Contacts of the strand formed by residues 191 - 204 (chain B) in PDB entry 6D6U
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 TYR 191 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.5 33.9 - - + -
55B ASP* 3.0 13.0 + - - -
141B MET* 4.3 5.0 - - + -
151B HIS* 3.2 28.7 - + - -
188B LEU* 3.8 32.9 - - + +
189B ASN 4.2 1.4 - - - +
190B GLN* 1.3 87.3 - - + +
192B ASP* 1.3 64.5 + - - +
219B LEU* 3.7 29.2 - - + -
220B LYS 3.4 8.5 - - - +
221B ARG* 2.8 67.1 + - + -
222B LYS* 4.0 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.5 1.8 - - - -
191B TYR* 1.3 81.0 - - - +
193B LEU* 1.3 77.2 + - - +
194B LEU* 3.5 5.7 + - - +
219B LEU* 4.3 2.8 - - - -
220B LYS* 3.2 26.3 + - + +
222B LYS* 4.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.9 14.8 - - + -
181B VAL* 4.1 19.7 - - + -
186B SER* 4.3 23.4 + - - +
188B LEU* 4.1 9.1 - - + +
192B ASP* 1.3 85.0 + - - +
194B LEU* 1.3 62.8 + - - +
195B GLY 4.5 5.6 - - - +
196B GLN* 3.6 25.1 - - - +
217B PHE* 4.2 24.7 - - + -
218B HIS 3.5 18.4 - - - +
219B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASP 3.5 5.6 + - - +
193B LEU* 1.3 80.7 - - - +
195B GLY* 1.3 60.9 + - - +
218B HIS* 3.6 27.3 + - + +
219B LEU* 4.8 3.4 - - - +
220B LYS* 5.3 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 4.5 3.8 - - - +
194B LEU* 1.3 82.6 - - - +
196B GLN* 1.3 75.2 + - - +
217B PHE* 4.0 1.4 - - - -
218B HIS* 3.2 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 4.0 31.1 - - + +
181B VAL* 3.4 36.7 - - - +
193B LEU* 3.6 24.5 - - - +
195B GLY* 1.3 78.3 - - - -
197B THR* 1.3 67.8 + - - +
198B VAL* 5.5 1.3 - - + -
215B THR* 5.2 2.5 - - + -
216B HIS 3.8 3.6 - - - +
217B PHE* 3.6 28.1 - - + -
92I TYR* 4.2 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLN* 1.3 77.7 + - - +
198B VAL* 1.3 67.5 + - - +
215B THR* 3.3 5.9 - - - +
216B HIS* 2.8 50.4 + - + +
218B HIS* 3.0 27.3 + - + +
28I TYR* 3.4 43.5 - - + +
92I TYR* 4.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TRP* 4.3 17.3 - - + +
175B PRO* 3.2 38.8 - - + +
179B VAL* 3.8 31.9 - - + +
196B GLN* 5.5 1.3 - - + -
197B THR* 1.3 82.6 - - - +
199B ASP* 1.3 65.7 + - - +
214B THR 3.6 5.8 - - - +
215B THR* 4.2 7.0 - - + +
216B HIS* 5.6 0.4 - - - -
28I TYR* 4.0 10.0 - - - -
30I GLY 4.7 1.0 - - - +
32I TYR* 4.4 5.0 - - + -
92I TYR* 3.5 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TRP* 5.0 1.5 - - - +
198B VAL* 1.3 79.4 - - - +
200B SER* 1.3 82.3 + - - +
214B THR* 2.9 43.1 + - - +
216B HIS* 5.0 11.7 - - + +
28I TYR* 4.0 15.4 + - - +
30I GLY* 3.3 8.2 - - - +
31I THR* 2.6 35.5 + - - +
32I TYR* 4.1 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 5.6 2.6 + - - -
171B TRP* 3.5 3.3 + - - -
199B ASP* 1.3 87.3 + - - +
201B GLY* 1.3 59.1 + - - +
212B VAL 3.7 4.3 - - - -
213B MET* 3.0 34.5 - - - +
31I THR* 3.5 10.4 + - - +
32I TYR* 2.6 27.0 + - - -
102J ARG* 3.2 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP 4.2 0.4 + - - -
200B SER* 1.3 75.4 - - - +
202B ILE* 1.3 71.5 + - - +
211B VAL* 3.9 6.8 - - - +
212B VAL* 3.1 30.4 + - - +
214B THR* 5.3 1.8 + - - -
102J ARG* 4.1 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.3 43.3 - - - +
201B GLY* 1.3 79.8 - - - +
203B VAL* 1.3 74.5 + - - +
204B GLN* 5.1 1.1 - - + +
209B GLU* 4.7 14.1 - - + -
210B TYR 3.4 16.8 - - - +
211B VAL* 5.1 3.4 - - + -
212B VAL 4.8 0.9 - - - +
53I ASN* 4.8 14.6 - - - +
102J ARG* 4.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 5.8 4.7 - - + -
156B LYS* 6.2 1.8 - - + -
202B ILE* 1.3 84.2 - - - +
204B GLN* 1.3 72.8 + - - +
205B SER* 4.2 3.3 + - - -
209B GLU 4.0 0.2 - - - -
210B TYR* 3.1 34.5 + - + +
212B VAL* 3.6 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.4 1.7 + - + +
203B VAL* 1.3 81.0 - - - +
205B SER* 1.3 75.9 + - - +
208B GLY* 4.0 11.4 - - - +
209B GLU* 4.4 25.6 + - + +
----------------------------------------------------------
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