Contacts of the helix formed by residues 1244 - 1255 (chain A) in PDB entry 1WUF
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 SER1244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A GLN* 6.0 3.4 - - - -
1242A ILE 3.7 0.6 - - - -
1243A ARG* 1.3 82.8 - - - +
1245A VAL* 1.3 67.5 + - - +
1246A LYS* 3.7 11.7 + - - +
1247A ASP* 2.9 31.5 + - - +
1248A VAL* 3.0 15.8 + - - +
1267A VAL* 4.2 1.0 - - - +
1272A SER* 4.4 5.2 - - - -
1276A ILE* 3.7 13.4 - - - +
2220B LYS* 5.0 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244A SER* 1.3 72.9 - - - +
1246A LYS* 1.3 53.1 + - - +
1248A VAL* 2.9 7.3 + - + +
1249A GLU* 2.8 44.1 + - - +
1272A SER* 4.5 1.5 + - - +
1275A LYS* 3.3 50.0 - - + +
1276A ILE* 3.6 12.8 - - + +
1279A TYR* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244A SER* 3.7 10.9 + - - +
1245A VAL* 1.3 79.8 - - - +
1247A ASP* 1.3 64.1 + - - +
1249A GLU* 3.2 24.0 + - + +
1250A GLN* 3.2 40.5 + - - +
2218B GLY* 5.8 4.9 - - - +
2220B LYS* 5.7 4.7 - - + -
2221B ASP* 3.3 33.5 + - - +
2223B VAL* 6.1 0.2 - - - +
2224B ASP* 4.6 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A PHE* 4.2 10.5 - - + -
1241A ASN 3.6 16.3 - - - +
1242A ILE* 4.1 7.6 - - - +
1243A ARG* 2.9 32.1 + - - +
1244A SER* 2.9 18.0 + - - +
1246A LYS* 1.3 77.2 - - - +
1248A VAL* 1.3 65.3 + - - +
1250A GLN* 3.4 10.3 + - - +
1251A ALA* 3.2 21.7 + - - +
2220B LYS* 3.0 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242A ILE* 3.9 22.2 - - + -
1244A SER 3.0 13.2 + - - +
1245A VAL* 2.9 9.9 + - + +
1247A ASP* 1.3 73.4 - - - +
1249A GLU* 1.3 56.4 + - - +
1251A ALA* 3.1 4.2 + - + +
1252A HIS* 2.8 32.9 + - - +
1257A CYS* 6.2 0.4 - - - -
1260A ILE* 4.4 13.0 - - + -
1276A ILE* 3.8 26.5 - - + -
1279A TYR* 3.7 28.0 - - + -
1280A CYS* 4.3 8.3 - - - -
1285A ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245A VAL* 2.8 30.8 + - - +
1246A LYS* 3.4 27.5 + - + +
1248A VAL* 1.3 76.9 - - - +
1250A GLN* 1.3 56.8 + - + +
1252A HIS* 3.4 1.9 + - - +
1253A SER* 3.0 30.0 + - - -
1279A TYR* 3.4 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A PHE* 3.9 23.1 - - + -
1246A LYS* 3.2 26.2 + - - +
1247A ASP* 3.8 12.6 - - - +
1248A VAL 3.2 0.2 - - - -
1249A GLU* 1.3 76.2 - - - +
1251A ALA* 1.3 67.2 + - - +
1253A SER* 3.2 6.3 + - - -
1254A ILE* 2.9 34.2 + - + +
2220B LYS* 3.4 17.5 - - - +
2221B ASP* 3.4 6.4 + - - -
2222B PHE* 2.6 41.8 - - - +
2223B VAL* 2.8 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A PHE* 4.0 14.3 - - + -
1238A LEU* 3.8 29.2 - - + -
1242A ILE* 4.4 2.2 - - + -
1247A ASP 3.2 9.6 + - - +
1248A VAL* 3.1 11.5 + - - +
1250A GLN* 1.3 80.0 - - - +
1252A HIS* 1.3 57.5 + - - +
1254A ILE 3.6 0.2 + - - -
1255A GLY* 2.8 6.6 + - - -
1256A SER* 2.7 33.2 + - - -
1257A CYS* 3.9 16.9 + - - -
1260A ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248A VAL 2.8 16.8 + - - +
1249A GLU 3.4 5.2 - - - +
1250A GLN 3.0 0.2 - - - -
1251A ALA* 1.3 73.2 - - - +
1253A SER* 1.3 63.0 + - - +
1254A ILE 3.1 1.6 - - - -
1255A GLY* 2.8 21.3 + - - -
1257A CYS* 5.4 8.9 - - - -
1279A TYR* 3.0 22.4 + - - +
1283A ASN* 3.1 46.1 + - + +
1285A ILE* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A GLU 3.0 10.9 + - - -
1250A GLN 3.2 3.1 + - - -
1252A HIS* 1.3 80.8 - - - +
1254A ILE* 1.3 62.5 + - - +
2223B VAL* 3.2 34.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222A PHE* 3.9 28.3 - - + +
1223A VAL* 4.6 6.1 - - + +
1226A ALA* 3.3 18.5 - - + +
1230A LYS* 3.9 13.2 + - - -
1250A GLN* 2.9 28.3 + - + +
1253A SER* 1.3 77.5 - - - +
1255A GLY* 1.3 60.1 + - - +
1256A SER* 3.7 17.3 - - - +
2223B VAL* 3.5 22.4 - - + -
2254B ILE* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A ALA* 2.9 20.4 - - - +
1229A GLN* 3.6 13.0 - - - +
1230A LYS* 4.4 7.4 - - - +
1251A ALA 2.8 1.7 + - - -
1252A HIS* 2.8 17.0 + - - -
1254A ILE* 1.3 80.2 - - - +
1256A SER* 1.3 63.1 + - - +
1257A CYS 3.4 6.3 - - - -
----------------------------------------------------------
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