Contacts of the helix formed by residues 1461 - 1468 (chain D) in PDB entry 2A69
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 GLY1461 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103D HIS* 3.8 4.9 - - - -
1104D GLU* 3.6 31.6 + - - +
1106D VAL* 5.6 0.4 - - - +
1108D ARG* 4.7 2.0 - - - +
1460D ILE* 1.3 79.0 - - - +
1462D LEU* 1.3 71.8 + - - -
1463D LYS 3.6 1.3 - - - -
1464D GLU* 4.2 2.5 - - - -
1465D ASN* 3.5 12.8 + - - +
1473D PRO* 3.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041C GLU* 3.0 49.4 - - + +
1103D HIS* 3.3 19.8 - - + +
1106D VAL* 4.4 5.6 - - + -
1223D ILE* 4.0 14.8 - - + -
1461D GLY* 1.3 77.1 - - - -
1463D LYS* 1.3 67.7 + - - +
1465D ASN 3.8 0.2 - - - -
1466D VAL* 2.9 28.1 + - - +
1472D ILE* 3.5 26.9 - - + +
1473D PRO* 3.4 24.5 - - + -
1474D ALA* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037C VAL* 4.8 3.8 - - - +
1038C TRP* 3.3 26.4 - - - +
1041C GLU* 2.9 35.3 + - - -
618D LEU* 3.5 42.6 - - + +
1099D VAL* 4.5 13.7 - - - +
1100D ASP* 5.0 11.9 - - - +
1103D HIS* 3.2 31.2 - - + +
1436D SER* 4.5 8.1 - - - +
1439D SER* 5.4 6.5 - - - +
1440D PHE* 6.0 2.2 - - + -
1462D LEU* 1.3 80.3 - - - +
1464D GLU* 1.3 64.3 - - - +
1466D VAL* 3.2 12.4 + - + +
1467D ILE* 3.5 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103D HIS* 4.2 4.0 + - - -
1104D GLU* 5.1 0.9 - - - +
1432D LYS* 2.6 26.4 + - - -
1433D SER* 3.2 22.3 - - - +
1435D LEU* 3.5 27.2 - - + +
1436D SER* 3.5 12.8 + - - +
1457D ASP* 2.5 27.2 - - - +
1458D GLU 3.1 2.1 - - - +
1459D LEU* 3.7 8.7 - - + +
1460D ILE 2.6 29.3 - - - +
1461D GLY* 3.6 8.0 - - - +
1463D LYS* 1.3 80.0 - - - +
1465D ASN* 1.3 69.9 + - - +
1466D VAL 3.2 1.2 + - - -
1467D ILE* 3.5 19.5 + - - +
1468D LEU* 3.8 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459D LEU* 3.5 16.7 - - + +
1461D GLY 3.5 15.7 + - - +
1462D LEU 3.5 2.1 + - - +
1463D LYS 3.3 0.6 - - - -
1464D GLU* 1.3 78.6 - - - +
1466D VAL* 1.3 63.5 + - - +
1468D LEU* 3.3 21.9 - - - +
1469D GLY 3.7 0.7 + - - -
1470D ARG* 2.7 68.5 + - - +
1471D LEU 3.3 16.2 - - - +
1472D ILE* 4.8 0.9 - - - -
1473D PRO* 3.6 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037C VAL* 4.9 5.8 - - + -
1041C GLU* 3.9 8.3 - - - +
1049C LEU* 3.7 20.4 - - + -
1053C LEU* 4.3 23.9 - - + +
617D ASN 5.2 5.4 - - - +
618D LEU* 4.9 18.4 - - + -
1462D LEU 2.9 14.2 + - - +
1463D LYS* 3.6 7.4 - - + +
1464D GLU 3.2 0.2 - - - -
1465D ASN* 1.3 75.0 - - - +
1467D ILE* 1.3 61.4 + - + +
1468D LEU 3.0 1.8 - - - -
1469D GLY* 2.5 29.2 + - - -
1470D ARG 4.6 2.2 - - - +
1472D ILE* 3.3 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082C PRO* 5.6 0.2 - - - +
1084C SER* 4.9 3.6 + - - -
1085C PHE* 4.2 17.2 + - + +
1088C LEU* 3.8 28.7 - - + -
614D PHE* 5.4 12.6 - - + +
617D ASN* 4.3 28.0 - - + +
618D LEU* 5.6 11.9 - - + -
1435D LEU* 4.1 35.2 - - + +
1436D SER* 5.5 0.4 - - - -
1439D SER* 4.6 7.9 - - - +
1463D LYS* 3.5 16.8 - - + +
1464D GLU* 3.5 12.8 + - - +
1466D VAL* 1.3 81.1 - - + +
1468D LEU* 1.3 62.0 - - - +
1469D GLY* 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082C PRO* 3.7 10.2 - - - +
1085C PHE* 3.1 50.6 - - + -
5D VAL* 4.0 16.4 - - + +
8D VAL* 4.8 7.9 - - + -
1435D LEU* 5.7 2.4 - - + +
1459D LEU* 3.4 20.0 - - + -
1464D GLU 3.8 4.3 + - - +
1465D ASN* 3.3 33.6 + - - +
1466D VAL 3.0 0.2 - - - -
1467D ILE* 1.3 79.9 - - - +
1469D GLY* 1.3 62.5 + - - +
1470D ARG* 3.3 26.9 - - + -
9017D MG 3.2 21.9 - - - -
----------------------------------------------------------
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