Contacts of the strand formed by residues 188 - 194 (chain E) in PDB entry 1PF7
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 188 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E LYS* 4.0 20.8 + - - +
124E PHE* 3.7 31.1 - - + -
125E GLU* 4.8 3.4 + - - -
128E ASP* 2.8 34.8 + - + +
129E ILE 3.1 17.2 + - - +
130E MET* 3.9 7.2 - - + -
131E LEU* 2.7 32.5 + - - +
185E ARG* 5.5 2.2 - - - +
186E GLU* 3.8 15.4 + - - +
187E LEU* 1.3 76.6 - - - +
189E GLU* 1.3 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ASN* 5.3 1.0 + - - -
124E PHE* 4.2 9.6 - - - -
130E MET* 3.8 3.8 - - - -
131E LEU* 3.2 30.1 - - + +
133E ARG* 3.3 36.6 + - + +
171E ARG* 3.2 31.2 + - - +
175E LEU* 4.0 18.4 - - + +
187E LEU 3.9 2.6 + - - +
188E GLN* 1.3 76.6 + - - +
190E GLY* 1.3 56.9 + - - +
215E ASP* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E MET* 3.6 14.1 - - - +
131E LEU 3.1 7.1 + - - +
132E ILE* 3.6 7.1 - - - -
133E ARG* 2.9 42.9 + - - +
134E ASP 3.5 0.3 + - - -
189E GLU* 1.3 77.1 - - - +
191E THR* 1.3 61.7 - - - -
215E ASP* 3.2 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E MET* 4.3 1.6 - - - -
133E ARG* 3.2 20.1 + - - -
134E ASP* 3.1 29.9 + - + +
135E HIS* 3.6 9.6 - - - +
136E ILE* 3.8 28.5 - - + +
190E GLY* 1.3 71.8 - - - -
192E TYR* 1.3 63.6 + - - +
213E GLY 3.7 16.3 + - - +
214E ALA 3.7 0.7 - - - -
215E ASP* 2.8 36.7 + - - +
216E ALA 3.2 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E ASN* 3.4 36.4 + - - +
117E ALA* 3.9 3.6 - - + -
130E MET* 4.2 2.7 - - + -
132E ILE* 4.2 20.2 - - + -
134E ASP 2.7 13.3 + - - +
135E HIS* 2.9 10.8 - - + +
136E ILE 2.9 21.7 + - - -
166E TYR* 5.5 0.2 - - - -
190E GLY 3.9 0.8 + - - -
191E THR* 1.3 73.1 - - - +
193E VAL* 1.3 58.8 + - - +
194E MET* 3.8 8.9 + - - -
216E ALA* 3.2 17.9 - - + -
218E GLY* 2.9 44.9 - - - -
219E MET 3.1 3.5 + - - -
220E SER* 3.1 33.8 + - - -
221E THR* 4.0 8.3 - - + -
222E VAL* 3.7 18.2 - - + -
239E SER* 4.1 7.9 - - - -
293E SO4 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E LEU* 3.8 4.7 - - + -
136E ILE* 3.6 23.6 - - + +
138E LEU* 3.5 30.7 - - + -
191E THR 3.8 1.4 + - - -
192E TYR* 1.3 74.5 - - - +
194E MET* 1.3 63.2 + - - +
195E VAL* 5.3 0.2 - - + -
209E LEU* 3.9 13.7 - - + -
212E LEU* 5.5 2.0 - - + -
214E ALA* 3.2 30.7 - - + -
216E ALA 2.7 17.4 + - - +
217E VAL* 3.3 19.4 - - + +
218E GLY 3.2 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E MET* 3.2 33.2 - - + +
136E ILE 3.0 11.0 + - - +
137E ASN* 4.1 6.3 - - - +
138E LEU* 3.1 28.4 + - - +
139E PRO* 3.2 23.7 - - + +
192E TYR* 3.8 4.0 + - - -
193E VAL* 1.3 72.5 - - - +
195E VAL* 1.3 69.1 + - - +
196E ALA* 4.8 0.2 - - - -
218E GLY 3.4 6.1 - - - +
219E MET 3.6 23.3 - - - +
220E SER* 3.8 10.8 - - - +
222E VAL* 3.5 23.1 - - + -
223E PRO* 3.6 36.3 - - + -
----------------------------------------------------------
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