Contacts of the strand formed by residues 177 - 182 (chain M) in PDB entry 6E0P
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 VAL 177 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M MET* 3.7 33.9 - - + -
171M ALA* 3.7 18.6 - - + -
175M GLU* 4.4 1.3 - - + +
176M ARG* 1.3 77.9 - - - +
178M THR* 1.3 63.5 + - - +
179M ILE* 4.3 4.9 - - + -
231M LEU 3.7 0.9 - - - +
232M THR* 3.3 7.1 - - - +
233M ILE* 3.0 38.1 + - + +
236M LEU* 3.7 27.8 - - + -
262M LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M PRO* 4.4 2.6 - - - +
169M MET* 3.8 17.0 - - - +
176M ARG* 4.2 7.9 + - - +
177M VAL* 1.3 73.9 - - - +
179M ILE* 1.3 68.4 + - - +
180M THR* 4.3 15.6 - - + +
230M SER* 4.4 6.6 - - - -
231M LEU 3.3 6.9 + - - -
232M THR* 4.1 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLN* 3.3 26.2 - - - +
166M PRO* 4.4 6.7 - - + -
169M MET* 3.7 19.5 - - + -
177M VAL* 4.3 4.0 - - + -
178M THR* 1.3 80.2 + - - +
180M THR* 1.3 64.0 + - - +
193M TRP* 3.8 14.0 - - + -
230M SER* 3.2 1.7 - - - -
231M LEU* 2.5 67.4 + - + +
233M ILE* 4.1 11.4 - - + -
244M TYR* 4.0 27.8 - - + -
260M THR* 4.0 12.1 - - + +
262M LEU* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLN* 3.4 9.0 - - - +
165M SER* 2.3 54.2 + - - -
166M PRO* 4.1 5.3 - - - +
178M THR* 4.3 11.2 - - + +
179M ILE* 1.3 78.7 - - - +
181M CYS* 1.3 61.3 + - - +
182M LYS* 3.8 6.9 + - - +
193M TRP* 4.3 1.8 - - - -
229M PHE 3.4 14.4 - - - +
230M SER* 4.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 181 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M MET* 3.6 30.5 - - - +
163M THR 3.4 8.7 - - - -
164M GLN* 4.1 1.1 - - - +
180M THR* 1.3 73.3 - - - +
182M LYS* 1.3 66.9 + - - +
183M ALA 3.3 2.6 + - - -
191M LEU* 4.4 3.6 - - + -
193M TRP* 3.5 13.4 - - + -
229M PHE* 3.2 27.1 + - + -
246M CYS* 2.0 53.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M THR* 3.2 40.8 + - + +
165M SER* 6.2 2.2 - - - -
180M THR* 3.8 6.5 + - - +
181M CYS* 1.3 72.5 - - - +
183M ALA* 1.3 72.2 + - - +
227M GLN* 3.3 8.1 - - + +
228M ASP* 3.3 32.5 + - - +
229M PHE 4.5 2.0 + - - +
----------------------------------------------------------
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