Contacts of the helix formed by residues 1521 - 1540 (chain A) in PDB entry 3UVD
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 SER1521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1458A LEU* 4.2 5.4 - - - -
1462A MET* 3.1 21.8 - - - +
1519A TYR 3.5 0.8 - - - -
1520A ARG* 1.3 82.9 - - - +
1522A LEU* 1.3 62.7 + - - +
1523A ASN* 3.4 11.0 + - - +
1524A ASP* 3.1 36.6 + - - +
1525A LEU 3.3 7.6 + - - -
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Residues in contact with LEU1522 (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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1458A LEU* 3.9 18.4 - - + +
1461A LYS* 4.2 13.9 - - + -
1462A MET* 3.7 32.1 - - + +
1465A ILE* 4.1 24.7 - - + -
1521A SER* 1.3 71.0 - - - +
1523A ASN* 1.3 56.1 + - - +
1524A ASP 3.2 0.2 - - - -
1525A LEU* 3.2 8.6 + - + +
1526A GLU* 2.8 36.2 + - - +
1557A PHE* 4.8 1.5 - - + -
1561A ARG* 3.6 24.4 + - + +
1565A GLU* 3.4 42.4 - - + +
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Residues in contact with ASN1523 (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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1521A SER* 3.3 11.9 + - - +
1522A LEU* 1.3 76.4 - - - +
1524A ASP* 1.3 60.8 + - - +
1526A GLU* 3.3 6.7 + - - +
1527A LYS* 2.9 53.9 + - - +
1561A ARG* 3.8 17.1 + - - +
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Residues in contact with ASP1524 (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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1518A LYS 4.7 1.4 - - - +
1519A TYR* 3.5 29.6 - - + -
1520A ARG* 2.9 30.7 + - - +
1521A SER* 3.1 26.7 + - - +
1522A LEU 3.2 0.4 - - - -
1523A ASN* 1.3 77.6 + - - +
1525A LEU* 1.3 65.0 + - - +
1527A LYS* 3.6 15.5 + - - +
1528A ASP* 3.4 15.2 + - - +
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Residues in contact with LEU1525 (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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1462A MET* 3.8 43.7 - - + +
1465A ILE* 4.6 4.9 - - + -
1466A VAL* 3.8 12.6 - - + -
1510A ILE* 3.5 31.4 - - + -
1514A ILE* 4.5 1.1 - - + -
1519A TYR* 3.8 22.2 - - + -
1521A SER 3.3 8.7 + - - +
1522A LEU* 3.2 15.4 + - + +
1524A ASP* 1.3 78.1 - - - +
1526A GLU* 1.3 67.0 + - - +
1528A ASP* 3.1 4.7 + - - +
1529A VAL* 3.1 23.5 + - + +
1557A PHE* 4.0 17.5 - - + -
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Residues in contact with GLU1526 (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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1522A LEU 2.8 20.5 + - - +
1523A ASN* 3.6 9.9 - - - +
1525A LEU* 1.3 72.4 - - - +
1527A LYS* 1.3 55.9 + - + +
1529A VAL* 3.2 2.3 + - - +
1530A MET* 2.8 54.3 + - + +
1557A PHE* 3.3 37.6 - - + -
1558A THR* 4.7 5.3 + - - -
1561A ARG* 2.8 33.2 + - - +
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Residues in contact with LYS1527 (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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1523A ASN* 2.9 42.3 + - - +
1524A ASP* 3.8 14.9 + - - +
1526A GLU* 1.3 78.5 - - + +
1528A ASP* 1.3 56.9 - - - +
1530A MET* 3.4 6.3 + - - +
1531A LEU* 3.0 26.5 + - - +
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Residues in contact with ASP1528 (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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1505A VAL* 3.8 12.1 - - - +
1510A ILE* 4.2 5.6 - - + -
1513A ARG* 2.7 30.4 + - - -
1519A TYR* 2.7 41.2 + - + +
1524A ASP 3.4 2.3 + - - +
1525A LEU 3.1 7.4 + - - +
1527A LYS* 1.3 77.6 - - - +
1529A VAL* 1.3 60.2 + - - +
1531A LEU* 3.4 22.0 + - - +
1532A LEU* 3.0 26.9 + - - +
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Residues in contact with VAL1529 (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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1466A VAL* 5.0 3.1 - - + -
1469A VAL* 5.3 2.5 - - + -
1507A PHE* 4.6 19.7 - - + -
1510A ILE* 3.9 22.7 - - + -
1525A LEU* 3.1 24.8 + - + +
1526A GLU 3.7 5.6 - - - +
1528A ASP* 1.3 75.2 - - - +
1530A MET* 1.3 67.8 + - - +
1532A LEU* 3.2 5.1 + - + +
1533A CYS* 3.0 33.7 + - - -
1553A LEU* 5.1 3.1 - - + +
1557A PHE* 3.8 45.8 - - + -
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Residues in contact with MET1530 (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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1526A GLU* 2.8 38.9 + - + +
1527A LYS* 3.9 6.5 - - - +
1529A VAL* 1.3 79.0 - - + +
1531A LEU* 1.3 51.9 + - - +
1533A CYS* 3.4 4.2 + - - +
1534A GLN* 2.8 33.3 + - - +
1554A GLN* 3.6 53.9 - - + +
1557A PHE* 4.0 17.3 - - + -
