Contacts of the strand formed by residues 244 - 258 (chain B) in PDB entry 3HB8
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 LYS 244 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 4.7 14.3 + - - +
206B SER* 3.0 14.3 + - - +
207B GLU* 3.2 13.8 - - + -
208B LEU 2.7 31.9 + - - -
238B ALA* 4.5 1.6 - - - -
242B GLY 5.8 0.4 - - - +
243B LEU* 1.3 76.2 - - - +
245B PRO* 1.3 73.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.4 31.4 - - + +
68B ARG* 3.5 20.7 - - - +
207B GLU* 4.0 4.0 - - - +
208B LEU 3.8 3.4 - - - +
234B THR* 4.8 3.1 - - + -
235B TYR* 3.7 37.9 - - + -
238B ALA* 4.3 14.1 - - + -
243B LEU 4.0 3.6 - - - +
244B LYS* 1.3 94.0 - - + +
246B GLY* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 2.8 30.7 + - - +
68B ARG* 3.4 28.5 + - - -
207B GLU* 4.0 7.9 - - - -
208B LEU 2.6 20.9 + - - -
209B SER* 3.9 2.5 - - - -
244B LYS 3.4 0.2 + - - -
245B PRO* 1.3 73.2 - - - +
247B ASP* 1.3 60.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.5 31.8 + - + +
65B TYR 3.5 3.8 - - - +
66B SER* 3.6 14.2 - - - -
67B LEU* 4.0 6.2 - - - +
68B ARG* 2.8 38.2 + - - -
209B SER* 2.8 19.9 + - - +
210B CYS 2.9 24.8 + - - +
246B GLY* 1.3 73.8 - - - +
248B PHE* 1.3 60.4 + - - +
249B ILE* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA 3.7 1.7 - - - +
65B TYR* 2.8 50.1 + + + +
67B LEU* 4.0 21.1 - - + +
210B CYS* 3.2 19.3 - - + +
212B LEU* 4.0 23.8 - - + -
226B ASN 4.8 0.2 - - - -
227B ILE* 3.8 35.7 - - + -
230B TYR* 3.5 32.8 - - + -
231B ALA* 4.6 8.3 - - + -
234B THR* 4.8 1.1 - - - +
247B ASP* 1.3 74.3 - - - +
249B ILE* 1.3 64.3 + - - +
250B HIS* 3.7 33.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 3.8 25.1 - - + +
60A GLY* 4.2 3.6 - - - -
62B GLN* 3.6 27.6 - - + +
63B ALA 3.4 6.7 - - - +
64B ARG* 3.7 43.5 - - + +
210B CYS 2.8 16.9 + - - +
211B GLN* 3.1 34.3 - - + +
212B LEU 2.9 26.0 + - - -
247B ASP* 3.7 13.5 - - + -
248B PHE* 1.3 77.1 - - - +
250B HIS* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 5.0 8.0 + - - -
62B GLN* 3.3 3.0 - - - -
63B ALA* 2.8 42.1 + - + +
65B TYR* 4.1 6.0 - - + -
212B LEU* 3.8 19.7 - - + -
214B GLN* 2.8 31.1 + - - +
223B VAL* 3.5 28.9 - - + +
226B ASN* 4.8 1.5 - - + +
227B ILE* 3.1 22.6 - - + +
248B PHE* 3.7 20.0 + + + -
249B ILE* 1.3 71.4 - - - +
251B THR* 1.3 65.3 + - - +
252B LEU* 3.6 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.6 2.9 - - - +
211A GLN* 3.2 27.1 - - - +
251A THR* 3.5 18.4 - - + +
61B MET 3.4 10.3 - - - +
62B GLN* 3.2 10.0 + - - +
211B GLN* 2.7 30.7 + - - -
212B LEU 2.9 16.9 + - - +
213B TYR* 3.6 9.8 - - + -
214B GLN* 2.9 28.4 + - - +
249B ILE 3.7 0.2 + - - -
250B HIS* 1.3 74.2 - - - +
