Contacts of the helix formed by residues 1505 - 1521 (chain E) in PDB entry 5JCZ
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 GLY1505 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500E VAL 4.7 0.8 + - - -
1503E ILE 3.5 0.2 + - - -
1504E PRO* 1.3 72.3 - - - +
1506E LEU* 1.3 65.5 + - - +
1507E PRO* 3.4 3.6 - - - +
1508E ALA* 3.0 15.1 + - - +
1509E TYR* 3.0 22.5 + - - -
1554E PHE* 5.7 2.2 - - - -
1557E SER* 5.8 1.1 - - - -
1558E ASN* 3.3 24.3 + - - +
1561E ARG* 4.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499E ALA* 4.0 33.7 - - + +
1500E VAL* 4.5 7.9 - - + +
1503E ILE* 3.2 34.0 + - + +
1504E PRO 3.2 0.6 + - - -
1505E GLY* 1.3 75.9 - - - +
1507E PRO* 1.4 70.7 - - + +
1509E TYR* 3.2 12.1 + - + +
1510E ILE* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489E LEU* 3.9 31.7 - - + +
1493E LEU* 4.0 14.1 - - + -
1500E VAL* 3.8 16.8 - - + -
1505E GLY* 4.3 1.3 - - - +
1506E LEU* 1.4 95.2 - - + +
1508E ALA* 1.3 55.2 + - - +
1510E ILE* 3.5 1.6 + - + +
1511E LEU* 2.9 37.4 + - + +
1554E PHE* 3.7 21.3 - - + -
1555E TRP* 4.2 11.7 - - + -
1558E ASN* 3.2 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505E GLY 3.0 10.1 + - - +
1507E PRO* 1.3 76.4 - - - +
1509E TYR* 1.3 61.0 + - - +
1511E LEU* 3.4 8.4 + - - -
1512E PHE* 3.0 28.9 + - - +
1558E ASN* 3.3 32.9 + - - +
1561E ARG* 3.6 13.7 - - + -
1562E PHE* 3.6 23.2 - - - +
1565E CYS* 4.7 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1509 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503E ILE* 4.9 9.4 - - + -
1504E PRO 3.7 18.6 - - - -
1505E GLY 3.0 28.0 + - - -
1506E LEU* 3.2 14.1 + - + +
1508E ALA* 1.3 74.1 - - - +
1510E ILE* 1.3 59.5 + - - +
1512E PHE* 3.3 7.1 + + - +
1513E MET* 2.9 43.0 + - + +
1561E ARG* 3.5 30.7 + - + -
1565E CYS* 3.7 25.8 - - - -
1569E TYR* 6.0 4.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475E LEU* 3.6 26.0 - - + +
1485E LEU* 5.4 2.7 - - + -
1489E LEU* 3.7 33.4 - - + -
1506E LEU* 2.9 47.3 + - + +
1507E PRO 3.8 3.1 - - - +
1509E TYR* 1.3 75.3 - - + +
1511E LEU* 1.3 62.2 + - - +
1513E MET* 3.3 8.0 + - - +
1514E CYS* 3.1 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1511 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485E LEU* 5.4 3.6 - - + -
1486E VAL* 5.2 4.9 - - + -
1489E LEU* 3.7 20.9 - - + -
1490E ILE* 4.1 20.9 - - + -
1507E PRO* 2.9 29.1 + - + +
1508E ALA* 3.6 8.7 - - - +
1510E ILE* 1.3 77.4 - - - +
1512E PHE* 1.3 61.3 + - - +
1514E CYS* 3.2 9.8 + - - +
1515E VAL* 3.1 23.4 + - - +
1530E LEU* 4.2 14.9 - - + +
1534E THR* 3.7 38.1 - - + +
1538E ILE* 5.6 2.0 - - + -
1555E TRP* 5.3 5.6 - - + -
1562E PHE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1512 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508E ALA 3.0 16.8 + - - +
1509E TYR* 3.3 5.4 + + - +
1511E LEU* 1.3 73.8 - - - +
1513E MET* 1.3 63.9 + - + +
1515E VAL* 3.1 6.8 + - + +
1516E ARG* 2.8 54.0 + - + +
1562E PHE* 3.6 8.9 - - + -
1565E CYS* 3.8 34.8 - - + -
1566E LEU* 3.8 31.4 - - + -
1569E TYR* 3.3 45.8 - + + -
1586E HIS 4.5 0.2 - - - -
1588E LEU* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1513 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473E GLY* 3.4 39.3 - - - +
1474E MET* 3.6 1.4 - - - +
1475E LEU* 3.0 52.4 + - + -
1509E TYR* 2.9 31.3 + - + +
1510E ILE* 3.3 9.6 + - - +
1512E PHE* 1.3 81.2 - - + +
1514E CYS* 1.3 60.6 + - - +
1516E ARG* 3.5 7.9 - - - +