1558A THR* 3.7 14.6 - - - +
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Residues in contact with LEU1531 (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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1503A LYS* 3.6 31.2 - - + +
1505A VAL* 3.8 11.0 - - + -
1513A ARG* 6.2 0.2 - - - +
1527A LYS 3.0 17.9 + - - +
1528A ASP* 3.5 22.2 - - - +
1530A MET* 1.3 72.4 - - - +
1532A LEU* 1.3 56.5 + - - +
1534A GLN* 3.7 22.4 - - - +
1535A ASN* 2.7 62.6 + - - +
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Residues in contact with LEU1532 (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* 3.9 34.5 - - + +
1505A VAL* 3.5 26.3 - - + +
1506A ASP* 3.6 22.9 - - - -
1507A PHE* 3.7 25.8 - - + +
1510A ILE* 3.5 25.1 - - + -
1528A ASP 3.0 13.6 + - - +
1529A VAL* 3.4 9.2 - - + +
1531A LEU* 1.3 75.9 - - - +
1533A CYS* 1.3 75.1 + - - +
1535A ASN* 3.6 3.7 - - - +
1536A ALA* 3.3 19.1 + - - +
1553A LEU* 5.5 0.7 - - + -
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Residues in contact with CYS1533 (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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1507A PHE* 6.2 0.2 - - - -
1529A VAL* 3.0 22.1 + - - +
1530A MET 3.7 7.9 - - - +
1532A LEU* 1.3 85.3 - - - +
1534A GLN* 1.3 64.5 + - - +
1536A ALA* 3.3 4.9 - - - +
1537A GLN* 3.1 30.5 + - - +
1550A SER* 3.3 31.9 - - - +
1553A LEU* 4.2 11.0 - - - -
1554A GLN* 3.6 36.8 - - + +
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Residues in contact with GLN1534 (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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1530A MET 2.8 19.1 + - - +
1531A LEU* 3.2 25.7 + - - +
1533A CYS* 1.3 75.1 - - - +
1535A ASN* 1.3 59.1 + - - +
1537A GLN* 3.1 14.8 + - + +
1538A THR* 3.0 39.8 + - - +
1554A GLN* 4.9 0.8 + - - -
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Residues in contact with ASN1535 (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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1497A TYR* 3.7 16.6 + - - +
1501A ILE* 3.4 31.4 - - + +
1503A LYS 2.8 28.0 + - - +
1504A PRO* 3.7 6.7 - - - +
1505A VAL* 3.9 11.2 - - - +
1531A LEU* 2.7 37.8 + - - +
1532A LEU* 3.6 5.2 - - - +
1534A GLN* 1.3 74.2 + - - +
1536A ALA* 1.4 51.6 + - - +
1538A THR* 3.2 3.8 + - - -
1539A PHE* 2.9 36.7 + - - +
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Residues in contact with ALA1536 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MB3 3.9 6.0 + - - +
1485A PHE* 3.5 22.9 - - + -
1497A TYR* 4.7 1.2 + - - -
1532A LEU 3.3 7.0 + - - +
1533A CYS 3.3 11.0 - - - +
1535A ASN* 1.4 75.2 - - - +
1537A GLN* 1.3 58.6 + - - +
1540A ASN* 2.8 47.7 + - - +
1546A ILE 4.3 2.7 - - - +
1547A TYR* 4.5 2.2 - - - -
1550A SER* 3.5 22.4 - - - +
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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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1533A CYS* 3.1 20.4 + - - +
1534A GLN* 3.1 13.1 + - + +
1536A ALA* 1.3 75.3 - - - +
1538A THR* 1.3 58.2 + - - +
1540A ASN 3.4 11.9 - - - +
1547A TYR* 3.6 43.3 + - + +
1550A SER* 2.9 24.5 + - - +
1551A ILE* 3.6 21.5 - - - +
1554A GLN* 2.9 29.6 + - - +
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Residues in contact with THR1538 (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 LEU* 3.5 26.2 - - + +
1501A ILE* 3.5 23.3 - - + -
1534A GLN* 3.0 27.7 + - - +
1535A ASN* 3.6 5.7 + - - -
1536A ALA 3.2 0.2 - - - -
1537A GLN* 1.3 79.3 - - - +
1539A PHE* 1.3 60.7 + - - +
1540A ASN 4.3 2.6 - - - +
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Residues in contact with PHE1539 (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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1A MB3 3.3 35.2 - + - -
1494A LEU* 3.8 27.8 - - + -
1496A GLU* 4.2 12.8 - - + -
1497A TYR* 3.5 42.2 - + + -
1500A LEU* 4.1 17.0 - - + -
1501A ILE* 4.4 5.4 - - + -
1535A ASN 2.9 15.8 + - - +
1538A THR* 1.3 80.0 - - - +
1540A ASN* 1.3 66.2 + - - +
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Residues in contact with ASN1540 (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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1A MB3 2.5 31.2 + - - +
1536A ALA 2.8 25.9 + - - +
1537A GLN 3.4 19.2 - - - +
1538A THR 4.3 1.7 - - - +
1539A PHE* 1.3 91.1 - - - +
1541A LEU* 1.3 64.8 + - - +
1542A GLU 3.6 0.3 + - - -
1544A SER* 3.5 17.0 + - - +
1546A ILE* 3.5 29.8 - - - +
1547A TYR* 3.4 10.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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