Contacts of the strand formed by residues 188 - 198 (chain E) in PDB entry 5MWF
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 ALA 188 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.0 22.0 - - + -
38E ARG 3.2 13.7 - - - +
39E ASN* 4.5 4.9 - - + +
148E ALA* 5.3 0.4 - - + -
163E ILE* 4.5 11.2 - - + -
164E GLU* 3.2 26.7 + - + -
184E SER* 4.1 0.2 - - - -
185E GLY 3.1 25.4 + - - +
187E VAL* 1.3 81.2 - - - +
189E HIS* 1.3 64.1 + - - +
190E LEU* 5.6 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
266A TYR* 4.3 9.6 - - - -
280A PRO* 5.4 2.7 - - + -
291A TRP* 4.4 4.8 - + - -
36E ALA 4.0 0.2 - - - +
37E LEU* 3.3 6.6 - - - +
38E ARG* 2.9 73.0 + - + +
182E HIS* 2.9 39.5 - + - -
183E PHE 3.2 16.8 - - - -
184E SER* 3.8 12.8 - - - +
188E ALA* 1.3 80.0 - - - +
190E LEU* 1.3 62.1 + - - +
191E GLU* 3.1 26.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 3.4 23.6 - - + -
36E ALA 3.1 18.4 - - - +
37E LEU* 3.4 35.0 - - + -
71E VAL* 5.4 5.6 - - + -
146E VAL* 3.9 28.5 - - + +
147E GLU 5.7 0.4 - - - -
148E ALA* 5.4 5.6 - - + -
164E GLU* 6.0 3.6 - - + -
166E VAL* 4.6 11.2 - - + -
181E LEU 4.1 0.6 - - - +
182E HIS* 3.5 4.3 - - - -
183E PHE* 2.5 58.5 + - + +
188E ALA* 5.6 1.3 - - + -
189E HIS* 1.3 74.2 + - - +
191E GLU* 1.3 65.8 + - - +
192E LEU* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 3.5 46.7 + - + +
34E LEU* 3.2 7.8 - - - +
35E SER* 2.7 41.2 + - - +
36E ALA* 3.0 18.2 + - + +
180E SER* 4.9 5.7 + - - -
181E LEU 3.8 4.0 - - - +
182E HIS* 2.5 49.0 + - - +
189E HIS* 3.1 12.8 + - + -
190E LEU* 1.3 76.0 - - - +
192E LEU* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 4.4 13.9 - - + -
33E GLN 3.3 15.7 - - - +
34E LEU* 4.0 10.5 - - + -
35E SER* 3.8 2.6 + - - -
144E LEU* 4.6 1.3 - - + -
146E VAL* 4.1 32.5 - - + -
180E SER* 3.7 3.0 + - - -
181E LEU* 2.8 58.2 + - + +
183E PHE* 3.9 19.1 - - + -
190E LEU* 4.7 10.3 - - + -
191E GLU* 1.3 79.1 + - - +
193E GLN* 1.3 66.9 + - - +
194E ILE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER* 6.0 3.2 - - - -
266A TYR* 5.9 5.7 - - - +
32E LEU* 3.4 2.9 - - - +
33E GLN* 2.8 47.7 + - + +
35E SER* 5.1 11.7 - - - +
107E PRO* 6.3 1.0 - - - +
178E TRP* 3.4 37.5 - - + +
179E LYS 3.2 13.2 - - - +
180E SER* 4.3 15.0 + - - +
192E LEU* 1.3 81.4 - - - +
194E ILE* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E PHE* 3.6 24.7 - - + -
31E GLU 3.1 11.2 - - - +
32E LEU* 3.9 20.0 - - + -
142E PHE* 3.8 30.7 - - + -
144E LEU* 3.9 8.7 - - + -
168E HIS* 5.1 0.9 - - + -
172E ILE* 5.1 11.1 - - + +
177E ARG 3.7 0.9 - - - +
178E TRP* 3.4 4.0 - - - -
179E LYS* 3.0 41.3 + - + +
181E LEU* 3.8 19.5 - - + -
192E LEU* 4.1 7.4 - - + -
193E GLN* 1.3 78.7 - - - +
195E ARG* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E PHE* 4.2 1.2 - - - -
31E GLU* 2.7 60.9 + - - +
172E ILE* 5.0 4.9 - - - -
177E ARG* 3.7 46.8 - - - +
178E TRP* 3.4 51.1 - - + +
194E ILE* 1.3 82.8 - - - +
196E VAL* 1.3 73.8 + - - +
197E ARG* 3.3 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 3.3 20.2 - - - +
30E PHE* 3.5 24.5 - - + -
134E PHE* 4.7 3.8 - - + -
138E TRP* 4.0 25.6 - - + +
172E ILE* 4.1 16.9 - - + +
173E ASN* 3.8 28.8 + - - +
174E PRO* 3.4 27.8 - - + +
177E ARG* 5.0 0.5 + - - -
195E ARG* 1.3 83.6 - - - +
197E ARG* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 2.4 92.3 + - - +
31E GLU* 2.8 53.7 + - - +
129E LEU* 5.6 0.8 - - - +
131E VAL* 4.5 15.2 - - - +
174E PRO* 5.0 4.0 - - - +
195E ARG* 3.3 45.8 - - - +
196E VAL* 1.3 75.2 - - - +
198E CYS* 1.3 64.7 + - - +
207E CYS* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET 4.2 0.4 - - - +
28E GLY* 4.0 1.3 - - - -
29E TYR* 4.9 4.2 + - - -
174E PRO* 4.1 13.3 - - - +
197E ARG* 1.3 76.5 - - - +
199E ASP* 1.3 72.8 + - - +
200E GLU 3.8 0.2 + - - -
202E TYR* 4.0 13.9 - - + +
203E TYR* 4.9 0.9 - - - -
204E SER 3.9 11.4 - - - -
207E CYS* 2.0 56.1 - - + -
----------------------------------------------------------
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