Contacts of the helix formed by residues 1464 - 1484 (chain D) in PDB entry 6CET
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 THR1464 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463D GLU* 1.3 94.1 + - + +
1465D TYR* 1.3 63.3 + - - +
1466D TRP* 3.2 6.4 + - - -
1467D ASP* 3.5 26.5 + - - +
1468D ARG* 3.6 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463D GLU* 4.8 4.5 - - - +
1464D THR* 1.3 74.8 - - - +
1466D TRP* 1.3 71.8 + + + +
1468D ARG* 3.2 31.3 + - + +
1469D MET* 2.9 47.5 + - + +
1472D PHE* 6.5 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464D THR* 3.2 2.5 - - - -
1465D TYR* 1.3 86.4 - + + +
1467D ASP* 1.3 62.6 + - - +
1469D MET* 3.5 10.3 + - + +
1470D HIS* 3.0 28.6 + - - +
1543D ARG* 5.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464D THR* 3.5 20.4 + - - +
1466D TRP* 1.3 80.3 - - - +
1468D ARG* 1.3 57.1 + - + +
1470D HIS* 3.4 7.8 + - - +
1471D LEU* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463D GLU* 2.9 41.7 + - - +
1464D THR* 3.6 11.3 + - - +
1465D TYR* 3.2 38.0 + - + +
1467D ASP* 1.3 78.1 - - + +
1469D MET* 1.3 58.1 + - - +
1471D LEU* 3.1 14.8 + - + +
1472D PHE* 3.0 43.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443D LEU* 4.4 22.9 - - + -
1445D ILE* 5.6 13.2 - - + -
1465D TYR* 2.9 38.3 + - + +
1466D TRP* 4.1 12.1 - - + +
1468D ARG* 1.3 74.1 - - - +
1470D HIS* 1.3 59.6 + - - +
1472D PHE* 3.4 14.1 + - + +
1473D GLN* 2.9 42.7 + - + +
1476D ILE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466D TRP 3.0 18.6 + - - +
1467D ASP* 3.5 10.3 - - - +
1469D MET* 1.3 78.1 - - - +
1471D LEU* 1.3 57.5 + - - +
1473D GLN* 3.3 9.5 + - + +
1474D GLU* 3.0 63.8 + - + +
1500D PRO* 3.3 37.5 - - + +
1513D LEU* 4.4 14.8 + - + +
1514D PRO 5.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467D ASP* 2.9 23.3 + - + +
1468D ARG* 3.1 17.4 + - + +
1470D HIS* 1.3 77.0 - - - +
1472D PHE* 1.3 64.3 + - + +
1474D GLU* 3.1 25.7 + - - +
1475D ALA* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1465D TYR* 6.5 1.3 - + - -
1468D ARG* 3.0 38.6 + - + +
1469D MET* 3.4 19.3 + - + +
1471D LEU* 1.3 78.8 - - + +
1473D GLN* 1.3 60.5 + - - +
1475D ALA* 3.6 14.5 - - + +
1476D ILE* 2.9 36.5 + - + +
1594D CYS* 5.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443D LEU* 3.3 22.2 - - - +
1469D MET* 2.9 20.5 + - + +
1470D HIS* 3.3 15.7 - - + +
1472D PHE* 1.3 76.1 - - - +
1474D GLU* 1.3 56.8 + - - +
1476D ILE* 3.2 27.6 - - - +
1477D ALA* 2.9 29.5 + - - +
1513D LEU* 3.5 37.2 - - + +
1545D GLY 5.4 1.6 - - - +
1546D TYR* 3.3 35.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1470D HIS* 3.0 48.3 + - + +
1471D LEU* 3.1 26.1 + - - +
1473D GLN* 1.3 76.9 - - - +
1475D ALA* 1.3 58.3 + - - +
1477D ALA* 3.3 8.2 - - - +
1478D HIS* 2.9 30.5 + - - +
1502D TYR* 4.0 24.8 + - + +
1513D LEU* 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471D LEU 2.8 15.5 + - - +
1472D PHE* 3.6 22.9 - - + +
1473D GLN 3.2 0.2 - - - -
1474D GLU* 1.3 76.0 - - - +
1476D ILE* 1.3 61.1 + - + +
1478D HIS* 3.5 3.2 + - - +
1479D ARG* 2.9 29.0 + - - +
1594D CYS* 5.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443D LEU* 4.9 13.2 - - + -
