Contacts of the helix formed by residues 1483 - 1496 (chain A) in PDB entry 2FR1
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 ALA1483 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478A LYS* 4.2 2.7 - - + -
1482A THR* 1.3 81.1 - - + +
1484A ASP* 1.3 59.6 + - - +
1485A GLU* 3.4 3.1 - - - +
1486A THR* 3.9 4.3 - - - +
1487A SER* 2.9 29.1 + - - -
1531A LEU* 4.1 17.4 - - + +
1534A VAL* 3.6 42.2 - - + +
1535A ASP* 4.0 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478A LYS* 3.4 24.1 + - - -
1481A GLY* 3.8 20.9 + - - -
1482A THR 4.2 5.3 + - - -
1483A ALA* 1.3 73.2 - - - +
1485A GLU* 1.3 79.8 + - - +
1487A SER* 3.2 6.1 + - - -
1488A THR* 3.0 27.8 + - - +
1503A GLU* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A ALA* 3.4 0.8 - - - +
1484A ASP* 1.3 90.2 + - - +
1486A THR* 1.3 63.2 + - - +
1488A THR* 3.5 6.3 + - - -
1489A ALA* 3.2 21.3 + - - +
1618A VAL* 4.0 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A ALA* 3.4 8.8 + - - +
1484A ASP 3.2 0.4 - - - -
1485A GLU* 1.3 75.7 - - - +
1487A SER* 1.3 59.8 + - - +
1489A ALA* 3.2 2.2 + - - +
1490A ALA* 2.9 27.0 + - - +
1531A LEU* 4.0 17.9 - - + -
1534A VAL* 3.7 26.9 - - + +
1571A VAL* 5.4 0.9 - - + -
1573A GLU* 4.6 3.5 + - - -
1613A VAL* 5.9 2.5 - - + -
1616A GLY 5.7 1.0 - - - -
1617A SER 4.5 5.3 + - - +
1618A VAL* 3.5 21.8 - - + +
1621A LEU* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476A VAL* 3.9 11.3 - - - +
1478A LYS* 3.6 16.9 - - - +
1483A ALA 2.9 18.5 + - - -
1484A ASP* 3.2 6.5 + - - -
1486A THR* 1.3 77.0 - - - +
1488A THR* 1.3 57.4 + - - +
1490A ALA* 3.1 3.4 + - - +
1491A ARG* 2.8 33.6 + - - +
1503A GLU* 2.8 28.7 + - - +
1531A LEU* 3.6 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484A ASP* 3.0 14.3 + - - +
1485A GLU* 3.7 9.1 - - - -
1487A SER* 1.3 75.6 - - - +
1489A ALA* 1.3 62.8 + - - +
1491A ARG* 3.3 15.7 + - + +
1492A GLU* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485A GLU 3.2 6.2 + - - +
1486A THR* 3.2 9.7 + - + +
1488A THR* 1.3 80.2 - - - +
1490A ALA* 1.3 61.1 + - - +
1492A GLU* 3.2 27.5 - - - +
1493A ALA* 3.2 6.2 + - - +
1618A VAL* 3.5 36.1 - - + +
1621A LEU* 5.4 2.2 - - + -
1622A ALA* 3.2 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476A VAL* 5.0 4.0 - - + -
1486A THR 2.9 17.0 + - - +
1487A SER* 3.1 8.5 + - - +
1489A ALA* 1.3 75.7 - - - +
1491A ARG* 1.3 58.8 + - - +
1493A ALA* 3.3 1.2 + - - +
1494A LEU* 2.9 39.0 + - + +
1529A LEU* 3.5 31.9 - - + -
1531A LEU* 4.6 3.1 - - + -
1621A LEU* 4.5 7.1 - - + +
1625A LEU* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476A VAL* 5.5 0.6 - - + +
1487A SER* 2.8 20.5 + - - +
1488A THR* 3.6 15.2 + - - +
1490A ALA* 1.3 77.3 - - - +
1492A GLU* 1.3 52.4 - - - +
1494A LEU* 3.2 2.1 + - - +
1495A GLU* 2.7 69.1 + - + +
1501A VAL* 3.5 45.7 + - + +
1502A ARG* 4.7 1.4 - - - +
1503A GLU* 3.4 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1488A THR* 3.2 15.1 + - + +
1489A ALA* 3.2 29.8 + - - +
1491A ARG* 1.3 79.1 - - - +
1493A ALA* 1.3 59.9 + - - +
1495A GLU* 4.1 9.4 - - - -
1496A SER* 2.7 41.1 + - - +
1622A ALA* 4.5 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489A ALA 3.2 15.6 + - - +
1490A ALA 3.6 4.7 - - - +
1491A ARG 3.2 0.6 - - - -
1492A GLU* 1.3 85.4 - - - +
1494A LEU* 1.3 63.9 + - - +
1496A SER* 3.7 5.0 + - - -
1497A ALA* 3.6 16.5 + - - +
1622A ALA* 3.7 28.0 - - - +
1625A LEU* 4.0 20.2 - - + -
1626A ALA* 3.9 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1470A LEU* 3.9 23.7 - - + +
1474A TRP* 4.2 27.4 - - + -
1476A VAL* 4.5 13.9 - - + -
1490A ALA 2.9 23.6 + - - +
1493A ALA* 1.3 74.8 - - - +
1495A GLU* 1.3 60.4 + - - +
1497A ALA* 2.9 22.9 + - - +
1498A GLY 3.3 4.2 + - - -
1499A ALA* 3.6 13.7 + - + +
1501A VAL* 3.7 25.4 - - + -
1529A LEU* 4.6 7.4 - - + -
1625A LEU* 4.0 25.6 - - + -
1626A ALA* 5.1 2.0 - - - -
1629A VAL* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491A ARG* 2.7 56.2 + - - +
1492A GLU* 4.1 7.0 + - - +
1494A LEU* 1.3 66.3 - - - +
1496A SER* 1.3 56.9 + - - +
1497A ALA 2.9 4.7 - - - -
1498A GLY* 2.9 19.1 + - - -
1499A ALA 3.4 22.7 + - - +
1500A ARG* 5.5 0.3 - - - -
1501A VAL* 3.9 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492A GLU* 2.7 28.7 + - - +
1493A ALA* 4.0 6.1 - - - -
1495A GLU* 1.3 76.4 - - - +
1497A ALA* 1.3 58.7 + - - +
1498A GLY 3.3 0.2 - - - -
----------------------------------------------------------
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