Contacts of the helix formed by residues 1505 - 1521 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500B VAL 5.6 0.4 + - - -
1503B ILE 3.9 0.2 + - - -
1504B PRO* 1.3 73.6 - - - +
1506B LEU* 1.3 64.0 + - - +
1507B PRO* 3.4 3.5 - - - +
1508B ALA* 3.1 6.2 + - - +
1509B TYR* 3.0 27.2 + - - -
1554B PHE* 5.9 2.4 - - - -
1557B SER* 5.6 1.3 - - - -
1558B ASN* 3.2 24.3 + - - +
1561B ARG* 4.2 17.7 - - - -
1676B HIS 4.5 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499B ALA 3.6 24.9 - - - +
1500B VAL* 4.7 5.8 + - + +
1502B LEU* 5.9 0.4 - - + -
1503B ILE* 3.8 33.6 + - + +
1504B PRO 3.2 2.8 - - - -
1505B GLY* 1.3 77.2 - - - +
1507B PRO* 1.4 71.9 - - + +
1509B TYR* 3.2 7.4 + - + +
1510B ILE* 3.0 41.3 + - + +
1839B ILE* 4.0 26.9 - - + -
1840B GLN 4.6 4.9 - - - +
1842B PRO* 4.5 13.9 - - + -
1845B LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489B LEU* 3.8 32.3 - - + +
1493B LEU* 4.1 20.4 - - + -
1500B VAL* 4.5 7.4 - - + -
1505B GLY* 4.4 0.7 - - - +
1506B LEU* 1.4 93.9 - - + +
1508B ALA* 1.3 55.5 + - - +
1510B ILE* 3.4 1.7 + - - +
1511B LEU* 2.9 37.6 + - + +
1554B PHE* 3.9 22.4 - - + -
1555B TRP* 4.4 10.5 - - + -
1558B ASN* 3.2 17.9 - - - +
1845B LEU* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B GLY 3.1 10.8 + - - +
1507B PRO* 1.3 78.6 - - - +
1509B TYR* 1.3 62.6 + - - +
1511B LEU* 3.5 6.3 + - - -
1512B PHE* 3.1 20.3 + - - +
1558B ASN* 3.2 34.5 + - + +
1561B ARG* 3.6 11.7 - - + -
1562B PHE* 3.5 31.5 - - - +
1565B CYS* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503B ILE* 4.5 2.5 - - + -
1504B PRO 3.8 13.2 - - - -
1505B GLY 3.0 29.9 + - - -
1506B LEU* 3.2 11.0 + - + +
1508B ALA* 1.3 74.3 - - - +
1510B ILE* 1.3 65.2 + - - +
1512B PHE* 3.3 3.9 + - - +
1513B MET* 3.0 29.1 + - - +
1561B ARG* 3.6 23.5 + - + -
1565B CYS* 3.8 26.0 - - - -
1568B GLN* 5.9 0.4 - - - -
1569B TYR* 5.8 2.5 - + - -
1832B SER* 2.5 35.5 + - - -
1834B LEU* 3.5 33.8 - - + +
1836B LEU* 4.0 21.3 - - + +
1839B ILE* 3.7 19.7 - - + -
130D HIS 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475B LEU* 3.6 21.9 - - + +
1489B LEU* 3.6 24.9 - - + -
1506B LEU* 3.0 38.3 + - + +
1507B PRO 3.7 3.6 - - - +
1509B TYR* 1.3 74.7 - - - +
1511B LEU* 1.3 63.7 - - - +
1513B MET* 3.3 11.6 + - - +
1514B CYS* 3.3 20.3 + - - -
1839B ILE* 5.0 4.9 - - + -
1841B ILE* 4.0 23.6 - - + -
1845B LEU* 3.7 29.8 - - + -
1847B LEU* 4.6 2.0 - - + -
1850B ILE* 4.7 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485B LEU* 5.1 9.2 - - + -
1486B VAL* 5.9 1.8 - - + -
1489B LEU* 3.6 20.0 - - + -
1490B ILE* 3.8 23.6 - - + -
1507B PRO* 2.9 24.7 + - + +
1508B ALA* 3.7 7.0 - - - +
1510B ILE* 1.3 77.7 - - - +
1512B PHE* 1.3 60.1 + - - +
1514B CYS* 3.3 16.2 + - - +
1515B VAL* 3.3 15.6 + - - +
1530B LEU* 4.3 14.0 - - + +
1534B THR* 3.7 37.5 - - + +
1538B ILE* 5.5 2.2 - - + -
1555B TRP* 5.4 4.9 - - + -
1562B PHE* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508B ALA 3.1 14.8 + - - +
1509B TYR 3.8 3.6 - - - +
1510B ILE 3.3 0.2 - - - -
1511B LEU* 1.3 77.2 - - - +
1513B MET* 1.3 66.2 + - - +
1515B VAL* 3.0 17.5 + - + +
1516B ARG* 3.0 36.9 + - + +
1562B PHE* 3.7 9.2 - - + -
1565B CYS* 3.7 30.5 - - + -
1566B LEU* 3.6 34.8 - - + -
1569B TYR* 3.3 47.1 - + + -
1588B LEU* 4.4 15.0 - - + -
1836B LEU* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473B GLY* 3.7 28.0 - - - +
