Contacts of the strand formed by residues 186 - 195 (chain B) in PDB entry 3LQM
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 THR 186 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 3.6 3.8 - - - -
161B GLN* 2.7 64.8 + - + +
185B THR* 1.3 75.7 - - - +
187B TYR* 1.3 55.2 + - - +
209B CYS* 4.0 14.8 - - + -
210B GLU 3.3 14.1 - - - +
211B GLN* 3.5 13.6 + - - +
607B SO4 2.8 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.1 20.3 - - + +
158B TYR* 4.6 17.3 - + + -
159B TRP* 3.3 20.0 - - - -
160B LYS* 3.5 22.1 - - + +
178B LEU* 6.1 0.4 - - + -
181B LEU* 3.6 37.1 - - + +
182B GLU* 2.8 49.5 + - - +
185B THR* 3.5 19.5 - - + -
186B THR* 1.3 75.9 - - - +
188B CYS* 1.3 66.3 + - - +
189B VAL* 5.1 2.0 - - + -
208B VAL 3.8 0.9 - - - +
209B CYS* 3.1 2.3 - - - +
210B GLU* 2.8 31.3 + - - +
212B THR* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.2 5.5 - - - -
159B TRP* 2.7 60.8 + - + +
161B GLN* 3.7 18.2 - - - -
187B TYR* 1.3 73.6 - - - +
189B VAL* 1.3 65.5 + - - +
207B PRO* 4.6 1.6 - - + -
208B VAL 3.3 4.7 - - - +
209B CYS* 2.1 45.3 - - - -
605B SO4 3.5 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 3.7 24.2 - - + +
120B VAL* 3.8 20.2 - - + -
127B LEU* 4.1 16.6 - - + -
129B MET* 4.1 25.1 - - + -
156B VAL* 5.0 2.0 - - + -
157B GLN 3.3 6.7 - - - +
158B TYR* 3.5 17.9 - - + -
159B TRP* 4.6 1.1 - - - -
178B LEU* 4.2 1.3 - - + -
187B TYR* 5.1 1.1 - - + -
188B CYS* 1.3 83.3 - - - +
190B GLN* 1.3 61.7 + - - +
207B PRO* 3.3 4.6 - - - +
208B VAL* 2.8 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 4.6 3.8 - - - -
156B VAL* 3.4 6.4 - - - +
157B GLN* 2.9 59.7 + - + +
159B TRP* 3.8 20.7 - - + -
166B LYS* 5.1 1.9 + - - -
189B VAL* 1.3 76.0 - - - +
191B VAL* 1.3 61.7 + - - +
204B TRP* 3.6 32.7 + - + +
205B SER* 3.7 24.7 + - - +
207B PRO* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 3.5 17.1 - - + +
117B GLY 4.4 0.2 - - - +
118B MET* 4.0 23.6 - - + -
131B PHE* 3.8 30.7 - - + -
154B TYR* 3.8 17.9 - - + -
155B ASN 3.4 13.2 - - - +
156B VAL* 4.0 7.4 - - + -
190B GLN* 1.3 75.6 - - - +
192B ARG* 1.3 70.5 + - - +
204B TRP* 3.6 2.9 - - - -
205B SER* 2.9 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 3.8 9.6 - - - -
154B TYR* 3.4 7.8 - - - -
155B ASN* 3.0 58.5 + - + +
168B GLN* 3.9 12.1 + - - +
191B VAL* 1.3 75.7 - - - +
193B GLY* 1.3 66.8 + - - +
194B PHE* 4.2 11.1 - - - -
201B ALA* 3.7 21.0 - - - +
202B GLY 3.4 16.9 + - - +
203B GLU 3.4 20.9 - - - +
204B TRP* 3.6 49.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 5.5 1.1 - - - -
114B GLY 5.3 1.2 + - - -
116B PRO* 3.9 6.9 - - - +
152B TRP* 3.5 33.4 - - - -
153B THR 3.6 5.8 - - - -
154B TYR* 4.5 0.2 - - - -
192B ARG* 1.3 82.4 - - - +
194B PHE* 1.3 58.7 + - - +
195B LEU* 5.7 0.2 - - - -
201B ALA* 3.7 0.5 - - - -
202B GLY* 2.8 32.8 + - - +
203B GLU 4.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TRP* 4.8 2.4 - - - -
153B THR* 2.9 42.0 + - - +
155B ASN* 3.5 39.7 - - + +
170B THR* 6.5 0.2 - - + -
192B ARG* 4.2 7.2 - - - -
193B GLY* 1.3 73.3 - - - +
195B LEU* 1.3 68.0 + - - +
196B PRO* 3.6 38.5 - - + +
199B ASN* 4.8 9.4 - - - -
200B LYS 3.6 22.9 - - - -
201B ALA* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.6 30.5 - - + -
149B TYR* 3.6 53.4 - - + -
151B SER* 3.9 11.4 - - - +
152B TRP* 3.8 25.8 - - + -
194B PHE* 1.3 76.8 - - - +
196B PRO* 1.3 69.2 - - - +
197B ASP* 3.4 2.0 - - - -
198B ARG* 3.1 15.1 + - + -
199B ASN* 3.0 17.7 + - - -
200B LYS* 2.8 30.7 + - + +
----------------------------------------------------------
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