Contacts of the helix formed by residues 177 - 180 (chain I) in PDB entry 2FRV
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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I GLU* 2.9 40.9 + - + +
170I LEU 3.6 27.1 - - - +
171I ASP* 3.7 13.7 - - + +
175I ARG 3.0 1.8 + - - -
176I PRO* 1.3 69.9 - - - +
178I MET* 1.3 61.8 + - - +
179I PHE 3.1 0.4 - - - -
180I PHE 4.5 1.1 - - - -
181I GLY* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I GLY 5.2 1.8 - - - +
158I THR* 5.3 0.9 - - - -
161I HIS* 4.6 26.5 - - + -
165I LYS* 4.8 7.6 - - - +
168I PRO* 4.5 19.7 - - + -
169I GLU 4.7 1.0 + - - -
176I PRO* 2.8 10.3 + - + -
177I VAL* 1.3 76.5 - - - +
179I PHE* 1.3 103.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I MET* 3.9 35.2 - - + -
154I ASN* 3.5 48.2 - - + +
157I GLY* 4.0 14.1 - - - -
158I THR* 3.3 26.7 - - - -
176I PRO* 2.9 9.9 + - + -
178I MET* 1.3 120.1 - - + +
180I PHE* 1.3 68.8 + + + +
181I GLY 3.5 2.8 + - - -
182I GLU 5.2 0.9 + - - -
226I ASN* 3.9 1.9 - - - +
227I ASN* 3.5 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I ILE* 4.1 13.0 - - + -
146I ALA* 3.3 43.7 - - - -
154I ASN* 3.7 15.0 - - + -
171I ASP* 4.3 8.8 - - - +
175I ARG* 3.6 42.8 - - + +
176I PRO* 3.2 27.4 + - + +
177I VAL* 4.0 3.4 - - - -
179I PHE* 1.3 86.6 - + + +
181I GLY* 1.3 60.1 + - - +
182I GLU 3.5 2.9 - - - -
225I TYR* 3.3 44.5 - - + +
226I ASN* 3.6 20.2 - - - +
250I SER* 4.4 1.3 - - - -
----------------------------------------------------------
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