Contacts of the strand formed by residues 184 - 190 (chain B) in PDB entry 6H25
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 GLN 184 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER* 6.5 0.4 - - - -
162B ALA 3.7 3.1 - - - -
173B LEU* 4.9 3.8 - - + -
178B GLU* 3.3 63.4 + - + +
182B GLY* 3.3 11.4 + - - +
183B PRO* 1.3 77.3 - - - +
185B LEU* 1.3 61.7 + - - +
186B ALA 5.5 0.2 - - - +
201B MET* 3.2 28.4 - - - +
202B ASP* 3.4 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 5.2 4.7 - - + -
161B SER* 3.4 3.5 - - - -
162B ALA* 2.9 43.1 + - + +
184B GLN* 1.3 77.0 - - - +
186B ALA* 1.3 66.3 + - - +
187B LEU* 4.2 1.3 + - + -
199B LEU* 4.6 9.2 - - + -
200B GLU 3.2 11.4 - - - +
201B MET* 3.7 23.1 - - + -
205B LEU* 5.6 4.0 - - + -
210B LEU* 4.6 14.6 - - + -
213B VAL* 4.2 23.3 - - + +
214B LEU* 4.0 26.5 - - + -
217B ALA* 4.1 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 4.3 25.8 - - + -
136B ALA* 5.6 1.1 - - + -
160B CYS 3.2 7.4 - - - +
161B SER* 3.4 19.7 - - - +
184B GLN* 5.5 0.6 - - - +
185B LEU* 1.3 77.1 - - - +
187B LEU* 1.3 63.9 + - - +
198B LEU* 5.3 0.2 - - - +
199B LEU* 3.7 0.5 - - - -
200B GLU* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 5.2 4.0 - - - -
158B CYS 4.3 0.2 - - - +
159B ALA* 3.2 5.4 - - - +
160B CYS 2.9 41.3 + - - +
185B LEU* 4.9 1.8 - - + -
186B ALA* 1.3 76.9 - - - +
188B ALA* 1.3 62.7 + - - +
189B LEU* 4.8 9.0 - - + -
196B ILE* 3.9 30.1 - - + -
198B LEU 3.1 12.8 - - - +
199B LEU* 3.9 13.5 - - + -
214B LEU* 4.6 10.1 - - + -
217B ALA* 3.7 37.5 - - + +
218B ALA* 4.5 18.2 - - + +
221B ALA* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 4.6 4.9 - - + -
135B TYR* 4.5 10.0 - - + +
139B VAL* 4.6 11.4 - - + -
157B VAL* 4.9 4.5 - - + -
158B CYS 3.7 4.5 - - - +
159B ALA* 3.8 12.8 - - + -
187B LEU* 1.3 74.3 - - - +
189B LEU* 1.3 55.4 + - - +
196B ILE* 3.7 2.8 - - - +
197B ALA* 2.6 38.6 + - + -
198B LEU* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.8 5.2 - - - +
158B CYS* 2.8 38.2 + - + +
187B LEU* 4.8 6.5 - - + -
188B ALA* 1.3 75.1 - - - +
190B LEU* 1.3 67.2 + - - +
191B PRO* 3.9 9.6 - - + +
194B GLY* 4.0 15.3 - - - +
195B GLN 3.3 28.7 - - - +
196B ILE* 3.9 14.6 - - + -
197B ALA* 4.2 0.4 - - - +
218B ALA* 4.0 22.7 - - + +
221B ALA* 3.7 26.5 - - + -
222B ARG* 4.5 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A MET* 3.8 40.4 - - + -
110B ALA* 4.6 9.9 - - + -
154B ARG* 4.7 7.9 - - + -
155B ASP* 3.1 33.2 - - + +
156B PHE 3.7 4.5 - - - +
157B VAL* 4.8 9.2 - - + -
189B LEU* 1.3 75.6 - - - +
191B PRO* 1.3 64.9 - - - +
192B ALA* 3.4 1.6 + - + -
193B SER* 3.9 12.3 + - - +
194B GLY* 3.5 13.3 + - - -
195B GLN* 3.3 22.2 + - - +
197B ALA* 3.8 20.0 - - + -
----------------------------------------------------------
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