Contacts of the strand formed by residues 245 - 259 (chain I) in PDB entry 2AAZ
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 GLU 245 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ALA* 4.9 1.1 - - + -
60I ASP* 4.5 13.5 + - - -
61I ASN* 4.9 7.1 + - - -
206I LYS* 4.2 29.2 + - + +
207I PRO 2.8 15.2 + - - +
208I LYS* 3.3 22.6 - - + +
209I LEU* 2.8 25.9 + - - -
244I THR* 1.3 73.7 - - - +
246I PRO* 1.3 93.1 - - - +
247I HIS 3.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LEU* 3.6 35.3 - - + +
59I ALA* 3.9 5.4 - - - +
61I ASN* 5.6 2.9 - - - +
208I LYS* 5.9 0.3 + - - -
209I LEU* 3.7 7.6 - - + +
235I THR* 4.5 5.6 - - + -
236I HIS* 3.5 33.2 - - + +
239I ALA* 3.6 24.8 - - + -
244I THR 3.8 1.3 - - - +
245I GLU* 1.3 105.7 - - - +
247I HIS* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I SER* 3.7 6.6 + - - -
58I LEU* 2.8 24.0 + - - +
59I ALA* 3.7 11.5 + - + +
196I SER* 5.5 4.7 - - - -
208I LYS* 3.8 45.9 + - + +
209I LEU 2.7 17.3 + - - +
210I SER* 3.5 17.7 - - - +
246I PRO* 1.3 76.3 - - - +
248I GLU* 1.3 74.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 2.6 53.9 + - - +
56I PHE 3.5 16.2 - - - +
57I SER* 5.0 1.3 - - - -
58I LEU* 4.1 8.6 - - - +
209I LEU 3.7 0.7 + - - +
210I SER* 3.1 16.4 + - - +
211I CYS 2.9 24.3 + - - -
247I HIS* 1.3 97.2 + - + +
249I PHE* 1.3 66.9 + - - +
250I ILE* 3.8 12.0 - - + +
49J PHE* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I PHE 3.8 0.3 - - - +
55I ARG* 3.5 2.1 - - - -
56I PHE* 2.9 53.3 + + + +
58I LEU* 4.0 21.5 - - + +
211I CYS* 3.3 24.7 - - + -
213I MET* 3.8 16.2 - - + -
227I ASN 4.5 3.4 - - - -
228I ILE* 3.8 34.3 - - + -
231I TYR* 3.5 29.6 - + + -
232I ALA* 4.8 6.7 - - + -
248I GLU* 1.3 75.2 - - - +
250I ILE* 1.3 71.9 + - - +
251I LEU* 3.9 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I SER* 3.8 21.8 - - - +
54I PHE 3.2 11.0 - - - +
55I ARG* 3.8 31.2 - - + +
210I SER* 4.8 0.4 - - - -
211I CYS 2.7 21.6 + - - +
212I LEU* 3.2 21.8 - - + -
213I MET 2.8 26.7 + - - -
248I GLU* 3.8 25.6 - - + +
249I PHE* 1.3 86.5 - - - +
251I LEU* 1.3 64.1 + - - +
252I GLN* 4.2 1.1 - - + -
49J PHE* 4.3 10.1 - - + -
50J ALA* 4.0 15.9 - - + +
252J GLN* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I SER* 3.3 5.7 - - - -
54I PHE* 2.9 46.0 + - + +
213I MET* 3.4 41.7 - - + +
215I GLN* 4.1 16.4 - - + +
224I VAL* 4.5 3.8 - - + -
227I ASN* 5.0 0.2 - - + -
228I ILE* 3.7 32.5 - - + +
249I PHE* 3.9 15.9 + - + -
250I ILE* 1.3 73.2 - - - +
252I GLN* 1.3 66.1 + - - +
253I MET* 4.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ALA* 4.0 4.2 - - - +
51I PRO 3.3 14.6 + - - +
52I PRO* 5.1 0.2 - - - +
53I SER* 3.1 32.7 - - - +
212I LEU* 4.7 7.6 - - + +
213I MET 2.9 9.4 + - - +
214I TYR* 3.4 30.4 - - + -
215I GLN 2.9 25.5 + - - -
250I ILE* 4.2 1.4 - - + +
251I LEU* 1.3 74.5 - - - +
253I MET* 1.3 78.6 + - - +
53J SER* 4.7 7.1 + - - -
212J LEU* 3.7 13.5 - - + +
250J ILE* 5.4 1.5 - - - +
252J GLN* 3.6 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 3.9 18.4 - - + -
