Contacts of the helix formed by residues 242 - 261 (chain A) in PDB entry 3EJW
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 ASP 242 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TRP* 1.3 75.6 - - - +
243A VAL* 1.3 55.7 + - - +
244A THR* 3.6 10.7 + - - -
245A GLN* 3.1 48.9 + - + +
246A GLN* 2.9 24.8 + - - +
299A LEU* 4.5 4.6 - - + +
301A GLU* 4.7 16.9 + - + +
303A THR* 5.5 0.8 + - - -
315A PHE* 5.2 7.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
15A PHE* 3.5 56.3 - - + +
18A SER* 3.9 14.1 - - - -
19A GLY* 3.6 7.8 - - - -
89A TRP* 3.9 10.8 - - + -
240A LEU* 4.7 0.2 - - + -
241A TRP* 2.9 11.4 + - - +
242A ASP* 1.3 69.2 + - - +
244A THR* 1.3 68.0 + - - +
246A GLN* 3.3 16.4 - - - +
247A GLY 3.0 18.0 + - - -
315A PHE* 3.6 33.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.8 24.9 + - - +
21A ALA* 5.1 1.6 - - + -
22A GLY* 3.4 26.4 - - - +
25A LYS* 6.0 4.3 - - + -
242A ASP* 3.7 8.5 - - - -
243A VAL* 1.3 80.4 - - - +
245A GLN* 1.3 63.1 + - - +
247A GLY 3.1 3.1 + - - -
248A LYS* 3.1 17.8 + - + +
315A PHE* 4.4 14.2 - - - +
----------------------------------------------------------
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 ASP* 3.1 38.1 + - - +
244A THR* 1.3 76.3 - - - +
246A GLN* 1.3 61.1 + - - +
248A LYS* 3.1 8.7 + - + +
249A ILE* 2.8 40.4 + - + +
273A GLY 4.4 3.6 - - - +
274A VAL* 4.0 37.5 - - + +
299A LEU* 5.5 2.0 - - - +
300A PRO* 4.2 27.7 - - - +
301A GLU* 5.3 5.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A PHE* 4.2 1.0 - - - -
89A TRP* 3.8 19.3 - - + -
90A ASP* 3.5 8.5 - - - +
102A ILE* 3.2 29.7 + - + +
104A GLN* 2.8 31.3 + - - +
241A TRP* 3.0 23.0 + - - -
242A ASP 2.9 13.6 + - - +
243A VAL* 3.3 19.1 - - - +
244A THR 3.2 0.2 - - - -
245A GLN* 1.3 77.5 - - - +
247A GLY* 1.3 60.0 + - - +
249A ILE* 3.4 3.5 + - - +
250A SER* 2.9 28.8 + - - +
299A LEU* 3.8 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.9 18.1 - - - -
19A GLY* 3.6 19.0 - - - -
23A ALA* 3.5 16.8 - - - +
243A VAL 3.0 10.5 + - - -
244A THR 3.1 4.4 + - - -
246A GLN* 1.3 75.4 - - - +
248A LYS* 1.3 63.3 + - - +
250A SER* 3.3 4.0 + - - -
251A VAL* 3.2 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 3.8 7.4 - - - +
25A LYS* 6.2 2.5 - - + -
26A ALA* 3.7 15.7 - - + +
29A GLU* 2.9 35.6 + - - +
244A THR* 3.1 11.0 + - + +
245A GLN* 3.1 14.0 + - + +
247A GLY* 1.3 75.5 - - - +
249A ILE* 1.3 64.4 + - - +
251A VAL* 3.1 4.0 + - - +
252A PHE* 3.0 47.8 + - + -
272A PRO 3.0 26.2 + - - -
273A GLY* 4.1 12.1 + - - -
274A VAL* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.0 18.6 - - + -
245A GLN* 2.8 39.8 + - + +
246A GLN 3.7 4.0 - - - +
248A LYS* 1.3 72.5 - - - +
250A SER* 1.3 63.7 + - - +
252A PHE* 3.9 0.5 - - - +
253A VAL* 2.9 37.6 + - + +
271A ILE* 4.2 13.2 - - + -
274A VAL* 4.0 26.7 - - + -
277A VAL* 4.2 21.1 - - + -
297A ILE* 4.5 4.3 - - + -
299A LEU* 3.6 26.7 - - + -
300A PRO* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.9 7.8 - - - -
63A ILE* 3.6 28.8 - - - +
87A MET* 3.7 4.4 - - - +
89A TRP* 3.8 12.0 - - - +
102A ILE* 3.4 28.4 - - - +
246A GLN 2.9 15.7 + - - -
247A GLY 3.5 9.0 - - - -
248A LYS 3.2 0.6 - - - -
249A ILE* 1.3 76.3 - - - +
251A VAL* 1.3 59.6 + - - +
254A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.2 9.1 - - + +
6A PHE* 5.1 0.2 - - + -
23A ALA* 3.4 29.8 - - + +
26A ALA* 3.7 9.4 - - + -
