Contacts of the helix formed by residues 1577 - 1588 (chain A) in PDB entry 3PPX
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 ASN1577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1542A TYR* 3.5 13.6 - - + +
1543A SER 3.0 18.7 + - - +
1544A TYR* 2.9 29.8 + - - +
1545A MET* 5.9 0.4 - - - -
1546A VAL* 4.8 0.6 - - + +
1575A ARG* 3.8 15.8 - - - +
1576A THR* 1.3 67.1 - - - +
1578A THR* 1.3 62.9 + - - +
1579A GLY 3.3 2.9 - - - -
1580A LEU* 3.2 16.4 + - + +
1581A ALA 3.2 16.3 + - - -
1613A SER* 3.5 19.9 - - - -
1614A ASP* 3.4 23.3 - - - +
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Residues in contact with THR1578 (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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1542A TYR* 3.0 27.5 + - - +
1576A THR* 3.0 17.1 + - - +
1577A ASN* 1.3 73.4 - - - +
1579A GLY* 1.3 58.6 + - - +
1581A ALA* 3.2 3.4 + - - +
1582A LEU* 3.0 34.7 + - + +
1606A MET* 3.7 36.1 - - + -
1608A THR* 4.5 4.8 + - + +
1610A ASN 5.0 0.5 + - - -
1612A ALA* 3.8 19.3 + - + +
1614A ASP* 3.2 0.8 + - - -
1616A ILE* 4.5 0.7 - - + -
1639A LEU* 5.9 0.7 - - + -
1642A ILE* 4.6 9.6 - - + -
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Residues in contact with GLY1579 (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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1578A THR* 1.3 79.1 - - - +
1580A LEU* 1.3 55.0 + - - +
1582A LEU* 3.4 7.6 + - - +
1583A ARG* 3.1 25.6 + - - +
1614A ASP* 2.9 15.5 + - - -
1615A GLU 3.4 22.0 - - - -
1616A ILE* 3.8 13.2 - - - +
1617A LYS 5.3 1.5 + - - -
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Residues in contact with LEU1580 (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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1544A TYR 4.2 18.8 - - - +
1545A MET* 4.3 8.1 - - + -
1546A VAL* 3.8 19.5 - - + +
1577A ASN* 3.2 15.9 + - + +
1579A GLY* 1.3 72.8 - - - +
1581A ALA* 1.3 66.7 + - - +
1583A ARG* 3.2 38.0 + - - +
1584A TYR* 3.0 44.2 + - + -
1614A ASP* 2.9 12.2 + - - +
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Residues in contact with ALA1581 (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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1502A VAL* 4.1 14.1 - - + -
1540A LEU* 4.4 2.0 - - + +
1542A TYR* 3.8 37.7 - - + -
1546A VAL* 3.7 14.5 - - + +
1577A ASN 3.2 6.0 + - - +
1578A THR* 3.2 10.3 + - - +
1580A LEU* 1.3 76.9 - - - +
1582A LEU* 1.3 59.5 + - - +
1584A TYR* 3.3 7.9 + - - +
1585A LEU* 3.3 26.2 + - - +
1606A MET* 5.2 3.1 - - - -
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Residues in contact with LEU1582 (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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1578A THR* 3.0 20.3 + - + +
1579A GLY* 3.7 7.6 - - - +
1581A ALA* 1.3 74.8 - - - +
1583A ARG* 1.3 62.4 + - - +
1585A LEU* 3.1 24.4 + - + +
1586A SER 3.2 3.8 + - - -
1606A MET* 4.1 19.5 - - - -
1616A ILE* 4.4 12.3 - - + -
1617A LYS 4.1 18.6 - - - +
1618A ARG* 5.9 0.2 - - - -
1619A LEU* 3.2 45.8 - - + +
1625A VAL* 4.5 5.2 - - + -
1642A ILE* 4.0 41.3 - - + -
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Residues in contact with ARG1583 (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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1579A GLY 3.1 14.1 + - - +
1580A LEU* 3.2 37.7 + - + +
1582A LEU* 1.3 74.5 - - - +
1584A TYR* 1.3 60.1 + - + +
1586A SER* 3.2 5.8 + - - +
1587A ASP* 2.8 59.0 + - + +
1619A LEU* 5.0 0.4 - - - -
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Residues in contact with TYR1584 (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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1540A LEU* 4.0 11.9 - - + -
1545A MET* 5.5 2.6 - - - +
1546A VAL* 3.7 50.1 + - + -
1548A VAL* 4.3 21.5 - - + -
1580A LEU* 3.0 41.3 + - + -
1581A ALA 3.3 10.1 + - - +
1583A ARG* 1.3 78.0 - - + +
1585A LEU* 1.3 51.2 + - - +
1587A ASP* 5.3 0.2 - - - -
1588A HIS* 2.8 30.0 + + + +
1589A SER* 2.8 31.8 + - - -
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Residues in contact with LEU1585 (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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1500A ALA* 3.9 22.0 - - + -
1502A VAL* 3.9 25.4 - - + -
1540A LEU* 4.0 7.0 - - + -
1581A ALA 3.4 14.8 - - - +
1582A LEU* 3.1 28.8 + - + +
1584A TYR* 1.3 77.3 - - - +
1586A SER* 1.3 60.1 + - - +
1589A SER* 3.7 16.1 + - - +
1590A PHE* 3.2 47.7 + - + +
1604A VAL* 3.8 25.1 - - + -
1606A MET* 5.5 1.3 - - - -
1619A LEU* 4.2 10.3 - - + -
1623A ILE* 4.2 0.7 - - - -
1625A VAL* 5.2 0.2 - - + -
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Residues in contact with SER1586 (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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1582A LEU 3.2 6.2 + - - -
1583A ARG* 3.2 10.4 + - - +
1585A LEU* 1.3 80.3 - - - +
1587A ASP* 1.3 81.4 + - - +
1588A HIS 3.6 0.4 + - - -
1590A PHE* 5.3 1.7 - - - +
1591A LEU* 4.0 13.7 - - - +
1619A LEU* 3.7 20.9 - - - +
1620A PRO* 4.0 21.2 - - - +
1623A ILE* 3.6 13.4 - - - +
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Residues in contact with ASP1587 (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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1583A ARG* 2.8 35.7 + - + +
1584A TYR* 5.3 0.2 - - - -
1586A SER* 1.3 104.9 + - - +
1588A HIS* 1.3 61.7 + - - +
1591A LEU* 3.4 19.7 - - - +
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Residues in contact with HIS1588 (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 VAL* 4.0 29.7 - - + +
1551A PRO* 6.1 1.4 - - - +
1584A TYR* 2.8 29.3 + + + +
1586A SER 3.6 1.8 + - - -
1587A ASP* 1.3 80.4 + - - +
1589A SER* 1.3 72.2 + - - +
1590A PHE 3.4 1.6 - - - -
1591A LEU* 3.3 15.0 + - - +
1594A GLN* 3.2 59.9 + - + +
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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