1469D MET* 6.2 0.9 - - + -
1472D PHE* 2.9 22.0 + - + +
1473D GLN* 3.2 37.7 - - - +
1475D ALA* 1.3 75.8 - - + +
1477D ALA* 1.3 64.9 + - - +
1479D ARG* 3.7 7.9 - - + +
1480D PHE* 2.9 59.4 + - + -
1546D TYR* 4.7 7.6 - - + +
1587D LEU* 5.5 11.2 - - + -
1590D PHE* 5.6 10.1 - - + -
1594D CYS* 5.7 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473D GLN* 2.9 20.6 + - - +
1474D GLU* 3.3 11.0 - - - +
1476D ILE* 1.3 82.5 - - + +
1478D HIS* 1.3 58.2 + - - +
1480D PHE* 3.3 3.0 + - - -
1481D GLY 2.8 20.1 + - - -
1487D TYR* 3.1 38.6 - - + -
1502D TYR* 5.7 7.2 - - + -
1511D LEU* 6.2 0.7 - - + -
1513D LEU* 5.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381D ASN* 4.4 17.7 + - - -
1474D GLU 2.9 19.3 + - - +
1475D ALA* 4.3 3.1 - - - +
1477D ALA* 1.3 70.4 - - - +
1479D ARG* 1.3 60.1 + - - +
1481D GLY* 3.0 5.3 - - - +
1482D PHE* 2.8 47.4 + + + -
1486D LYS* 3.2 42.9 + - + +
1487D TYR* 4.7 12.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475D ALA 2.9 18.5 + - - +
1476D ILE* 3.7 10.3 - - + +
1477D ALA 3.2 0.2 - - - -
1478D HIS* 1.3 72.6 - - - +
1480D PHE* 1.3 60.3 + - + +
1481D GLY 3.0 0.9 - - - -
1482D PHE* 2.7 39.5 + - - +
1483D VAL* 3.0 32.9 + - - +
1590D PHE* 4.0 39.1 - - + -
1593D SER* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443D LEU* 6.6 0.4 - - + -
1476D ILE* 2.9 44.3 + - + -
1477D ALA* 3.4 8.5 - - - +
1479D ARG* 1.3 75.0 - - + +
1481D GLY* 1.3 62.9 + - - +
1483D VAL* 3.3 20.8 - - + +
1485D ASP* 2.9 20.6 + - - +
1487D TYR* 3.9 7.1 - - + -
1546D TYR* 4.6 11.4 - - - -
1576D PHE* 3.4 39.2 - + + -
1579D PHE* 3.6 55.4 - + + -
1580D CYS* 5.9 1.6 - - - -
1587D LEU* 6.1 0.9 - - + -
1590D PHE* 3.9 23.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1481 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477D ALA 2.8 12.8 + - - -
1478D HIS* 3.0 15.5 - - - -
1479D ARG 3.0 0.2 - - - -
1480D PHE* 1.3 78.2 - - - +
1482D PHE* 1.3 63.3 + - - -
1483D VAL 3.3 0.9 + - - -
1484D GLN 3.9 1.4 + - - -
1485D ASP 3.2 28.2 + - - -
1486D LYS* 3.5 21.8 + - - +
1487D TYR* 3.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1482 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478D HIS* 2.8 34.4 + + - -
1479D ARG* 2.7 36.9 + - + +
1481D GLY* 1.3 72.3 - - - -
1483D VAL* 1.3 63.3 + - - +
1486D LYS* 3.3 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306D SER* 4.9 3.6 - - - -
1316D LEU* 4.7 19.1 - - + -
1479D ARG* 3.0 23.6 + - - +
1480D PHE* 3.3 35.4 - - + +
1482D PHE* 1.3 81.2 - - - +
1484D GLN* 1.3 96.2 + - + +
1485D ASP 4.9 0.2 - - - +
1575D ASP* 5.6 3.6 - - - +
1576D PHE* 5.6 2.7 - - + -
1579D PHE* 4.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306D SER* 2.8 57.2 + - - +
1307D GLU* 5.7 3.1 - - - +
1309D PRO* 4.3 13.4 - - - +
1310D ALA* 4.2 17.3 + - + +
1314D PRO* 5.8 3.8 - - - +
1316D LEU* 5.2 11.0 - - + +
1481D GLY 4.1 2.9 - - - -
1483D VAL* 1.3 110.7 + - + +
1485D ASP* 1.3 64.4 + - + +
1486D LYS 4.2 1.3 + - - -
1505D VAL* 6.1 0.7 - - - +
1568D PHE* 6.1 2.6 - - + -
1572D LEU* 5.8 5.2 - - + -
1575D ASP* 5.9 2.7 - - - +
----------------------------------------------------------
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