1517E HIS 3.5 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1514 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475E LEU* 3.6 26.4 - - - +
1476E GLU 5.9 0.2 - - - -
1477E TYR* 4.1 25.6 - - + -
1485E LEU* 4.4 15.5 - - - -
1510E ILE* 3.1 26.0 + - - -
1511E LEU* 3.4 11.7 - - - +
1512E PHE 3.1 0.2 - - - -
1513E MET* 1.3 76.2 - - - +
1515E VAL* 1.3 64.0 + - - +
1517E HIS* 3.3 4.5 + - - +
1518E ALA* 3.2 21.5 + - - +
1526E LYS* 6.0 0.2 - - - -
1530E LEU* 3.7 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1515 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511E LEU 3.1 14.7 + - - +
1512E PHE* 3.1 12.9 + - + +
1514E CYS* 1.3 77.2 - - - +
1516E ARG* 1.3 57.0 + - - +
1518E ALA* 3.2 5.2 + - - +
1519E ASP* 2.8 29.2 + - + +
1527E VAL* 4.9 8.9 - - + +
1530E LEU* 3.8 18.2 - - + -
1531E LEU* 3.9 23.1 - - + -
1562E PHE* 4.1 12.3 - - + -
1566E LEU* 4.5 7.0 - - + -
1588E LEU* 4.4 12.1 - - + -
1593E LEU* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1516 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472E GLN* 2.8 34.5 + - - +
1473E GLY* 2.9 22.5 + - - -
1474E MET* 3.6 27.0 - - + +
1512E PHE* 2.8 44.5 + - + +
1513E MET* 3.5 11.7 - - - +
1514E CYS 3.2 0.2 - - - -
1515E VAL* 1.3 76.3 - - - +
1517E HIS* 1.3 56.3 + - - +
1519E ASP* 3.2 4.3 + - - +
1520E TYR* 2.8 28.1 + - - +
1585E GLU 4.2 4.0 + - - -
1586E HIS* 3.2 53.5 + - - +
1587E CYS 5.3 1.4 + - - -
1588E LEU* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1517 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474E MET* 3.8 33.3 - - + -
1475E LEU 3.2 25.4 - - - +
1476E GLU* 3.4 38.8 - - + +
1513E MET 3.5 3.0 + - - +
1514E CYS 3.3 2.6 + - - +
1515E VAL 3.3 0.6 - - - -
1516E ARG* 1.3 76.0 - - - +
1518E ALA* 1.3 60.3 + - - +
1520E TYR* 3.2 5.0 + + - +
1521E LEU* 2.9 67.2 + - + +
1526E LYS* 4.9 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1518 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514E CYS 3.2 13.6 + - - +
1515E VAL* 3.5 10.3 - - - +
1517E HIS* 1.3 76.0 + - - +
1519E ASP* 1.3 61.6 + - - +
1521E LEU* 3.4 6.2 + - - +
1522E ASN 3.3 2.6 + - - -
1523E ASP* 3.1 27.9 + - - +
1526E LYS* 4.2 31.2 - - + +
1527E VAL* 3.6 23.7 - - + +
1530E LEU* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1519 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515E VAL* 2.8 14.8 + - + +
1516E ARG 3.4 8.7 - - - +
1518E ALA* 1.3 75.2 - - - +
1520E TYR* 1.3 55.4 + - - +
1522E ASN 3.0 6.4 + - - -
1527E VAL* 4.1 1.9 - - + +
1587E CYS 5.0 0.2 - - - +
1588E LEU* 3.5 26.5 - - + +
1589E THR* 3.0 27.1 + - - -
1590E ASN* 2.6 39.5 + - - +
1591E PHE* 2.9 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1520 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472E GLN* 5.5 11.1 + - - -
1474E MET* 3.9 29.6 - - + -
1516E ARG 2.8 20.1 + - - +
1517E HIS* 3.2 8.0 + + - +
1519E ASP* 1.3 76.4 + - - +
1521E LEU* 1.3 80.4 + - + +
1522E ASN* 3.1 1.8 + - - +
1589E THR* 5.4 3.1 - - - -
1590E ASN* 4.0 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1521 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517E HIS* 2.9 51.5 + - + +
1518E ALA* 3.8 7.6 - - - +
1519E ASP 3.2 0.2 - - - -
1520E TYR* 1.3 96.7 - - + +
1522E ASN* 1.3 69.9 - - - +
1523E ASP* 3.2 15.3 + - + +
1526E LYS* 4.8 13.7 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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