50I ALA* 3.3 13.3 - - - -
51I PRO* 4.3 15.0 + - + -
53I SER* 5.3 0.4 - - - +
54I PHE* 3.3 46.0 - - + -
214I TYR* 4.3 3.1 - - - -
215I GLN 3.5 3.6 - - - -
218I CYS* 3.4 30.5 - - - -
220I LEU* 4.4 4.0 - - + -
224I VAL* 4.2 19.3 - - + -
251I LEU* 4.0 17.0 + - + +
252I GLN* 1.3 95.6 + - - +
254I GLY* 1.3 60.7 + - - +
256I ALA* 3.9 13.7 - - + -
212J LEU* 3.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU 3.5 0.2 - - - +
49I PHE* 3.3 16.2 - - - -
50I ALA* 2.9 23.3 + - - -
51I PRO* 4.0 0.9 - - - +
214I TYR* 3.4 20.8 + - - -
215I GLN 2.8 12.5 + - - -
216I ARG 3.7 1.3 - - - -
218I CYS* 4.3 0.2 - - - -
253I MET* 1.3 74.1 - - - +
255I ASP* 1.3 59.1 + - - +
256I ALA 3.1 7.1 + - - -
192J GLN* 3.5 9.0 - - - -
212J LEU* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ARG* 4.6 8.3 + - - -
47I ALA* 3.6 14.6 - - - +
48I LEU 4.2 2.5 - - - -
49I PHE* 4.1 4.4 - - - -
216I ARG 2.7 18.7 + - - +
217I SER* 4.3 0.4 - - - -
218I CYS* 2.8 27.1 + - - -
254I GLY* 1.3 70.8 - - - +
256I ALA* 1.3 57.3 + - - +
257I HIS* 3.0 18.2 + - - +
165J THR 4.8 0.5 - - - +
166J ASP 5.2 0.7 - - - +
167J ARG* 3.2 37.3 - - + +
192J GLN* 4.3 5.5 - - - +
194J PHE* 3.6 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.7 0.4 - - + -
30I ILE* 3.8 11.8 - - + +
47I ALA* 3.1 2.5 - - - +
48I LEU* 3.0 40.1 + - + +
51I PRO* 4.0 18.4 - - + -
218I CYS* 4.0 7.4 - - - -
220I LEU* 4.0 9.6 - - + -
253I MET* 3.9 25.8 - - + -
254I GLY 3.1 2.2 + - - -
255I ASP* 1.3 69.2 - - - +
257I HIS* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 257 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE* 4.5 0.9 - - - -
45I THR* 3.8 15.3 - - + +
46I VAL 3.3 12.1 - - - +
47I ALA* 3.5 11.7 - - + -
217I SER* 3.1 26.9 - - - -
218I CYS 3.0 36.0 + - - +
219I ASP* 3.9 1.0 - - - -
220I LEU* 3.2 20.6 + - - +
255I ASP* 3.0 26.0 + - - +
256I ALA* 1.3 74.1 - - - +
258I VAL* 1.3 63.8 + - - +
259I TYR* 3.6 21.5 - + - -
350I UMP 3.0 21.0 + - - -
167J ARG* 3.5 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ILE* 4.4 11.7 - - + +
30I ILE* 3.8 26.2 - - + -
31I ILE* 4.7 5.6 - - + -
45I THR* 4.2 2.2 - - - -
46I VAL* 3.0 40.0 + - + +
219I ASP* 5.6 0.2 - - - -
220I LEU* 4.4 9.6 - - + +
221I GLY 5.5 1.8 - - - +
257I HIS* 1.3 77.4 - - - +
259I TYR* 1.3 74.0 + - - +
260I ARG* 4.5 0.3 - - - -
262I HIS* 4.1 3.4 - - + -
263I VAL* 4.2 16.8 - - + +
266I LEU* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ASP* 3.5 7.9 - - - -
41I THR* 3.5 27.4 - - + +
43I THR* 3.0 20.0 - - - -
44I GLY 3.7 3.1 - - - -
45I THR* 3.6 11.0 - - + -
219I ASP* 3.5 33.2 - - - -
257I HIS* 3.6 17.3 - + - -
258I VAL* 1.3 77.2 - - - +
260I ARG* 1.3 61.7 + - - +
261I ASP* 3.2 15.3 - - - +
262I HIS* 2.9 39.0 + + + +
263I VAL* 3.5 5.4 + - - +
316I SER* 3.7 19.5 + - - -
350I UMP 3.2 25.7 + - - -
167J ARG* 3.3 20.8 + - - -
----------------------------------------------------------
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