Contacts of the helix formed by residues 246 - 261 (chain A) in PDB entry 2WWA
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 ASN 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 3.7 32.0 - - + +
219A ASN* 3.4 36.4 + - - +
220A LEU* 3.9 11.9 - - + -
236A ILE* 3.9 16.0 - - - +
244A LEU* 3.3 26.3 + - - +
245A PRO* 1.4 80.7 + - - +
247A LEU* 1.4 58.1 + - - -
248A THR* 3.3 3.9 - - - +
249A THR* 3.5 11.5 - - - +
250A THR* 2.9 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.8 35.7 - - + +
236A ILE 5.0 0.2 - - - +
237A SER* 3.2 41.7 - - - +
238A ALA* 5.7 1.1 - - + -
245A PRO 3.0 3.6 + - - -
246A ASN* 1.4 74.2 - - - +
248A THR* 1.4 64.9 + - - +
250A THR* 3.3 2.4 + - + -
251A ILE* 3.1 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER 4.8 0.2 + - - -
244A LEU* 5.3 5.2 - - + -
245A PRO* 3.8 35.7 - - + +
246A ASN 4.3 4.0 - - - +
247A LEU* 1.4 81.1 - - - +
249A THR* 1.4 66.0 + - + +
251A ILE* 3.7 3.7 + - - +
252A ILE* 3.2 33.8 + - - +
356A PHE 5.1 2.7 - - - +
357A PHE* 4.0 16.9 + - - +
358A LYS* 3.6 30.3 - - + +
444A LEU 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 3.3 29.2 + - - +
197A THR* 5.2 4.9 + - - +
216A ALA* 3.4 33.4 - - + -
244A LEU* 5.9 8.1 - - + -
246A ASN* 3.5 8.7 - - - +
248A THR* 1.4 81.0 - - + +
250A THR* 1.4 62.6 + - - +
252A ILE* 3.8 13.8 - - - +
253A VAL* 3.7 21.8 - - - +
356A PHE* 4.9 13.2 + - - +
446A LEU* 4.4 8.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
197A THR* 4.3 8.8 + - - +
216A ALA* 4.2 9.7 - - - +
217A LEU* 3.9 28.6 + - + -
220A LEU* 3.7 19.5 - - + +
221A ILE* 5.1 2.9 - - + -
246A ASN 2.9 15.3 + - - -
247A LEU* 3.3 8.4 + - + -
249A THR* 1.4 76.7 - - - +
251A ILE* 1.4 66.5 + - + +
253A VAL* 3.4 21.3 - - + +
254A LEU* 4.0 6.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
247A LEU* 3.1 48.0 + - + +
248A THR* 3.7 5.6 + - - +
250A THR* 1.4 78.9 - - + +
252A ILE* 1.4 63.7 + - + +
253A VAL 3.3 0.9 - - - -
254A LEU* 3.3 11.3 + - + +
255A ALA* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 3.2 25.4 - - + +
249A THR* 3.8 18.6 - - - +
250A THR 3.4 0.4 - - - -
251A ILE* 1.4 83.1 - - + +
253A VAL* 1.4 60.4 + - - +
255A ALA* 4.2 9.0 - - + -
256A ILE* 3.3 26.6 - - - +
356A PHE 5.3 2.7 - - - -
357A PHE 3.7 17.5 - - - +
444A LEU* 3.9 28.0 - - + +
445A GLY* 3.8 7.4 - - - +
446A LEU* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.6 31.0 - - + -
196A ASP* 5.6 0.4 - - - +
197A THR* 5.7 4.9 - - + +
249A THR* 3.7 11.9 - - - +
250A THR* 3.4 17.7 - - + +
252A ILE* 1.4 76.4 - - - +
254A LEU* 1.4 66.5 + - + +
255A ALA 3.5 0.2 - - - -
256A ILE* 4.2 3.0 + - - +
257A ALA* 3.4 21.1 + - - +
446A LEU* 3.6 35.4 - - + -
449A LYS* 4.4 0.9 - - - +
453A ILE* 4.0 19.5 - - + +
