Contacts of the strand formed by residues 164 - 171 (chain F) 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 GLU 164 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 4.9 12.4 - - - +
146F VAL 4.3 0.3 - - - +
147F GLU* 3.5 0.9 - - - -
148F ALA* 2.8 32.0 + - + +
162F LEU* 3.3 8.6 - - - +
163F ILE* 1.3 81.4 - - - +
165F ARG* 1.3 78.2 + - - +
166F VAL* 4.1 19.1 - - + -
185F GLY* 3.6 6.8 - - - -
186F HIS* 3.1 19.1 + - - +
187F VAL* 3.0 32.2 + - - +
188F ALA* 3.4 30.4 + - + +
190F LEU* 4.4 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 5.8 1.4 - - + +
84F PRO* 3.7 36.2 + - - +
145F ILE* 4.2 15.5 - - + -
146F VAL 3.7 3.4 - - - -
147F GLU* 2.6 38.9 + - + -
149F TRP* 4.4 4.9 - - - -
159F GLU* 3.6 30.5 + - - -
162F LEU* 3.8 24.7 - - + +
164F GLU* 1.3 88.9 + - - +
166F VAL* 1.3 65.7 + - - +
167F SER* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F ILE* 3.4 12.0 - - - +
146F VAL* 3.0 54.6 + - + +
164F GLU* 4.1 10.3 - - + -
165F ARG* 1.3 79.2 - - - +
167F SER* 1.3 62.4 + - - +
183F PHE* 3.5 52.0 - - + -
185F GLY* 5.8 3.6 - - - +
190F LEU* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F VAL* 3.6 39.3 - - - +
144F LEU 3.3 9.4 - - - -
145F ILE* 4.3 5.6 - - - +
165F ARG* 6.2 0.2 - - - -
166F VAL* 1.3 78.5 - - - +
168F HIS* 1.3 65.1 + - - +
183F PHE* 3.3 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F VAL* 5.2 2.0 - - - -
142F PHE* 4.3 20.0 - + - -
143F THR* 3.6 2.7 - - - -
144F LEU* 2.7 44.4 + - + +
167F SER* 1.3 77.6 + - - +
169F ALA* 1.3 79.7 + - - +
170F GLY* 4.1 7.7 + - - -
181F LEU* 4.0 37.4 - - + +
183F PHE* 3.8 19.2 - - + -
194F ILE* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TYR* 3.6 25.5 + - + +
79F GLN 4.0 12.3 - - - +
82F VAL* 4.6 9.0 - - + +
142F PHE 3.6 4.3 - - - -
143F THR* 3.7 21.1 - - + +
168F HIS* 1.3 88.6 + - - +
170F GLY* 1.3 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TYR* 3.8 9.9 - - - -
141F SER* 3.4 3.5 - - - -
142F PHE* 3.0 40.3 + - - +
168F HIS* 4.1 13.8 + - - -
169F ALA* 1.3 75.0 - - - +
171F MET* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TYR* 5.8 5.2 - - + -
140F ARG* 3.3 58.3 - - + +
141F SER* 4.0 17.7 - - - -
142F PHE* 3.7 3.9 - - - -
170F GLY* 1.3 80.3 - - - +
172F ILE* 1.3 64.4 + - - +
176F ASP* 4.5 2.8 - - - +
179F LYS* 5.8 3.1 - - - +
----------------------------------------------------------
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