Contacts of the helix formed by residues 1578 - 1588 (chain A) in PDB entry 5G04
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 ASN1578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1307A LEU* 3.5 32.5 + - + +
1308A GLY* 5.2 4.0 + - - -
1376A LEU* 3.6 29.2 + - - +
1377A LYS* 4.1 20.4 - - - +
1576A THR 4.0 0.2 - - - -
1577A SER* 1.3 77.7 + - - +
1579A SER* 1.3 64.0 + - - +
1580A SER 3.2 1.6 - - - -
1581A ILE* 3.2 21.9 + - - +
1582A ALA 3.7 3.3 + - - -
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Residues in contact with SER1579 (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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1217A LEU* 4.6 14.2 - - - +
1262A GLN* 3.7 21.1 + - - +
1307A LEU* 3.5 20.2 - - - +
1577A SER* 3.3 3.3 + - - -
1578A ASN* 1.3 76.7 - - - +
1580A SER* 1.3 60.2 + - - +
1582A ALA* 3.0 23.3 - - - +
1583A ALA* 3.4 5.4 + - - +
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Residues in contact with SER1580 (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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1575A SER* 2.4 33.0 + - - -
1576A THR* 3.3 1.8 - - - -
1577A SER* 2.9 18.1 + - - -
1579A SER* 1.3 76.5 - - - +
1581A ILE* 1.3 63.0 + - - +
1582A ALA 3.2 0.2 - - - -
1583A ALA* 3.1 9.9 + - - +
1584A LEU* 3.0 23.3 + - - +
1612A LEU 4.6 4.9 - - - -
1613A ALA* 3.1 25.7 + - - +
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Residues in contact with ILE1581 (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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1376A LEU* 4.3 15.7 - - + -
1377A LYS* 4.2 6.1 - - - -
1413A LEU* 3.9 15.7 - - + -
1416A TRP* 3.3 36.3 - - + -
1474A PHE* 4.0 21.1 - - + +
1576A THR* 3.0 33.8 + - - +
1577A SER 4.1 7.4 - - - +
1578A ASN 3.2 7.7 + - - +
1580A SER* 1.3 74.8 - - - +
1582A ALA* 1.3 64.7 + - - +
1584A LEU* 3.4 8.8 + - + +
1585A LEU* 2.9 41.6 + - + +
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Residues in contact with ALA1582 (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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1262A GLN* 2.8 35.0 - - - +
1304A MET* 4.1 3.4 - - + -
1307A LEU* 3.8 13.2 - - + -
1373A MET* 3.6 22.6 - - + +
1578A ASN 3.7 3.4 + - - -
1579A SER 3.0 10.0 + - - +
1581A ILE* 1.3 79.5 - - - +
1583A ALA* 1.3 57.2 + - - +
1585A LEU* 3.3 6.6 + - - +
1586A CYS* 2.8 26.2 + - - -
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Residues in contact with ALA1583 (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 SER 3.4 4.1 + - - +
1580A SER* 3.1 11.3 + - - +
1582A ALA* 1.3 75.9 - - - +
1584A LEU* 1.3 64.9 + - - +
1586A CYS* 3.7 5.6 + - - +
1587A ALA* 3.4 20.6 + - - +
1609A LEU* 3.7 33.6 - - + +
1612A LEU* 3.7 28.9 - - + -
1613A ALA* 3.8 9.9 - - - +
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Residues in contact with LEU1584 (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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1474A PHE* 3.5 22.7 - - + -
1477A ALA* 4.1 11.2 - - + -
1525A MET* 3.8 22.9 - - - -
1564A LEU* 6.1 1.1 - - + -
1574A LEU* 3.8 29.2 - - + -
1575A SER 5.2 5.4 - - - +
1580A SER* 3.0 10.7 + - - +
1581A ILE* 3.6 9.6 - - + +
1582A ALA 3.4 0.2 - - - -
1583A ALA* 1.3 77.2 - - - +
1585A LEU* 1.3 53.7 + - - +
1587A ALA* 3.1 3.5 + - - -
1588A LEU* 2.6 59.3 + - + +
1610A TYR* 4.9 7.0 - - + -
1613A ALA* 3.6 25.8 - - + +
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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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1300A LEU* 4.5 3.9 - - + +
1369A LEU* 3.7 26.7 - - + +
1372A ALA* 4.9 3.8 - - + -
1373A MET* 3.7 35.2 - - + -
1376A LEU* 5.6 0.2 - - + -
1409A LEU* 3.6 26.5 - - + -
1413A LEU* 4.0 11.4 - - + -
1474A PHE* 3.4 25.1 - - + -
1581A ILE* 2.9 28.4 + - + +
1582A ALA 3.3 4.9 + - - +
1584A LEU* 1.3 76.0 - - - +
1586A CYS* 1.3 58.8 + - - +
1588A LEU 3.8 1.2 - - - +
1589A TYR* 3.1 31.2 + - - +
1590A PRO* 6.4 0.9 - - + -
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Residues in contact with CYS1586 (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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1300A LEU* 3.7 21.1 - - + -
1304A MET* 3.4 32.3 - - - -
1582A ALA 2.8 28.0 - - - -
1583A ALA* 3.9 7.6 - - - +
1584A LEU 3.3 0.2 - - - -
1585A LEU* 1.3 77.7 - - - +
1587A ALA* 1.3 61.1 + - - +
1589A TYR 3.9 0.5 + - - -
1602A HIS* 2.9 31.6 + - - -
1606A LEU* 3.8 26.0 - - + -
1609A LEU* 4.4 10.5 - - + -
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Residues in contact with ALA1587 (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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1560A MET* 4.1 8.2 - - - +
1583A ALA 3.4 11.2 + - - +
1584A LEU* 3.1 7.9 + - - +
1586A CYS* 1.3 77.1 - - - +
1588A LEU* 1.3 71.6 + - + +
1589A TYR 3.4 0.4 - - - -
1606A LEU 3.7 11.3 + - - +
1607A ARG* 3.0 52.1 + - - +
1610A TYR* 3.8 19.1 - - + +
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Residues in contact with LEU1588 (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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1086A MET* 5.2 0.4 - - + -
1470A LEU* 4.4 13.4 - - + +
1474A PHE* 4.1 11.7 - - + -
1518A VAL* 5.4 0.2 - - - +
1521A LEU* 4.8 23.4 - - + +
1525A MET* 3.5 36.8 - - + -
1560A MET* 4.6 12.1 - - - -
1564A LEU* 4.4 20.0 - - + -
1584A LEU* 2.6 50.1 + - + +
1585A LEU* 3.8 3.1 - - - -
1587A ALA* 1.3 86.4 - - + +
1589A TYR* 1.3 65.5 + - - +
1590A PRO* 3.3 8.3 - - - +
1592A PHE* 5.7 0.2 - - - -
1607A ARG* 4.8 0.4 - - - +
1610A TYR* 5.2 3.4 - - + -
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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