58B PHE* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR 4.2 8.3 - - - +
251A ILE* 3.3 11.4 + - + +
253A VAL* 1.4 82.8 - - + +
255A ALA* 1.4 63.5 + - - +
257A ALA* 3.2 16.7 + - + +
258A ILE* 3.2 39.7 + - + +
54B VAL* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 2.9 25.4 + - + +
252A ILE* 4.2 8.5 - - + -
253A VAL 3.5 0.2 - - - -
254A LEU* 1.4 78.2 - - - +
256A ILE* 1.4 59.6 + - - +
258A ILE* 3.9 11.8 + - - +
259A ILE* 3.4 19.2 + - - +
444A LEU* 3.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE 3.3 24.5 - - - +
253A VAL* 4.2 2.9 + - - +
254A LEU 3.4 0.4 - - - -
255A ALA* 1.4 73.8 - - - +
257A ALA* 1.4 64.1 + - - +
259A ILE* 3.2 13.7 + - + +
260A VAL* 3.1 24.2 + - + +
437A ILE 5.1 2.2 - - - +
441A GLY* 3.3 44.6 - - - +
442A GLU 4.5 0.2 - - - +
444A LEU* 4.7 4.9 - - + -
445A GLY 4.0 6.7 - - - +
446A LEU* 4.0 17.9 - - + -
450A ALA 4.2 11.2 - - - +
453A ILE* 4.6 4.5 - - + -
454A VAL* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL 3.4 19.0 + - - +
254A LEU* 3.2 13.3 + - + +
256A ILE* 1.4 78.7 - - - +
258A ILE* 1.4 62.0 + - + +
260A VAL* 4.2 1.1 - - - -
261A CYS* 3.2 26.3 + - - +
453A ILE* 5.8 2.0 - - + -
457A ILE* 3.3 27.5 - - + +
50B ILE* 5.3 2.1 - - - +
54B VAL* 5.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.2 42.1 + - + +
255A ALA* 4.1 9.2 - - - +
256A ILE 3.3 0.2 - - - -
257A ALA* 1.4 76.9 - - + +
259A ILE* 1.4 67.4 + - + +
261A CYS* 4.2 2.2 - - - +
262A TYR* 3.4 24.5 + - + +
47B TYR* 6.0 8.1 - - + -
50B ILE* 5.5 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA 3.4 20.2 - - - +
256A ILE* 3.5 20.6 - - + +
258A ILE* 1.4 87.4 - - + +
260A VAL* 1.4 62.3 + - + +
261A CYS 3.5 0.4 - - - -
262A TYR* 3.9 9.4 - - + +
263A LEU* 3.5 11.6 + - - +
437A ILE* 3.2 45.7 - - + +
440A ILE* 4.8 5.2 - - + -
441A GLY* 4.8 6.7 - - - -
444A LEU* 5.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 3.1 21.4 + - + +
257A ALA* 4.2 0.4 - - - -
259A ILE* 1.4 80.6 - - + +
261A CYS* 1.4 64.3 + - - +
262A TYR 3.3 1.6 - - - -
263A LEU* 3.8 4.7 + - - +
264A GLN 4.1 0.9 + - - -
289A LEU* 3.4 29.3 - - + +
434A LEU* 5.0 1.8 - - + -
437A ILE* 4.0 27.1 - - + +
454A VAL* 3.4 49.8 - - + +
457A ILE* 3.9 16.6 - - + -
458A ALA* 3.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA 3.2 19.2 + - - +
258A ILE 4.2 2.7 - - - +
260A VAL* 1.4 77.5 - - - +
262A TYR* 1.4 58.7 + - - +
263A LEU 3.5 0.2 - - - -
264A GLN* 4.1 3.9 + - - +
265A SER* 3.9 14.0 + - - -
457A ILE* 3.8 15.7 - - + -
458A ALA* 4.4 6.7 - - - -
461A PHE* 3.5 50.7 - - - -
50B ILE* 3.9 30.3 - - + +
54B VAL* 5.4 1.6 - - - -
----------------------------------------------------------
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