Contacts of the helix formed by residues 1575 - 1580 (chain H) in PDB entry 6X34
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 LEU1575 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295H VAL* 6.1 0.2 - - - +
1433H TYR* 4.4 13.6 - - + +
1434H TYR 4.2 16.1 + - - +
1435H TYR* 4.7 19.1 - - + -
1452H TRP* 5.7 6.5 - - + -
1574H PRO* 1.3 72.9 - - - +
1576H SER* 1.3 59.7 + - - +
1577H ALA 3.2 0.2 - - - -
1578H ALA* 3.3 3.8 + - - +
1579H MET* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1576 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1566H LEU* 5.8 4.9 - - - +
1574H PRO* 3.8 6.3 - - - +
1575H LEU* 1.3 76.5 - - - +
1577H ALA* 1.3 61.3 + - - +
1579H MET* 3.5 13.8 + - - +
1580H PHE* 3.6 15.4 + - - +
1583H GLU 5.1 0.7 - - - +
1588H ALA 3.6 14.6 + - - -
1589H PRO* 3.8 11.6 + - - +
1590H GLN 3.3 28.1 + - - -
1591H CYS* 4.7 8.1 - - - -
1592H PRO* 5.0 7.4 - - - +
1595H LEU* 5.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1577 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433H TYR* 5.2 2.0 - - + -
1573H MET* 4.9 7.9 - - + -
1574H PRO* 3.4 17.6 + - + +
1575H LEU 3.2 0.8 - - - -
1576H SER* 1.3 81.6 + - - +
1578H ALA* 1.3 56.4 + - - +
1580H PHE 3.0 18.5 - - - +
1583H GLU 3.9 10.5 - - - +
1584H ARG* 3.3 38.4 - - - +
1586H ASN 3.8 17.0 - - - +
1588H ALA 5.3 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1578 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294H PRO 4.7 2.9 - - - +
1295H VAL* 4.7 19.7 - - + +
1296H GLN 5.5 4.0 + - - +
1433H TYR* 3.5 41.7 - - + +
1574H PRO 3.9 0.6 + - - -
1575H LEU* 3.3 8.4 + - - +
1577H ALA* 1.3 76.8 - - - +
1579H MET* 1.3 65.4 + - - +
1580H PHE 3.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1579 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293H LEU* 4.2 34.0 - - + +
1294H PRO* 4.0 17.6 - - - +
1295H VAL* 5.7 2.4 - - + +
1575H LEU 2.9 16.7 + - - +
1576H SER* 3.9 9.6 - - - +
1577H ALA 3.4 0.8 - - - -
1578H ALA* 1.3 80.3 - - - +
1580H PHE* 1.3 59.3 + - + +
1592H PRO* 6.0 5.4 - - + -
1595H LEU* 5.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1580 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591H ASP* 5.3 10.8 - - + +
592H LYS* 5.9 8.1 - - + -
1293H LEU* 5.6 5.2 - - + -
1576H SER 3.6 11.4 + - - +
1577H ALA 3.0 19.3 - - - +
1578H ALA* 3.8 4.4 - - - +
1579H MET* 1.3 81.2 - - + +
1581H LEU* 1.3 61.0 - - - +
1582H SER* 4.3 12.1 - - - +
1583H GLU 5.2 3.6 - - - +
1584H ARG* 4.9 2.8 - - - +
1592H PRO* 5.3 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