1474B MET* 3.4 9.8 - - - +
1475B LEU* 3.0 50.4 + - + -
1509B TYR 3.0 23.0 + - - +
1510B ILE* 3.3 7.1 + - - +
1512B PHE* 1.3 75.4 - - - +
1514B CYS* 1.3 61.6 + - - +
1516B ARG* 3.7 6.0 + - - +
1517B HIS 3.6 9.2 + - - -
1836B LEU* 3.5 35.9 - - + +
1839B ILE* 4.1 39.9 - - - +
1841B ILE* 5.1 0.9 - - + -
1852B ARG* 5.4 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475B LEU* 3.5 30.6 - - - +
1477B TYR* 3.9 18.1 - - + -
1485B LEU* 4.1 22.7 - - + -
1510B ILE* 3.3 21.8 - - - -
1511B LEU* 3.4 10.3 - - - +
1512B PHE 3.1 0.6 - - - -
1513B MET* 1.3 76.5 - - - +
1515B VAL* 1.3 63.1 + - - +
1517B HIS* 3.3 5.5 + - - +
1518B ALA* 3.1 20.8 + - - +
1530B LEU* 3.8 17.0 - - + +
1850B ILE* 5.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511B LEU 3.4 14.6 - - - +
1512B PHE* 3.0 16.7 + - + +
1514B CYS* 1.3 75.5 - - - +
1516B ARG* 1.3 59.1 + - - +
1518B ALA* 3.2 5.4 + - - +
1519B ASP* 2.8 28.9 + - + +
1527B VAL* 4.8 9.1 - - + +
1530B LEU* 3.7 19.3 - - + -
1531B LEU* 4.2 21.5 - - + -
1562B PHE* 4.3 9.0 - - + -
1566B LEU* 4.6 5.6 - - + -
1588B LEU* 4.6 12.8 - - + -
1593B LEU* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472B GLN* 3.3 12.5 + - - +
1473B GLY* 2.8 38.0 + - - -
1474B MET* 3.4 35.4 - - + +
1512B PHE* 3.0 43.4 + - + +
1513B MET* 3.7 9.0 - - - +
1514B CYS 3.3 0.2 - - - -
1515B VAL* 1.3 76.9 - - - +
1517B HIS* 1.3 51.4 + - - +
1519B ASP* 3.2 4.2 + - - +
1520B TYR* 2.6 35.0 + - - +
1585B GLU 4.0 4.6 + - - -
1586B HIS* 2.9 62.8 + - - +
1587B CYS 5.2 0.4 + - - -
1588B LEU* 4.0 11.7 - - + -
1836B LEU* 3.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474B MET* 3.7 27.8 - - + -
1475B LEU 3.7 14.8 + - - +
1476B GLU* 3.5 35.0 - - + +
1477B TYR* 5.0 2.9 + - - -
1513B MET 3.6 1.6 + - - +
1514B CYS 3.3 9.3 + - - +
1515B VAL 3.3 0.6 - - - -
1516B ARG* 1.3 75.7 - - - +
1518B ALA* 1.3 56.2 + - - +
1520B TYR* 3.2 7.2 + + - +
1521B LEU* 2.8 72.9 + - + +
1526B LYS* 5.6 6.5 + - - +
1853B VAL* 4.4 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514B CYS 3.1 12.7 + - - +
1515B VAL* 3.5 10.5 - - - +
1517B HIS* 1.3 76.8 + - - +
1519B ASP* 1.3 62.0 + - - +
1521B LEU* 3.2 6.5 + - - +
1522B ASN 3.2 2.8 + - - -
1523B ASP* 3.1 28.3 + - - +
1526B LYS* 3.7 33.4 - - + +
1527B VAL* 3.6 22.9 - - + +
1530B LEU* 5.3 2.7 - - + -
1591B PHE* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515B VAL* 2.8 14.7 + - + +
1516B ARG 3.4 7.6 - - - +
1518B ALA* 1.3 76.4 - - - +
1520B TYR* 1.3 61.4 + - - +
1522B ASN* 3.1 5.2 + - - -
1527B VAL* 4.0 2.4 - - + +
1587B CYS 4.8 0.3 - - - +
1588B LEU* 3.5 25.2 - - + +
1589B THR* 2.9 30.5 + - - +
1590B ASN* 3.0 31.7 + - - +
1591B PHE* 3.0 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472B GLN* 6.4 2.0 - - - -
1474B MET* 3.8 28.0 - - + -
1516B ARG 2.6 19.8 + - - +
1517B HIS* 3.2 13.9 + + - +
1519B ASP* 1.3 76.7 + - - +
1521B LEU* 1.3 81.3 + - + +
1522B ASN* 3.1 1.8 + - - +
1589B THR* 5.3 3.6 - - - -
1590B ASN* 4.3 6.6 + - - +
1853B VAL* 6.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517B HIS* 2.8 52.5 + - + +
1518B ALA* 3.7 7.4 - - - +
1519B ASP 3.2 0.4 - - - -
1520B TYR* 1.3 94.0 - - + +
1522B ASN* 1.3 70.0 + - - +
1523B ASP* 3.1 17.3 + - + +
1526B LYS* 5.6 8.1 - - + +
----------------------------------------------------------
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