Contacts of the strand formed by residues 179 - 187 (chain B) in PDB entry 1OFG
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 LEU 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.7 27.8 - - + +
176B LEU* 3.8 26.9 - - + -
177B GLY 3.6 14.6 - - - +
178B LYS* 1.3 81.4 - - - +
180B GLY* 1.3 58.6 + - - +
181B MET 5.3 0.4 - - - +
182B VAL* 5.9 0.2 - - + -
225B LEU 4.3 3.8 - - - +
226B LEU* 3.7 38.1 - - + +
261B SER* 5.2 2.1 + - - +
262B GLY 5.4 0.2 - - - -
263B ALA* 3.9 14.6 + - + +
281B VAL* 3.9 18.8 - - + -
282B GLN 3.5 4.0 - - - +
283B GLY* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 3.1 39.8 + - - -
272A SER* 5.5 0.9 - - - -
273A THR* 3.7 14.0 - - - +
178B LYS 3.7 1.8 + - - -
179B LEU* 1.3 74.8 - - - +
181B MET* 1.3 63.5 + - - +
263B ALA* 4.3 3.4 - - - -
264B LEU* 3.1 16.1 + - - +
282B GLN 2.9 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP* 4.4 7.6 - - - +
252A ARG* 3.9 28.7 - - + -
254A ILE* 4.1 9.9 - - + -
268A ALA* 3.9 18.2 - - + -
269A SER 4.6 2.9 - - - +
270A SER* 4.9 4.7 - - - -
273A THR* 4.1 4.0 - - + +
180B GLY* 1.3 78.9 - - - +
182B VAL* 1.3 68.1 + - - +
183B THR* 4.4 2.7 - - - +
264B LEU* 3.4 30.5 - - + +
266B HIS* 3.9 18.4 - - - -
280B SER 3.7 0.9 - - - +
281B VAL* 3.5 1.6 - - - +
282B GLN* 2.6 70.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 5.9 0.2 - - + -
181B MET* 1.3 81.0 - - - +
183B THR* 1.3 68.1 + - - +
184B THR* 4.2 10.1 - - + -
222B THR* 3.8 28.7 - - + +
225B LEU* 5.3 4.0 - - + -
226B LEU* 3.8 37.7 - - + -
264B LEU 3.0 8.6 + - - +
265B SER* 3.2 12.1 - - - -
266B HIS* 2.9 27.7 + - - -
279B PHE* 6.0 0.2 - - + -
280B SER 3.2 9.4 - - - +
281B VAL* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 3.8 16.4 - - + -
185A ASP* 2.7 31.3 + - - +
266A HIS* 4.0 3.6 - - + -
181B MET* 4.4 3.1 - - - +
182B VAL* 1.3 74.4 - - - +
184B THR* 1.3 67.3 + - - +
185B ASP* 4.4 3.1 - - - +
266B HIS* 3.1 34.4 + - + +
278B ARG 3.7 1.6 - - - +
279B PHE* 3.3 3.5 - - - -
280B SER* 2.8 49.1 + - - -
282B GLN* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A HIS* 3.8 1.7 - - - -
182B VAL* 4.2 8.3 - - + -
183B THR* 1.3 78.4 - - - +
185B ASP* 1.3 68.6 + - - +
186B ASN* 4.7 0.5 + - - -
218B GLY* 3.5 21.3 + - - +
222B THR* 3.5 25.7 + - - +
225B LEU* 6.1 0.7 - - + -
255B TRP* 4.1 6.6 + - - -
265B SER* 6.4 0.2 - - - -
266B HIS 3.2 6.3 + - - +
267B GLY* 3.2 16.5 - - - -
268B ALA 3.2 17.1 + - - -
278B ARG 3.4 5.2 - - - -
279B PHE* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 4.4 1.0 - - - +
183A THR* 2.7 33.2 + - - +
266A HIS* 2.9 22.3 + - - -
280A SER* 5.2 2.5 + - - -
282A GLN* 3.7 14.7 + - - +
183B THR* 4.4 2.1 - - - +
184B THR* 1.3 80.6 - - - +
186B ASN* 1.3 63.4 + - - +
268B ALA* 3.5 14.7 - - - +
276B THR* 3.6 21.4 - - + +
277B SER* 3.4 3.8 - - - -
278B ARG* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 4.5 0.3 + - - -
185B ASP* 1.3 81.0 + - - +
187B SER* 1.3 60.2 + - - +
214B ILE* 3.4 33.1 + - + +
215B GLY* 4.7 2.6 - - - +
217B TYR* 3.7 11.8 - - - +
218B GLY* 3.3 27.0 + - - -
255B TRP* 5.7 0.5 - - - -
268B ALA 3.1 10.2 + - - +
269B SER* 3.2 24.8 - - - -
270B SER 3.2 1.7 + - - -
276B THR 3.2 3.5 + - - +
277B SER* 3.8 11.1 + - - +
279B PHE* 3.5 9.8 - - - -
294B THR* 3.6 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 2.6 24.8 + - - -
186B ASN* 1.3 76.3 + - - +
188B ASP* 1.3 66.8 + - - +
214B ILE* 3.6 4.6 - - - +
270B SER* 3.3 31.8 + - - -
273B THR* 3.6 11.2 - - - -
274B THR 3.8 2.7 - - - -
275B THR* 3.3 4.0 - - - +
276B THR* 2.8 39.7 + - - +
----------------------------------------------------------
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