Contacts of the helix formed by residues 1532 - 1546 (chain A) in PDB entry 5A31
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 ASN1532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A ARG* 3.8 5.7 + - - +
1485A PHE* 3.8 10.5 - - - -
1527A MET* 3.4 30.7 - - - +
1530A SER* 3.4 6.6 + - - +
1531A GLY* 1.3 75.5 - - - +
1533A LEU* 1.3 70.2 + - - +
1534A LYS* 2.6 27.5 + - - +
1535A VAL* 2.7 27.9 + - + +
1536A LEU* 2.9 12.0 + - - -
1565A LEU* 4.3 7.2 - - + +
1566A PHE* 4.5 0.8 - - - -
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Residues in contact with LEU1533 (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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1031A ASP* 5.6 10.5 - - + +
1033A ARG* 3.7 33.9 - - + +
1532A ASN* 1.3 71.2 - - - +
1534A LYS* 1.4 99.7 + - + +
1536A LEU* 4.2 14.8 - - + +
1537A GLN* 2.9 44.7 + - - +
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Residues in contact with LYS1534 (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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1485A PHE* 3.7 22.0 - - + -
1489A HIS* 3.8 34.0 - - + +
1493A LYS* 6.0 2.2 - - - +
1532A ASN* 2.6 22.1 + - - +
1533A LEU* 1.4 100.6 - - + +
1535A VAL* 1.3 61.6 + - - +
1537A GLN* 3.3 36.0 - - - +
1538A LEU* 3.4 9.2 + - - +
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Residues in contact with VAL1535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485A PHE* 4.1 4.3 - - + -
1489A HIS* 5.3 0.4 - - - -
1520A LEU* 4.5 6.1 - - + -
1523A LEU* 3.6 38.8 - - + -
1524A ALA* 4.4 9.4 - - + +
1527A MET* 3.7 24.2 - - + -
1532A ASN* 2.7 17.9 + - + +
1534A LYS* 1.3 70.5 - - - +
1536A LEU* 1.3 58.3 + - - +
1538A LEU* 3.1 12.5 - - - +
1539A CYS* 2.9 31.7 + - - -
1565A LEU* 3.6 30.5 - - + -
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Residues in contact with LEU1536 (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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1031A ASP* 5.7 0.4 - - - +
1033A ARG* 4.6 17.5 - - + +
1036A ASP* 5.9 4.5 - - + -
1037A VAL* 4.3 9.2 - - + +
1040A LEU* 4.1 26.0 - - + -
1532A ASN 2.9 13.0 + - - +
1533A LEU* 4.1 13.9 - - + +
1535A VAL* 1.3 75.7 - - - +
1537A GLN* 1.3 61.6 + - - +
1539A CYS* 3.1 4.5 + - - +
1540A ARG* 2.8 45.0 + - + +
1562A LEU* 4.3 4.7 - - + -
1565A LEU* 3.7 13.2 - - + +
1566A PHE* 3.8 32.3 - - + -
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Residues in contact with GLN1537 (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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1489A HIS* 5.8 0.8 - - - -
1533A LEU* 2.9 37.4 + - - +
1534A LYS* 3.3 40.2 + - - +
1536A LEU* 1.3 77.8 - - - +
1538A LEU* 1.3 63.3 + - + +
1540A ARG* 3.2 17.8 + - - +
1541A PHE* 3.0 24.6 + - - +
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Residues in contact with LEU1538 (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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1489A HIS* 4.3 17.0 - - + -
1492A ALA* 3.8 29.2 - - + -
1493A LYS* 5.5 1.3 - - + +
1496A MET* 3.6 31.6 - - + -
1516A LEU* 5.3 1.8 - - + -
1520A LEU* 3.9 11.7 - - + -
1523A LEU* 3.8 18.2 - - + -
1534A LYS 3.6 6.5 - - - +
1535A VAL* 3.1 13.6 + - - +
1537A GLN* 1.3 86.1 - - + +
1539A CYS* 1.3 57.4 + - - +
1541A PHE* 3.5 16.3 - - + +
1542A LEU* 3.5 18.5 + - + +
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Residues in contact with CYS1539 (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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1040A LEU* 5.2 0.7 - - - -
1520A LEU* 4.6 7.4 - - - -
1535A VAL* 2.9 21.2 + - - -
1536A LEU* 3.1 8.5 + - - +