27A GLY* 3.8 16.8 - - - +
30A VAL* 4.2 10.8 - - + -
32A ALA* 5.1 0.2 - - + -
34A VAL* 3.8 27.6 - - + -
63A ILE* 4.3 14.6 - - + -
247A GLY 3.2 10.9 + - - +
248A LYS 3.1 7.7 + - - +
250A SER* 1.3 73.9 - - - +
252A PHE* 1.3 61.2 + - - +
254A ALA* 3.3 3.5 + - - +
255A ASP* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.7 17.5 - - + -
29A GLU* 3.7 27.4 - - + -
30A VAL* 3.6 27.2 - - + +
248A LYS* 3.0 56.8 + - + +
249A ILE 4.0 2.9 - - - +
251A VAL* 1.3 75.8 - - - +
253A VAL* 1.3 59.3 + - - +
255A ASP* 3.4 4.4 + - - +
256A HIS* 2.9 30.8 + - - +
269A LEU* 4.1 3.2 - - + +
270A GLU 5.7 0.7 - - - -
271A ILE* 3.7 29.8 - - + -
272A PRO* 3.8 27.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
87A MET* 3.6 22.9 - - + -
100A TYR* 4.7 5.6 - - + -
102A ILE* 4.5 0.9 - - + -
249A ILE* 2.9 32.8 + - + +
250A SER 3.9 2.5 - - - +
252A PHE* 1.3 75.2 - - - +
254A ALA* 1.3 65.5 + - - +
256A HIS* 3.2 2.3 + - - +
257A VAL* 3.0 34.6 + - + +
263A MET* 4.7 6.5 - - - -
269A LEU* 4.0 20.2 - - + -
271A ILE* 4.4 1.1 - - + -
277A VAL* 4.3 7.9 - - + -
297A ILE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.0 15.7 - - + -
61A ALA* 4.4 6.7 - - + -
63A ILE* 4.0 10.5 - - + -
85A LEU* 3.7 12.1 - - + +
87A MET* 3.8 21.3 - - - -
250A SER 2.9 19.1 + - - +
251A VAL 3.6 4.5 - - - +
253A VAL* 1.3 78.7 - - - +
255A ASP* 1.3 58.0 + - - +
257A VAL 3.3 0.5 + - - -
258A LEU* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 3.0 30.8 + - - +
4A ILE* 4.3 7.4 - - + +
30A VAL* 3.6 31.9 - - + +
31A GLY 4.8 0.7 - - - +
32A ALA* 3.9 7.8 - - - +
251A VAL 2.9 17.6 + - - +
252A PHE 3.9 2.9 - - - +
254A ALA* 1.3 76.4 - - - +
256A HIS* 1.3 62.5 + - - +
258A LEU* 3.4 5.0 + - - +
259A LYS* 2.7 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE 2.9 17.9 + - - +
253A VAL 3.6 3.1 - - - +
255A ASP* 1.3 77.4 + - - +
257A VAL* 1.3 59.7 + - + +
259A LYS* 3.2 1.5 + - - -
260A ASN* 2.8 73.8 + - + +
261A GLY 4.6 3.0 + - - -
263A MET* 3.7 40.8 - - + +
268A LYS 5.6 1.6 + - - -
269A LEU* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.9 29.6 - - + -
100A TYR* 3.8 25.4 - - + +
253A VAL* 3.0 25.3 + - + +
254A ALA 3.8 3.4 - - - +
256A HIS* 1.3 76.0 - - + +
258A LEU* 1.3 62.0 + - + +
261A GLY* 2.9 47.0 + - - +
262A PRO* 4.1 8.3 - - + -
263A MET* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 3.3 46.9 - - + +
4A ILE* 4.4 4.7 - - + -
60A ASN* 3.6 35.4 - - + +
61A ALA* 4.0 12.6 - - + -
83A GLY 5.5 2.7 - - - +
85A LEU* 4.0 17.7 - - + +
254A ALA 3.0 24.4 + - - +
255A ASP 3.7 1.1 - - - +
256A HIS 3.3 0.2 - - - -
257A VAL* 1.3 79.9 - - + +
259A LYS* 1.3 59.6 + - - +
261A GLY 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASN* 4.1 12.8 - - - +
30A VAL* 3.6 16.6 + - - +
31A GLY 4.7 5.7 + - - -
255A ASP* 2.7 51.0 + - - +
256A HIS* 5.5 0.7 - - - -
258A LEU* 1.3 77.0 - - - +
260A ASN* 1.3 78.3 + - - +
261A GLY 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 2.8 56.5 + - + +
259A LYS* 1.3 89.7 - - - +
261A GLY* 1.3 63.0 + - - +
262A PRO 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 4.4 5.9 + - - +
257A VAL* 2.9 30.9 + - - +
258A LEU 4.6 0.6 + - - -
259A LYS 3.8 0.8 - - - -
260A ASN* 1.3 82.2 - - - +
262A PRO* 1.3 78.4 - - - +
263A MET 3.6 0.5 + - - -
----------------------------------------------------------
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