Contacts of the helix formed by residues 1386 - 1399 (chain A) in PDB entry 1Y8Z
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 ASP1386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A PRO* 4.1 0.2 - - - -
1178A MET 3.2 4.0 - - - +
1179A ASP* 3.7 4.0 - - - +
1180A ILE* 2.9 37.9 + - - +
1181A VAL* 3.7 6.7 + - - +
1381A LEU 3.9 0.8 + - - -
1382A TYR* 3.0 46.8 + - + +
1384A HIS 4.0 0.2 - - - -
1385A GLN* 1.3 78.9 - - - +
1387A SER* 1.3 65.8 - - - +
1388A SER* 2.7 33.8 + - - -
1389A PHE* 3.0 20.0 + - + +
1390A CYS* 3.1 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A GLU* 3.8 4.4 + - - -
1026A TRP* 3.5 14.1 + - - -
1177A PRO* 3.4 16.3 + - - +
1178A MET* 3.0 37.2 + - - -
1179A ASP* 3.3 10.2 + - - -
1385A GLN 3.6 1.0 + - - -
1386A ASP* 1.3 72.8 - - - +
1388A SER* 1.3 62.7 + - - +
1389A PHE 3.1 0.9 + - - -
1391A PHE* 3.1 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A TRP* 4.5 9.5 + - - +
1029A LYS* 6.0 4.7 - - - -
1382A TYR* 4.0 14.5 + - - -
1386A ASP* 2.7 23.5 + - - -
1387A SER* 1.3 78.3 - - - +
1389A PHE* 1.3 75.0 + - - +
1392A LYS* 3.7 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A ARG* 3.5 39.4 + - - +
1382A TYR* 3.6 62.8 - + - -
1383A GLN* 3.9 22.2 - - - -
1386A ASP* 3.0 7.7 + - + +
1388A SER* 1.3 90.6 - - - +
1390A CYS* 1.3 65.6 + - - +
1391A PHE 3.5 0.2 - - - -
1392A LYS* 3.3 8.2 + - + +
1393A GLU* 3.1 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A GLN* 3.9 17.9 - - + +
1177A PRO* 3.4 23.6 - - + -
1332A ARG* 3.8 21.1 - - - +
1384A HIS 3.9 1.3 - - - -
1385A GLN* 3.6 35.9 - - - -
1386A ASP 3.1 5.7 + - - +
1389A PHE* 1.3 77.3 - - - +
1391A PHE* 1.3 60.7 + - - +
1393A GLU* 3.1 11.3 + - - +
1394A GLN* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A PHE* 3.7 16.4 - + - -
1022A GLU 3.6 19.5 - - - -
1023A GLN* 3.3 38.6 - - + -
1026A TRP* 3.4 42.8 - + + -
1027A PHE* 5.4 2.7 - + - -
1112A TYR* 5.0 0.2 - - - -
1177A PRO* 3.5 28.7 - - + -
1387A SER* 3.1 34.8 + - - +
1390A CYS* 1.3 77.3 - - - +
1392A LYS* 1.3 57.4 + - - +
1394A GLN* 3.5 30.2 - - + +
1395A PHE* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A TRP* 4.0 16.4 - - + +
1030A ASN* 6.0 3.8 - - - +
1387A SER 4.1 1.4 + - - -
1388A SER 3.7 18.0 + - - +
1389A PHE* 3.3 11.3 + - + +
1390A CYS 3.1 0.8 - - - -
1391A PHE* 1.3 76.8 - - - +
1393A GLU* 1.3 65.2 + - - +
1395A PHE* 3.2 4.5 + - + +
1396A ASP* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173A ASN 4.1 8.1 - - - +
1174A PHE* 5.3 0.7 - - - -
1175A GLN* 4.7 1.2 + - - -
1303A ARG* 2.8 44.5 + - - -
1332A ARG* 4.5 13.7 + - - +
1389A PHE 3.1 11.9 + - - +
1390A CYS* 3.1 12.2 + - - +
1392A LYS* 1.3 78.2 - - - +
1394A GLN* 1.3 65.0 + - - +
1396A ASP* 3.4 8.0 + - - +
1397A ILE* 3.1 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A PHE* 4.0 1.2 - - - -
1112A TYR* 2.5 49.5 + - - +
1138A PHE* 3.9 19.4 - - + -
1173A ASN 5.6 0.2 - - - +
1174A PHE* 4.2 6.5 - - + -
1175A GLN 2.9 30.5 + - - +
1177A PRO* 3.6 9.0 - - - +
1390A CYS* 3.0 16.2 + - - +
1391A PHE* 3.5 29.6 - - + +
1393A GLU* 1.3 79.2 - - + +
1395A PHE* 1.3 59.0 + - - +
1397A ILE* 3.1 3.7 + - + +
1398A ILE* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A GLY 3.9 10.1 - - - -
1001A MET* 3.8 28.5 - - + -
1026A TRP* 3.7 28.5 - + + -
1027A PHE* 3.9 16.8 - + + -
1032A HIS* 3.7 25.4 - - - -
1077A ILE* 5.6 1.3 - - + -
1391A PHE 2.8 19.0 + - - +
1392A LYS* 3.2 6.7 + - + +
1394A GLN* 1.3 77.0 - - - +
1396A ASP* 1.3 66.2 + - - +
1398A ILE* 3.2 10.9 + - + +
1399A THR* 2.8 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392A LYS* 3.0 29.1 + - - +
1393A GLU* 3.6 10.1 - - - +
1394A GLN 3.3 0.2 - - - -
1395A PHE* 1.3 86.5 - - - +
1397A ILE* 1.3 59.7 + - + +
1399A THR* 3.6 5.7 + - - -
1400A LYS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136A VAL* 4.2 7.7 - - + +
1138A PHE* 3.8 26.2 - - + -
1172A TYR* 3.6 54.2 - - + -
1173A ASN 4.7 2.5 - - - +
1393A GLU* 3.1 35.3 + - + +
1394A GLN* 3.6 6.3 - - - +
1396A ASP* 1.3 76.6 - - + +
1398A ILE* 1.3 64.5 + - - +
1400A LYS* 3.2 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A PHE* 4.9 16.4 - - + -
1077A ILE* 4.0 25.1 - - + -
1079A ILE* 5.0 5.2 - - + -
1108A ARG* 3.0 27.8 + - - -
1110A VAL* 3.8 33.7 - - + -
1112A TYR* 3.8 22.9 - - + +
1136A VAL* 4.1 11.2 - - + +
1138A PHE* 3.8 16.4 - - + -
1394A GLN* 2.8 23.9 + - + +
1395A PHE* 3.6 9.9 - - + +
1397A ILE* 1.3 78.8 - - - +
1399A THR* 1.3 60.7 + - + +
1400A LYS 3.5 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A MET* 4.2 16.4 - - + -
1077A ILE* 4.8 2.7 - - + -
1108A ARG* 3.6 12.2 + - - +
1395A PHE* 2.8 56.0 + - + +
1396A ASP* 3.6 7.3 + - - -
1398A ILE* 1.3 82.3 - - + +
1400A LYS* 1.3 68.1 + - - +
----------------------------------------------------------
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