1538A LEU* 1.3 72.7 - - - +
1540A ARG* 1.3 68.3 + - - +
1542A LEU* 3.5 9.9 + - - +
1543A HIS* 3.2 20.8 + - - +
1558A HIS* 4.1 8.7 - - - +
1559A HIS* 5.6 0.2 - - - -
1561A ALA* 3.9 16.4 - - - -
1562A LEU* 3.9 46.9 - - + -
1565A LEU* 4.3 10.1 - - - -
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Residues in contact with ARG1540 (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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1036A ASP* 4.5 26.7 + - - +
1040A LEU* 4.3 28.8 - - + +
1536A LEU* 2.8 29.3 + - + +
1537A GLN* 3.6 18.8 - - - +
1539A CYS* 1.3 75.9 - - - +
1541A PHE* 1.3 65.2 + - - +
1543A HIS* 2.8 21.3 + - - +
1544A MET* 2.9 48.6 + - + +
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Residues in contact with PHE1541 (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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1496A MET* 3.4 44.6 - - + -
1537A GLN 3.0 10.9 + - - +
1538A LEU* 3.5 11.4 - - + +
1540A ARG* 1.3 81.3 - - - +
1542A LEU* 1.3 60.5 + - - +
1544A MET* 3.5 13.9 + - + +
1545A LYS* 3.4 32.7 + - + +
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Residues in contact with LEU1542 (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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1496A MET* 3.4 29.8 - - + -
1516A LEU* 4.0 16.8 - - + -
1520A LEU* 3.4 33.7 - - + -
1538A LEU* 3.5 23.9 + - + +
1539A CYS* 3.9 4.9 - - - +
1540A ARG 3.1 0.6 - - - -
1541A PHE* 1.3 71.5 - - - +
1543A HIS* 1.3 67.9 + - - +
1544A MET 3.1 2.0 - - - -
1545A LYS* 3.1 36.7 + - + +
1546A THR 3.8 3.3 + - - -
1550A MET* 4.9 2.9 - - + +
1555A HIS* 4.8 3.3 + - - -
1558A HIS* 3.7 37.2 + - + +
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Residues in contact with HIS1543 (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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1039A ARG 5.3 0.4 - - - -
1040A LEU* 3.5 50.1 + - + +
1076A ARG* 2.9 71.7 + - + +
1080A LEU* 4.6 2.2 - - + +
1539A CYS 3.2 11.3 + - - +
1540A ARG* 2.8 12.0 + - - +
1542A LEU* 1.3 79.4 - - - +
1544A MET* 1.3 71.6 + - + +
1545A LYS 3.5 0.5 + - - -
1546A THR* 3.6 4.3 + - - +
1555A HIS* 5.1 3.8 - - - -
1558A HIS* 4.8 2.6 + - + +
1559A HIS* 3.2 37.5 - + + -
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Residues in contact with MET1544 (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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1076A ARG* 5.3 2.2 - - - +
1540A ARG* 2.9 52.1 + - + +
1541A PHE* 3.7 12.6 - - + +
1542A LEU 3.1 0.4 - - - -
1543A HIS* 1.3 86.0 - - + +
1545A LYS* 1.3 64.6 + - - +
1546A THR* 3.4 9.9 + - - +
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Residues in contact with LYS1545 (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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1496A MET* 4.1 4.6 - - + +
1499A LEU* 3.5 27.9 - - - +
1513A GLU* 4.3 0.4 + - - -
1541A PHE* 3.4 35.2 + - + +
1542A LEU* 3.1 30.9 + - + +
1544A MET* 1.3 79.3 - - - +
1546A THR* 1.3 74.0 + - - +
1547A GLY* 3.2 2.9 + - - -
1550A MET* 3.4 29.9 - - + +
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Residues in contact with THR1546 (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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1069A ARG* 3.1 25.3 + - - +
1072A GLN 5.0 5.8 - - - -
1073A LEU* 4.3 10.8 - - + -
1076A ARG* 4.0 26.9 - - - +
1542A LEU 3.8 5.5 + - - -
1543A HIS 3.6 12.9 + - - +
1544A MET* 3.4 15.5 - - - +
1545A LYS* 1.3 80.8 + - - +
1547A GLY* 1.3 81.0 + - - -
1548A GLY 3.7 1.7 + - - +
1550A MET* 3.3 20.1 - - - +
1555A HIS* 3.6 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