.5 41.2 - + + -
1713D GLU* 5.2 5.8 - - - -
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Residues in contact with ASN1577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1573D PRO* 2.8 32.8 + - - +
1574D ASP* 3.2 12.7 + - - +
1576D TRP* 1.3 84.1 - - - +
1578D SER* 1.3 58.0 + - - +
1580D GLN* 3.5 6.3 + - - +
1581D ALA* 3.0 28.4 + - - +
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Residues in contact with SER1578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A SER* 6.3 0.2 - - - -
1534D GLN* 4.5 3.3 + - - -
1574D ASP* 3.0 16.9 + - - +
1575D LEU 3.7 2.0 - - - -
1577D ASN* 1.3 74.6 - - - +
1579D TYR* 1.3 66.1 + - - +
1581D ALA* 3.4 7.1 + - - +
1582D LYS* 3.2 25.6 + - - +
1708D TYR* 3.5 39.3 - - - +
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Residues in contact with TYR1579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575D LEU* 2.9 19.5 + - + +
1576D TRP* 3.6 10.1 - + - +
1578D SER* 1.3 75.5 - - - +
1580D GLN* 1.3 79.1 + - - +
1582D LYS* 3.0 8.7 + - - +
1583D LYS* 2.8 28.4 + - + +
1596D GLU* 2.8 37.2 + - - +
1661D ARG* 3.3 39.5 + - + +
1662D VAL 3.8 0.2 + - - -
1663D LEU* 3.6 19.9 - - + +
1708D TYR* 3.4 24.5 + - + +
1709D GLN 3.5 14.8 - - - -
1710D ALA 3.9 1.8 - - - +
1711D TYR* 3.8 27.8 - - + -
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Residues in contact with GLN1580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576D TRP* 2.9 69.4 + - + +
1577D ASN* 3.8 7.4 - - - +
1579D TYR* 1.3 94.3 - - - +
1581D ALA* 1.3 56.2 + - - +
1583D LYS* 3.6 23.0 + - - +
1584D LYS* 2.9 29.6 + - - +
1596D GLU* 4.6 2.0 + - - -
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Residues in contact with ALA1581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1577D ASN 3.0 17.9 + - - +
1578D SER* 3.7 8.5 - - - +
1579D TYR 3.2 0.2 - - - -
1580D GLN* 1.3 72.1 - - - +
1582D LYS* 1.3 67.2 + - + +
1584D LYS* 3.4 10.1 + - - +
1585D THR* 3.2 25.5 + - - -
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Residues in contact with LYS1582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1544A SER* 2.6 47.5 + - - +
1546A PRO* 5.0 4.2 - - - +
1549A ASN* 5.3 4.2 - - - +
1578D SER 3.2 12.5 + - - +
1579D TYR 3.0 8.6 + - - +
1581D ALA* 1.3 75.5 - - + +
1583D LYS* 1.3 66.9 + - - +
1585D THR* 3.3 8.9 + - - +
1586D MET* 3.0 27.1 + - + +
1663D LEU* 3.6 15.5 - - + -
1706D TYR* 6.2 4.3 - - - -
1708D TYR* 3.8 29.2 - - + +
1709D GLN* 5.3 1.1 - - - -
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Residues in contact with LYS1583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579D TYR* 2.8 18.3 + - + +
1580D GLN* 3.2 29.3 + - - +
1582D LYS* 1.3 74.3 - - - +
1584D LYS* 1.3 52.1 + - - +
1586D MET* 3.3 1.5 + - - +
1587D ASP* 2.7 69.8 + - - +
1595D ASN* 5.6 0.4 - - - +
1596D GLU* 3.8 42.6 - - - +
1663D LEU* 3.5 24.3 - - + +
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Residues in contact with LYS1584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1580D GLN 2.9 16.5 + - - +
1581D ALA* 3.9 9.6 - - - +
1582D LYS 3.2 0.2 - - - -
1583D LYS* 1.3 78.1 - - - +
1585D THR* 1.3 62.9 + - - +
1587D ASP* 3.3 7.6 + - + +
1588D ALA* 3.0 25.2 + - + +
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Residues in contact with THR1585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1581D ALA 3.2 13.0 + - - -
1582D LYS* 3.7 13.8 - - + +
1584D LYS* 1.3 78.3 - - - +
1586D MET* 1.3 64.5 + - - +
1588D ALA* 3.2 15.4 + - - +
1589D LYS* 3.2 15.6 + - + +
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Residues in contact with MET1586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1582D LYS* 3.0 17.7 + - + +
1583D LYS* 3.7 5.4 - - - +
1585D THR* 1.3 78.1 - - - +
1587D ASP* 1.3 57.0 + - - +
1589D LYS* 3.0 12.4 + - - +
1590D ASN* 3.0 46.7 + - - +
1595D ASN* 3.3 16.4 + - + +
1663D LEU* 3.9 37.5 - - + +
1665D GLY* 3.8 15.7 - - - -
1690D ASP* 3.5 33.9 - - + +
1706D TYR* 6.5 0.4 - - + -
1709D GLN* 4.5 6.5 - - + +
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Residues in contact with ASP1587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1583D LYS* 2.7 57.1 + - - +
1584D LYS* 3.7 7.9 - - - +
1586D MET* 1.3 73.3 - - - +
1588D ALA* 1.3 60.6 + - - +
1589D LYS 3.2 0.7 + - - -
1590D ASN 4.0 5.0 + - - -
1591D GLY* 4.2 13.3 + - - +
1593D THR 4.8 1.7 - - - +
1595D ASN* 2.5 38.8 + - - +
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Residues in contact with ALA1588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1584D LYS* 3.0 18.0 + - + +
1585D THR* 3.2 8.0 + - - +
1587D ASP* 1.3 75.6 - - - +
1589D LYS* 1.3 57.6 + - - +
1591D GLY 5.2 0.4 - - - -
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Residues in contact with LYS1589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1585D THR* 3.2 11.7 + - + +
1586D MET* 3.0 14.3 + - - +
1588D ALA* 1.3 79.9 - - - +
1590D ASN* 1.3 82.8 + - - +
1591D GLY 3.4 3.7 + - - -
1680D LYS* 4.7 13.5 - - - +
1687D ASP* 5.0 11.7 + - - +
1688D LEU 4.5 8.5 + - - -
1690D ASP* 2.8 30.0 + - - -
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Residues in contact with ASN1590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1586D MET* 3.0 22.4 + - - +
1587D ASP 4.0 1.3 + - - -
1589D LYS* 1.3 101.0 - - - +
1591D GLY* 1.3 63.4 + - - +
1592D GLN* 3.2 2.8 + - - +
1593D THR* 2.8 33.9 + - - +
1595D ASN* 2.7 31.6 + - - +
1665D GLY* 3.8 2.6 - - - -
1666D ILE* 3.3 23.9 - - + +
1680D LYS* 4.9 0.2 + - - -
1690D ASP* 3.0 23.4 + - - -
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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