Contacts of the helix formed by residues 1386 - 1400 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177B PRO* 4.0 0.2 - - - -
1178B MET 3.5 3.9 - - - +
1179B ASP* 3.9 4.3 - - - +
1180B ILE* 3.0 37.4 + - + +
1181B VAL* 3.7 7.0 + - - +
1381B LEU 4.0 0.6 + - - -
1382B TYR* 3.0 47.4 + - + +
1384B HIS 4.0 0.2 - - - -
1385B GLN* 1.3 78.6 - - - +
1387B SER* 1.3 66.4 + - - +
1388B SER* 2.6 34.8 + - - -
1389B PHE* 3.0 20.7 + - + +
1390B CYS* 3.1 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B GLU* 3.8 4.0 + - - -
1026B TRP* 3.6 12.4 + - - -
1029B LYS* 6.3 0.9 - - - -
1177B PRO* 3.4 15.0 + - - +
1178B MET* 2.9 39.3 + - - -
1179B ASP* 3.4 11.3 + - - -
1385B GLN 3.6 0.6 + - - -
1386B ASP* 1.3 72.2 - - - +
1388B SER* 1.3 63.3 + - - +
1391B PHE* 3.0 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B TRP* 4.5 9.0 + - - +
1029B LYS* 6.2 1.8 - - - -
1382B TYR* 4.0 10.9 + - - -
1386B ASP* 2.6 23.6 + - - -
1387B SER* 1.3 77.3 - - - +
1389B PHE* 1.3 73.8 + - - +
1392B LYS* 3.5 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332B ARG* 3.4 41.1 - - - +
1382B TYR* 3.5 60.3 - + - -
1383B GLN* 3.8 17.0 - - + -
1386B ASP* 3.0 7.9 + - + +
1387B SER 3.0 0.2 - - - -
1388B SER* 1.3 88.8 - - - +
1390B CYS* 1.3 61.2 + - - +
1391B PHE 3.5 0.2 - - - -
1392B LYS* 3.3 6.0 + - + +
1393B GLU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175B GLN* 3.7 36.3 - - + +
1177B PRO* 3.4 23.8 - - + -
1332B ARG* 4.0 8.5 - - - -
1385B GLN* 3.6 33.9 - - - -
1386B ASP 3.1 5.0 + - - -
1389B PHE* 1.3 78.0 - - - +
1391B PHE* 1.3 60.9 + - - +
1393B GLU* 3.2 11.5 + - - +
1394B GLN* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE* 3.6 26.7 - + - -
1022B GLU* 3.4 25.1 - - + -
1023B GLN* 3.3 36.8 - - + -
1026B TRP* 3.3 41.0 - + + -
1027B PHE* 5.6 2.5 - + - -
1112B TYR* 5.0 0.7 - - - -
1177B PRO* 3.4 29.2 - - + -
1387B SER* 3.0 27.4 + - - +
1390B CYS* 1.3 76.5 - - - +
1392B LYS* 1.3 58.8 + - - +
1394B GLN* 3.5 19.9 - - + +
1395B PHE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B TRP* 4.0 15.3 - - + +
1387B SER 3.9 2.0 + - - -
1388B SER 3.5 18.6 - - - +
1389B PHE* 3.3 11.5 + - + +
1390B CYS 3.2 0.2 - - - -
1391B PHE* 1.3 77.2 - - - +
1393B GLU* 1.3 64.2 + - - +
1395B PHE* 3.2 3.5 + - + +
1396B ASP* 3.0 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173B ASN 4.3 8.0 - - - +
1174B PHE* 5.3 0.5 - - - -
1175B GLN* 4.6 1.4 + - - -
1303B ARG* 3.0 41.6 + - - -
1332B ARG* 4.6 12.6 + - - +
1389B PHE 3.0 13.3 + - - +
1390B CYS* 3.3 12.6 - - - +
1392B LYS* 1.3 78.7 - - - +
1394B GLN* 1.3 64.9 + - - +
1396B ASP* 3.5 8.2 + - - +
1397B ILE* 3.2 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B PHE* 4.1 1.8 - - - -
1112B TYR* 2.6 49.4 + - - +
1138B PHE* 3.7 19.9 - - + -
1173B ASN 5.6 0.2 - - - +
1174B PHE* 3.9 9.1 - - + +
1175B GLN 2.9 32.2 + - - +
1177B PRO* 3.8 4.2 - - - +
1390B CYS* 2.9 23.2 + - - +
1391B PHE* 3.5 28.2 - - + +
1392B LYS 3.3 0.2 - - - -
1393B GLU* 1.3 78.6 - - + +
1395B PHE* 1.3 60.9 + - - +
1397B ILE* 3.2 4.1 + - + +
1398B ILE* 2.8 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B MET* 3.7 26.5 - - + -
1026B TRP* 3.6 27.4 - + + -
1027B PHE* 3.8 16.2 - + + -
1032B HIS* 3.7 26.5 - + - -
1077B ILE* 5.5 1.6 - - + -
1391B PHE 2.9 19.0 + - - +
1392B LYS* 3.6 4.9 - - + +
1394B GLN* 1.3 75.8 - - - +
1396B ASP* 1.3 69.1 + - - +
1398B ILE* 3.2 12.1 + - + +
1399B THR* 2.8 56.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392B LYS* 3.0 42.9 + - - +
1393B GLU* 3.8 7.4 - - - +
1394B GLN 3.3 0.2 - - - -
1395B PHE* 1.3 85.6 - - - +
1397B ILE* 1.3 66.0 + - + +
1399B THR* 3.9 4.7 - - - -
1400B LYS* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136B VAL* 4.4 7.5 - - + +
1138B PHE* 3.7 24.9 - - + -
1172B TYR* 3.4 60.9 + - + -
1173B ASN 4.7 2.9 - - - +
1393B GLU* 3.2 31.4 + - + +
1394B GLN* 3.2 7.5 + - + +
1396B ASP* 1.3 79.6 - - + +
1398B ILE* 1.3 64.4 + - - +
1399B THR 3.3 0.3 + - - -
1400B LYS 3.7 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B PHE* 4.8 16.2 - - + -
1077B ILE* 4.2 19.5 - - + -
1079B ILE* 5.1 5.2 - - + -
1108B ARG* 2.8 34.3 + - - +
1110B VAL* 3.9 34.1 - - + -
1112B TYR* 3.9 20.6 - - + +
1136B VAL* 4.4 10.5 - - + +
1138B PHE* 3.8 15.5 - - + -
1394B GLN* 2.8 27.1 + - + +
1395B PHE* 3.2 13.4 + - + +
1397B ILE* 1.3 78.5 - - - +
1399B THR* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B MET* 5.2 3.3 - - - +
1108B ARG* 3.0 23.0 + - - +
1395B PHE* 2.8 48.7 + - + -
1396B ASP* 3.9 6.1 - - - -
1397B ILE 3.2 0.2 - - - -
1398B ILE* 1.3 78.7 - - - +
1400B LYS* 1.3 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B TYR* 5.5 4.8 + - - -
1396B ASP 3.0 16.4 + - - +
1397B ILE* 3.7 15.2 - - - +
1399B THR* 1.3 85.6 - - + +
----------------------------------------------------------
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