Contacts of the helix formed by residues 244 - 258 (chain A) in PDB entry 1WXI
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 PRO 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASN* 5.5 3.4 - - - +
242A ASN 4.8 0.2 - - - +
243A VAL* 1.3 90.0 - - + +
245A GLN* 1.3 65.9 + - - +
246A GLN* 4.5 4.0 - - + +
247A VAL* 2.9 35.9 + - + +
248A ALA 3.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 5.3 3.5 - - - +
243A VAL 3.3 6.2 + - - +
244A PRO* 1.3 72.5 - - - +
246A GLN* 1.3 56.6 + - - +
248A ALA* 3.2 14.3 + - - +
249A ARG* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 5.9 1.6 - - - +
244A PRO* 3.2 3.7 - - + +
245A GLN* 1.3 78.6 - - - +
247A VAL* 1.3 71.6 + - + +
249A ARG* 3.5 27.2 + - - +
250A THR* 3.0 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.1 9.0 - - + -
233A ASN* 3.7 41.5 - - + +
243A VAL* 4.3 10.5 - - + -
244A PRO* 2.9 33.5 + - + +
246A GLN* 1.3 86.1 - - + +
248A ALA* 1.3 66.3 + - - +
250A THR* 3.2 6.2 + - - -
251A ILE* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 4.1 20.0 - - + -
243A VAL* 4.0 17.2 - - + +
244A PRO 3.0 11.4 + - - +
245A GLN* 3.2 19.7 + - - +
247A VAL* 1.3 78.0 - - - +
249A ARG* 1.3 57.7 + - - +
251A ILE* 3.3 2.6 + - - +
252A GLU* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 2.9 41.6 + - - +
246A GLN* 3.8 27.4 - - - +
248A ALA* 1.3 78.0 - - + +
250A THR* 1.3 58.4 + - - +
252A GLU* 3.8 11.1 - - - +
253A ASN* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU 3.8 17.9 - - - +
228A GLY* 4.6 5.2 + - - +
229A VAL* 3.8 22.4 - - + +
246A GLN* 3.0 32.7 + - - -
247A VAL 3.2 8.0 + - - -
249A ARG* 1.3 74.1 - - - +
251A ILE* 1.3 64.8 + - - +
253A ASN* 3.3 7.4 + - + +
254A TRP* 3.2 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 5.5 0.7 - - + -
167A ILE* 3.4 37.0 - - + +
168A THR* 5.2 4.9 - - + -
229A VAL* 4.4 17.9 - - + -
233A ASN* 4.0 13.0 - - + +
234A ILE* 4.2 13.0 - - + +
237A TYR* 3.7 39.9 - - + -
243A VAL* 5.5 0.2 - - + -
247A VAL* 3.1 24.8 + - + +
248A ALA* 3.7 6.3 - - - +
250A THR* 1.3 75.2 - - - +
252A GLU* 1.3 63.4 + - - +
254A TRP* 3.2 12.2 + - - +
255A TYR* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.5 34.8 - - + +
4A GLN* 4.1 8.1 + - - +
7A ILE* 4.2 2.2 - - + -
237A TYR* 2.7 37.7 + - + +
248A ALA* 2.9 27.0 + - - +
249A ARG* 3.9 11.1 - - - +
251A ILE* 1.3 74.2 - - - +
253A ASN* 1.3 64.9 + - - +
255A TYR* 3.4 6.6 + - - +
256A LEU* 3.1 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG 2.9 18.4 + - - +
250A THR* 3.5 8.9 + - + +
251A ILE 3.2 0.2 - - - -
252A GLU* 1.3 76.5 - - - +
254A TRP* 1.3 71.0 + - - +
256A LEU* 3.9 6.6 - - - +
257A LYS* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE 4.2 0.9 - - - -
168A THR* 4.0 39.5 - - + -
226A ALA* 3.5 26.0 - - + -
227A LEU* 2.9 36.6 + - + +
229A VAL* 5.4 2.2 - - + -
250A THR* 3.2 31.9 + - + +
251A ILE* 3.2 9.6 + - - +
253A ASN* 1.3 85.8 - - + +
255A TYR* 1.3 59.5 + - - +
257A LYS* 3.4 34.3 + - + +
258A THR* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.1 4.9 - - + -
6A GLN 5.7 0.2 - - - -
7A ILE* 3.7 44.0 - - + +
10A ALA* 3.8 22.2 - - - +
11A LEU* 4.7 10.1 - - + +
167A ILE* 3.3 32.3 + - + +
251A ILE 3.0 12.0 + - - +
252A GLU 3.6 7.6 - - - +
253A ASN 3.3 0.2 - - - -
254A TRP* 1.3 76.7 - - - +
256A LEU* 1.3 79.7 + - + +
258A THR* 3.2 8.7 + - - -
259A GLU* 3.4 13.0 + - - -
262A ARG* 2.7 55.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.5 24.0 - - + -
252A GLU* 3.1 18.7 + - + +
253A ASN* 4.0 5.8 - - - +
255A TYR* 1.3 95.9 - - + +
257A LYS* 1.3 62.5 + - - +
258A THR 3.3 0.7 + - - -
259A GLU* 3.6 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASN* 3.0 26.8 + - - +
254A TRP* 3.8 37.6 - - + +
256A LEU* 1.3 77.8 - - - +
258A THR* 1.3 62.4 + - + +
259A GLU 3.8 0.3 + - - -
260A HIS* 3.5 17.6 + - + -
300A AMP 4.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR 3.6 15.6 + - - +
169A GLY* 3.7 20.9 + - - +
254A TRP* 2.8 29.6 + - + +
255A TYR 3.4 1.2 + - - -
256A LEU 3.2 0.4 - - - -
257A LYS* 1.3 88.9 - - + +
259A GLU* 1.3 65.2 + - - +
260A HIS* 3.1 10.5 - - + -
261A LYS* 2.9 32.1 + - + +
262A ARG* 3.0 28.2 + - - -
----------------------------------------------------------
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