Contacts of the strand formed by residues 187 - 193 (chain E) in PDB entry 3O2Q
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 PHE 187 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D SER* 3.6 10.6 + - - +
137E VAL* 4.3 10.1 - - + -
138E ASN 3.3 16.6 - - - +
139E VAL* 3.3 31.9 - - + -
154E LEU* 4.7 4.9 - - + -
158E LEU* 4.1 19.3 - - + -
176E LEU* 4.1 24.4 - - + +
179E PHE* 3.5 37.0 - + + -
180E GLU* 2.7 49.7 + - + +
183E SER* 4.0 7.6 - - - -
185E ARG* 3.7 19.1 - - + -
186E THR* 1.3 73.4 - - - +
188E LEU* 1.3 64.6 + - - +
189E HIS* 3.6 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D SER* 3.8 8.5 - - - +
295D SER* 3.7 28.0 - - - -
296D SER* 3.5 18.2 - - - +
299D LYS* 4.2 7.0 - - + -
113E GLU* 4.0 33.2 - - + +
116E TYR* 3.7 31.4 - - + -
137E VAL* 3.2 5.9 - - - +
138E ASN* 2.8 44.4 + - + +
186E THR* 4.1 8.6 + - - +
187E PHE* 1.3 75.1 - - - +
189E HIS* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D SER* 4.4 5.0 + - - +
251D ILE* 3.5 27.4 - - + +
254D THR* 5.2 1.2 - - - +
293D GLN* 6.3 2.0 - - + -
296D SER* 3.1 24.7 + - - -
116E TYR* 3.6 2.0 - - - -
135E HIS* 2.8 43.0 - + + -
136E VAL 3.2 9.6 + - - -
137E VAL* 3.6 6.2 - - + +
172E ILE* 3.6 15.2 - - + +
173E ASP* 2.6 37.6 + - - +
176E LEU* 3.6 24.5 - - + -
187E PHE 3.6 2.4 + - - +
188E LEU* 1.3 77.1 - - - +
190E THR* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ILE* 4.0 9.0 - - - -
254D THR* 3.5 8.1 + - - -
296D SER* 5.2 0.4 - - - -
300D ASN* 2.9 29.0 + - - +
116E TYR* 3.2 22.7 - - + +
120E VAL* 3.6 28.0 - - + +
135E HIS* 3.6 3.5 - - - -
136E VAL* 2.8 40.7 + - + +
189E HIS* 1.3 76.0 + - - +
191E VAL* 1.3 80.9 + - - +
192E CYS* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D THR* 4.9 1.1 - - + -
251D ILE* 3.8 18.4 - - + +
254D THR* 4.1 10.5 + - - +
255D THR* 3.6 13.7 - - - +
133E PRO* 4.4 6.5 - - + -
134E VAL 3.2 7.6 - - - +
135E HIS* 3.3 48.5 - - + +
136E VAL 4.6 0.2 - - - +
169E GLU* 5.0 0.2 - - - +
190E THR* 1.3 84.5 + - - +
192E CYS* 1.3 70.8 + - - +
193E PHE* 3.6 29.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E VAL* 4.2 31.2 - - - -
123E LEU* 3.9 38.8 - - + -
124E ASN* 5.0 3.8 - - - -
133E PRO* 3.2 6.1 - - - +
134E VAL* 2.7 38.7 + - + -
136E VAL* 4.0 17.0 - - - +
190E THR* 4.8 0.7 - - - -
191E VAL* 1.3 78.4 - - - +
193E PHE* 1.3 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D THR* 4.0 7.6 - - + -
185D LYS* 3.8 32.1 - - + -
254D THR* 5.8 0.4 - - - -
255D THR* 3.5 41.1 - - + -
258D GLY* 6.5 1.1 - - - -
123E LEU* 4.6 13.3 + - - +
126E ARG* 5.1 1.9 - - - +
127E GLU 5.7 0.2 - - - -
128E GLN* 3.6 32.2 - - + +
131E CYS* 3.5 22.0 - - - -
132E GLN 3.3 4.0 - - - +
133E PRO* 3.7 20.9 - - + -
191E VAL* 3.6 23.8 - - + -
192E CYS* 1.3 83.9 - - - +
194E TYR* 1.3 69.0 + - - +
----------------------------------------------------------
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