Contacts of the strand formed by residues 188 - 194 (chain B) in PDB entry 3F12
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 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 6.0 1.4 - - - +
91B THR* 5.4 5.2 + - - +
122B THR* 5.6 4.9 - - - +
156B ASP 3.0 21.8 + - - -
157B TYR* 2.9 55.8 + + + +
158B PHE* 4.1 23.6 - + - -
159B PRO* 4.5 3.6 - - + -
160B GLU* 3.5 37.2 + - + +
180B ALA* 4.6 6.5 - - + -
181B VAL 3.9 6.3 - - - -
182B LEU* 3.8 46.8 - - + +
186B GLY 4.0 3.1 - - - -
187B LEU* 1.3 72.7 - - - +
189B SER* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 5.6 5.2 + - - +
153B LEU* 4.3 7.4 - - - +
154B VAL 3.2 7.1 + - - -
155B LYS* 3.5 32.0 - - - +
156B ASP 4.0 0.2 - - - -
157B TYR* 3.8 1.1 - - - -
180B ALA* 4.1 2.8 - - - +
181B VAL* 3.5 32.2 + - - +
183B GLN* 3.5 24.8 + - - -
188B TYR* 1.3 79.1 - - - +
190B LEU* 1.3 59.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
153B LEU* 3.9 8.5 - - - +
154B VAL* 2.9 62.5 + - + +
157B TYR* 4.3 3.9 - - - +
162B VAL* 3.4 35.2 - - + -
164B VAL* 4.1 10.5 - - + -
177B THR* 4.2 12.3 - - + -
178B PHE 3.7 20.0 - - - +
179B PRO 5.1 0.7 - - - -
180B ALA* 3.6 19.7 - - + +
181B VAL* 5.6 0.4 - - - -
189B SER* 1.3 75.1 - - - +
191B SER* 1.3 76.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.2 8.0 - - - +
177A SER* 3.4 26.7 + - - -
179A THR* 5.1 2.6 + - - -
136B LEU* 3.9 16.8 - - - +
152B CYS 3.6 10.7 + - - -
153B LEU* 4.6 6.1 - - - +
177B THR* 3.6 1.0 - - - -
178B PHE* 2.7 45.5 + - - +
190B LEU* 1.3 83.4 + - - +
192B SER* 1.3 56.2 + - - +
193B VAL* 4.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLY* 3.2 2.6 - - - -
152B CYS* 2.9 35.8 + - - +
154B VAL* 5.9 0.2 - - - -
164B VAL* 3.7 27.0 - - - +
166B TRP* 3.3 21.1 + - - -
175B VAL* 3.9 3.6 - - - +
176B HIS 3.5 5.6 - - - -
177B THR* 3.4 26.6 + - - -
190B LEU* 4.3 0.8 - - - +
191B SER* 1.3 74.9 - - - +
193B VAL* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.7 4.3 - - + -
134A VAL* 6.2 1.6 - - + -
136A LEU* 3.6 38.1 - - + -
138A ASN* 5.6 0.9 - - - +
177A SER* 6.0 0.4 - - - -
136B LEU* 4.3 19.7 - - + -
150B LEU 3.4 9.4 - - - +
151B GLY* 4.1 0.4 - - - -
166B TRP* 4.9 1.3 - - - +
174B GLY 3.4 0.7 - - - +
175B VAL* 3.3 5.9 - - - +
176B HIS* 2.9 43.8 + - + +
178B PHE* 3.7 26.9 - - + -
191B SER* 4.6 3.4 - - - +
192B SER* 1.3 83.4 - - - +
194B VAL* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 6.2 0.4 - - - -
149B ALA* 3.3 4.8 - - - +
150B LEU* 2.8 56.0 + - + -
166B TRP* 4.7 10.8 - - + -
171B LEU* 3.6 39.3 - - + -
173B SER 4.4 2.7 - - - +
174B GLY 3.0 21.5 - - - +
175B VAL* 3.8 9.4 - - + -
193B VAL* 1.3 76.7 - - - +
195B THR* 1.3 61.2 + - - +
196B VAL* 3.6 18.1 + - + -
----------------------------------------------------------
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