252B LEU* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.2 13.1 + - - +
36B GLN* 5.1 5.6 - - - +
61B MET* 2.8 43.9 + - + +
213B TYR* 5.2 1.1 - - - -
214B GLN* 3.5 33.4 - - + +
217B GLY* 3.8 25.8 - - - +
219B MET* 3.9 23.3 - - + -
223B VAL* 4.2 3.1 - - + -
250B HIS* 3.6 23.6 + - + +
251B THR* 1.3 74.4 - - - +
253B GLY* 1.3 60.5 + - - +
254B ASP 5.0 0.2 - - - +
255B ALA* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLN* 3.9 6.1 - - - -
211A GLN* 3.6 14.8 - - - -
58B VAL 3.3 2.3 - - - +
59B PHE* 3.0 19.3 - - - -
60B GLY 2.8 26.0 + - - -
213B TYR* 4.0 1.6 - - - -
214B GLN 2.8 14.3 + - - -
215B ARG 3.5 7.0 - - - -
252B LEU* 1.3 72.4 - - - +
254B ASP* 1.3 59.0 + - - +
255B ALA* 3.4 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.4 27.6 + - + +
200A GLN* 4.6 4.3 - - - +
202A TYR* 3.1 16.7 - - + -
47B LYS* 3.1 29.8 + - - +
57B SER* 2.7 24.7 + - - -
58B VAL 3.7 3.6 - - - -
59B PHE* 3.7 6.1 - - + -
215B ARG 2.7 16.8 + - - +
216B SER* 4.4 0.2 - - - -
217B GLY 3.1 16.1 + - - -
252B LEU* 5.2 0.2 - - - -
253B GLY* 1.3 68.5 - - - +
255B ALA* 1.3 57.0 + - - +
256B HIS* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.8 12.6 - - + +
57B SER* 3.3 1.7 + - - -
58B VAL 2.7 41.8 + - - +
61B MET* 3.5 32.8 - - + -
217B GLY 3.9 4.7 - - - -
219B MET* 4.7 0.2 - - - -
252B LEU* 3.5 28.0 - - + -
253B GLY 3.4 1.8 + - - +
254B ASP* 1.3 72.4 - - - +
256B HIS* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.3 29.7 + - - -
40B ILE* 4.3 2.3 - - - +
55B THR* 3.3 17.9 - - + +
56B LEU 3.2 8.7 - - - +
57B SER* 3.9 6.1 - - - +
216B SER* 3.2 26.9 - - - -
217B GLY 3.2 23.2 + - - +
218B ASP* 4.0 7.9 + - - +
219B MET* 3.1 29.7 + - - +
254B ASP* 2.9 27.3 + - - +
255B ALA* 1.3 74.1 - - - +
257B ILE* 1.3 63.7 + - - +
258B TYR* 3.9 26.0 + + - -
615B PO4 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.5 33.0 - - + +
40B ILE* 3.3 30.7 - - + -
41B LEU* 3.4 22.0 - - + -
55B THR* 2.5 16.2 + - - -
56B LEU* 3.0 17.2 + - + +
218B ASP* 5.4 0.9 - - - -
219B MET* 4.0 15.7 - - + +
220B GLY 5.5 1.1 - - - +
256B HIS* 1.3 77.0 - - - +
258B TYR* 1.3 66.7 + - - +
259B LEU* 3.4 0.7 + - - -
261B HIS* 4.5 2.2 - - + -
262B ILE* 3.7 23.8 - - + +
265B LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.0 20.1 + - - -
49B ASP* 2.9 30.4 + - - -
53B THR* 3.7 22.0 - - + -
54B GLY 3.5 15.5 - - - -
55B THR* 3.6 10.1 - - + -
218B ASP* 4.0 28.4 + - + -
256B HIS* 3.9 21.1 - + - -
257B ILE* 1.3 74.8 - - - +
259B LEU* 1.3 66.6 + - - +
260B ASN* 3.2 11.9 - - - +
261B HIS* 2.8 40.7 + + + +
262B ILE 3.3 6.4 + - - -
----------------------------------------------------------
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