Contacts of the helix formed by residues 234 - 247 (chain A) in PDB entry 1UU1
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 SER 234 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 4.8 0.3 + - - -
232A ASN 4.2 1.6 + - - -
233A VAL* 1.3 79.7 - - - +
235A TYR* 1.3 65.2 + - - +
237A SER* 2.9 30.7 + - - -
238A GLN* 2.9 21.7 + - - +
83B ASN* 5.5 0.6 + - - -
208B ALA 3.2 15.3 - - - -
209B GLN* 3.4 35.1 + - - -
210B ARG* 4.3 6.6 - - - +
234B SER* 4.6 1.2 + - - -
237B SER* 4.0 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 3.6 9.2 + - - -
45A LEU* 4.2 16.6 - - + -
46A ASN* 2.9 46.3 + - - +
49A ALA* 3.9 15.0 - - + -
50A LEU* 3.7 19.3 - - + -
54A TYR* 3.6 54.8 - + + +
233A VAL 3.7 0.6 + - - -
234A SER* 1.3 70.6 - - - +
236A VAL* 1.3 68.0 + - + +
238A GLN* 3.2 6.5 + - - +
239A MET* 3.1 40.0 + - + +
208B ALA* 2.9 26.4 + - + -
209B GLN* 3.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.3 10.8 - - + -
42A PHE* 5.0 1.8 - - + -
45A LEU* 4.1 20.6 - - + -
50A LEU* 3.8 15.3 - - + -
209A GLN* 4.8 0.7 - - - +
235A TYR* 1.3 82.1 - - + +
237A SER* 1.3 62.6 + - - +
239A MET* 3.0 7.2 + - - +
240A PHE* 2.9 45.9 + - + -
209B GLN* 2.9 30.9 - - - +
236B VAL* 3.9 15.9 - - + -
240B PHE* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 2.6 48.7 + - - -
210A ARG 4.7 0.4 - - - -
211A VAL* 3.7 17.3 - - - +
233A VAL* 3.9 7.6 - - - -
234A SER* 2.9 25.7 + - - -
236A VAL* 1.3 75.3 - - - +
238A GLN* 1.3 63.1 + - - +
240A PHE* 3.2 8.0 + - - +
241A ALA 3.0 18.9 + - - -
234B SER* 4.1 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.5 13.1 - - + -
55A ASP 3.1 12.5 - - - +
56A SER* 2.5 30.2 + - - +
58A ASP* 2.7 33.1 - - + +
61A LEU* 3.6 21.9 - - + +
211A VAL* 5.1 0.2 - - - -
233A VAL* 3.1 32.5 - - + +
234A SER 2.9 14.0 + - - +
235A TYR 3.5 7.6 - - - +
237A SER* 1.3 78.3 - - - +
239A MET* 1.3 55.4 + - - +
241A ALA* 3.4 4.7 + - - +
242A LYS* 3.0 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.7 30.3 - - + +
44A ARG* 3.5 49.4 - - + +
45A LEU* 3.8 12.1 - - + -
54A TYR* 5.5 0.4 - - - +
235A TYR* 3.1 44.5 + - + +
236A VAL 3.0 10.8 + - - +
238A GLN* 1.3 72.5 - - - +
240A PHE* 1.3 67.9 + - - +
242A LYS* 3.1 25.8 + - - +
243A VAL* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 26.7 - + - -
38A VAL* 4.3 11.0 - - + -
41A VAL* 3.6 27.1 - - + +
42A PHE* 4.5 12.8 - + - -
206A LEU* 3.9 20.4 - - + +
209A GLN* 3.8 17.7 - - + -
236A VAL* 2.9 39.6 + - + -
237A SER* 3.5 9.2 - - - +
239A MET* 1.3 77.2 - - - +
241A ALA* 1.3 61.8 + - - +
243A VAL* 3.3 3.5 - - - +
244A ALA* 3.0 24.3 + - - +
45B LEU* 5.0 1.1 - - + -
50B LEU* 3.6 31.0 - - + -
236B VAL* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.9 11.7 - - + -
200A PHE* 3.6 37.8 - - + -
206A LEU* 4.4 4.4 - - + +
211A VAL* 4.0 14.8 - - + +
237A SER 3.0 12.7 + - - +
238A GLN* 3.8 7.9 - - - +
239A MET 3.3 0.2 - - - -
240A PHE* 1.3 75.4 - - - +
242A LYS* 1.3 58.0 + - - +
244A ALA* 3.3 2.6 + - - +
245A LEU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.5 4.9 - - - +
54A TYR* 4.1 4.9 + - - -
58A ASP* 3.0 26.7 + - - -
60A GLU* 3.1 48.3 + - + +
61A LEU* 3.8 27.8 - - + +
64A LYS* 4.1 8.3 + - + +
238A GLN* 3.0 34.2 + - - +
239A MET* 3.5 29.0 - - - +
241A ALA* 1.3 75.7 - - - +
243A VAL* 1.3 63.6 + - - +
245A LEU* 3.2 7.3 + - - +
246A ASP* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.2 9.9 - - + -
37A LEU* 4.1 10.5 - - + +
40A GLU* 3.9 31.4 - - + +
41A VAL* 3.3 35.0 - - + -
44A ARG* 4.1 20.6 - - - +
239A MET* 2.9 14.3 + - + +
240A PHE* 3.3 9.0 - - - +
242A LYS* 1.3 76.6 - - - +
244A ALA* 1.3 69.3 + - - +
246A ASP* 3.0 16.8 + - - -
247A HIS* 3.0 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.2 2.2 - - + -
37A LEU* 4.9 0.7 - - - -
200A PHE* 4.5 1.8 - - + -
204A PHE* 3.8 22.7 - - + -
206A LEU* 4.1 14.6 - - + -
240A PHE 3.0 14.9 + - - +
241A ALA* 3.5 5.6 - - - +
242A LYS 3.2 0.2 - - - -
243A VAL* 1.3 82.9 - - - +
245A LEU* 1.3 59.7 + - - +
247A HIS 3.0 5.7 + - - -
248A ARG* 3.0 24.4 + - - -
251A PHE* 3.4 25.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.0 2.2 - - + -
64A LYS* 3.6 20.0 - - + +
65A ILE* 3.6 47.6 - - + +
68A TYR* 4.0 27.8 - - + -
200A PHE* 3.6 20.6 - - + -
204A PHE* 4.0 17.5 - - + -
241A ALA 2.9 19.7 + - - +
242A LYS 3.7 4.5 - - - +
244A ALA* 1.3 77.5 - - - +
246A ASP* 1.3 61.4 + - - +
247A HIS 3.0 1.3 + - - -
248A ARG* 3.1 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 4.7 3.5 - - - +
44A ARG* 3.7 14.9 + - - -
64A LYS* 2.7 44.8 + - - +
242A LYS 2.9 13.4 + - - +
243A VAL* 3.0 9.5 + - - +
245A LEU* 1.3 75.2 - - - +
247A HIS* 1.3 75.2 + - + +
248A ARG* 3.5 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.4 30.6 - - + +
40A GLU* 2.7 41.3 + - - -
243A VAL 3.0 21.8 + - - +
244A ALA 3.0 5.8 + - - +
246A ASP* 1.3 86.5 + - + +
248A ARG* 1.3 63.7 + - - +
249A GLU 2.9 5.7 + - - -
250A ILE* 3.0 33.0 + - + +
251A PHE* 3.4 8.1 - - - -
----------------------------------------------------------
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