Contacts of the strand formed by residues 1527 - 1530 (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 GLY1527 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473A THR 3.8 0.8 + - - -
1474A TRP* 3.3 28.3 - - - -
1475A LEU 3.0 22.3 + - - -
1525A VAL* 3.3 7.2 - - - +
1526A ALA* 1.3 82.1 - - - +
1528A VAL* 1.3 63.1 + - - -
1566A CYS* 4.0 4.7 - - - -
1567A PRO* 3.8 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474A TRP* 3.6 5.2 - - - -
1475A LEU* 3.4 22.4 - - + +
1477A ALA* 4.7 5.4 - - + -
1504A LEU* 5.2 3.1 - - + -
1519A LEU* 5.6 1.3 - - + -
1525A VAL* 4.1 8.1 - - + -
1527A GLY* 1.3 80.6 - - - +
1529A LEU* 1.3 65.2 + - - +
1555A LEU* 4.3 16.6 - - + -
1559A MET* 3.3 26.7 - - + -
1564A LEU* 4.6 6.5 - - + -
1566A CYS* 3.9 8.1 - - - -
1567A PRO 3.2 6.1 + - - +
1568A LEU* 3.5 23.6 - - + +
1569A TRP* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474A TRP* 4.2 10.2 - - + -
1475A LEU 2.8 13.6 + - - +
1476A VAL* 3.3 11.7 - - + +
1477A ALA 2.9 25.0 + - - +
1490A ALA* 3.5 33.0 - - + -
1494A LEU* 4.6 7.9 - - + -
1528A VAL* 1.3 75.2 - - - +
1530A SER* 1.3 59.9 + - - +
1531A LEU* 3.9 19.0 + - + -
1569A TRP* 3.4 25.1 - - + +
1571A VAL* 3.7 21.5 - - + -
1611A VAL* 6.4 0.2 - - + -
1621A LEU* 5.2 0.9 - - + -
1625A LEU* 3.8 28.3 - - + -
1629A VAL* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477A ALA* 3.8 5.2 - - - -
1528A VAL 4.0 0.8 + - - -
1529A LEU* 1.3 72.8 - - - +
1531A LEU* 1.3 66.1 + - - +
1532A LEU* 3.4 30.3 + - - +
1533A ALA 5.1 0.2 + - - -
1552A THR* 4.8 4.2 + - - -
1555A LEU* 4.6 6.5 - - - +
1568A LEU* 4.1 14.1 - - - -
1569A TRP 2.7 16.8 + - - +
1570A THR* 3.9 20.7 + - - +
1571A VAL* 3.1 25.9 + - - +
----------------------------------------------------------
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