Contacts of the helix formed by residues 1333 - 1348 (chain A) in PDB entry 1YW2
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 LEU1333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A ILE* 4.3 6.3 - - + -
1332A LEU* 1.3 77.8 - - - +
1334A ILE* 1.3 58.7 + - - +
1335A ASP* 3.1 6.5 - - + +
1336A GLU* 2.7 51.2 + - + +
1337A TRP* 3.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A PHE* 3.8 27.6 - - + +
1060A GLN 4.3 3.1 - - - +
1061A SER* 3.6 30.1 - - - +
1062A ILE* 3.7 21.9 - - + +
1065A ALA* 4.3 13.3 - - + +
1333A LEU* 1.3 73.0 - - - +
1335A ASP* 1.3 62.5 + - - +
1337A TRP* 3.4 2.7 + - - +
1338A LYS* 2.8 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A LEU* 5.6 0.2 - - - +
1333A LEU* 3.1 4.7 - - + +
1334A ILE* 1.3 83.7 - - - +
1336A GLU* 1.3 61.4 + - + +
1338A LYS* 3.5 16.1 - - - +
1339A SER* 2.9 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A LEU* 3.5 26.1 - - + +
1333A LEU* 2.7 50.3 + - + +
1335A ASP* 1.3 73.0 - - + +
1337A TRP* 1.3 60.2 + - - +
1339A SER* 3.5 4.2 + - - -
1340A LEU* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A PHE* 5.0 0.2 - - - -
1062A ILE* 4.1 13.5 + - + +
1065A ALA* 3.4 33.2 - - + -
1066A LYS* 3.6 46.5 - - + +
1069A TYR* 3.6 40.3 - + - -
1327A PHE* 3.8 25.4 - + + -
1330A ARG* 4.0 7.2 - - + -
1331A ASP* 4.8 0.8 - - - +
1332A LEU* 3.6 51.3 + - + +
1333A LEU 3.1 21.3 + - - -
1334A ILE 3.7 0.9 - - - +
1336A GLU* 1.3 76.3 - - - +
1338A LYS* 1.3 59.1 + - - +
1340A LEU* 3.3 9.7 + - + +
1341A THR* 2.8 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A PHE* 3.8 36.7 - - + +
1096A LEU* 4.1 14.1 - - + -
1097A GLU 5.5 2.0 + - - -
1099A PHE* 2.5 53.5 + - + -
1100A ASN* 3.0 22.4 + - - -
1334A ILE* 2.8 20.1 + - + +
1335A ASP* 3.5 19.3 - - - +
1336A GLU 3.1 0.4 - - - -
1337A TRP* 1.3 80.8 - - - +
1339A SER* 1.3 57.8 + - - +
1341A THR* 3.4 4.3 - - - -
1342A TYR* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A LEU* 3.9 33.4 - - - +
1335A ASP 2.9 16.0 + - - -
1336A GLU* 4.2 4.2 + - - -
1338A LYS* 1.3 73.2 - - - +
1340A LEU* 1.3 70.9 + - - +
1342A TYR* 3.7 1.5 - - - +
1343A ASP* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A TYR* 3.4 30.0 - - + +
1332A LEU* 3.8 24.5 - - + -
1336A GLU* 2.8 35.1 + - + +
1337A TRP* 3.4 14.4 - - + +
1339A SER* 1.3 84.0 + - - +
1341A THR* 1.3 64.5 + - - +
1343A ASP* 3.0 24.0 + - + +
1344A GLU* 3.3 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A PHE* 3.8 19.7 - - + -
1065A ALA 4.4 0.3 + - - -
1068A THR* 3.9 23.1 - - + -
1069A TYR* 3.6 27.3 + - - +
1072A LEU* 4.2 17.7 - - + -
1099A PHE* 4.0 9.0 - - + -
1102A VAL* 4.5 3.4 - - + -
1337A TRP 2.8 16.8 + - - -
1338A LYS 3.4 8.5 - - - -
1340A LEU* 1.3 75.8 - - - +
1342A TYR* 1.3 58.7 + - - +
1344A GLU* 3.1 7.8 + - - +
1345A VAL* 2.8 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091A THR* 4.8 9.6 - - + -
1093A ALA* 5.5 1.1 - - + -
1094A ARG 4.0 6.6 + - - -
1095A SER* 3.6 17.2 + - - -
1096A LEU* 3.6 42.0 + - + -
1099A PHE* 3.4 46.8 - + + -
1338A LYS 3.0 12.2 + - - +
1339A SER* 3.7 7.6 - - - +
1340A LEU 3.3 0.2 - - - -
1341A THR* 1.3 75.3 - - - +
1343A ASP* 1.3 62.7 + - - +
1345A VAL* 2.8 6.9 + - + +
1346A ILE* 2.7 65.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A SER* 2.9 26.9 + - - +
1340A LEU* 3.0 20.3 + - + +
1342A TYR* 1.3 86.1 - - - +
1344A GLU* 1.3 50.7 + - + +
1346A ILE* 3.4 9.5 + - - +
1347A SER* 2.8 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A TYR* 4.1 10.1 + - + -
1072A LEU* 3.5 17.4 - - + +
1073A ARG* 3.6 39.2 + - + -
1076A LYS* 2.8 54.9 + - + +
1089A VAL* 4.7 0.2 - - - +
1340A LEU 3.7 11.2 - - - +
1341A THR 3.1 8.6 + - - +
1343A ASP* 1.3 73.4 - - + +
1345A VAL* 1.3 69.3 + - - +
1347A SER* 3.8 6.0 + - - -
1348A PHE* 3.2 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072A LEU* 3.9 13.7 - - + -
1089A VAL* 4.3 31.4 - - + +
1090A PHE* 4.4 16.4 - - - +
1091A THR* 4.6 12.6 - - + -
1099A PHE* 3.8 24.0 - - + -
1102A VAL* 4.8 5.4 - - + -
1341A THR* 2.8 21.5 + - + +
1342A TYR* 2.8 6.9 + - + +
1344A GLU* 1.3 76.7 - - - +
1346A ILE* 1.3 73.0 + - + +
1348A PHE* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091A THR* 6.0 1.6 - - + -
1342A TYR* 2.7 56.5 + - + +
1343A ASP* 3.4 11.7 - - - +
1345A VAL* 1.3 82.9 - - + +
1347A SER* 1.3 64.7 + - - +
1348A PHE 3.2 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076A LYS* 3.1 17.3 + - - -
1343A ASP 2.8 20.6 + - - -
1344A GLU* 3.8 7.8 + - - -
1345A VAL 3.3 0.4 - - - -
1346A ILE* 1.3 76.9 - - - +
1348A PHE* 1.3 65.1 + - - +
1349A VAL* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076A LYS* 3.5 32.1 - - + +
1086A LEU* 3.9 23.8 - - + -
1087A LEU 3.7 12.6 - - - -
1088A ASP* 3.7 26.7 - - - -
1089A VAL* 3.5 35.9 - - + +
1344A GLU 3.2 8.1 + - - +
1345A VAL 3.1 11.2 + - - +
1346A ILE 3.2 4.0 + - - +
1347A SER* 1.3 78.1 - - - +
1349A VAL* 1.3 74.7 + - - +
1350A PRO* 3.5 35.1 - - + +
1351A PRO* 3.8 6.1 - - + -
----------------------------------------------------------
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