Contacts of the helix formed by residues 145 - 153 (chain C) in PDB entry 3FUV
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 LYS 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C VAL 3.7 0.6 + - - -
144C GLN* 1.3 71.7 - - - +
146C GLU* 1.3 53.2 + - - +
148C ALA* 3.2 4.5 + - - +
149C GLU* 2.9 55.4 + - - +
175C ARG* 3.4 27.8 - - - +
178C ASP* 4.2 10.8 + - + +
190C VAL* 5.4 2.1 - - + +
191C TRP* 2.8 44.1 + - + +
193C SER* 3.5 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 4.6 10.7 + - - -
144C GLN* 4.5 14.5 - - + +
145C LYS* 1.3 78.4 - - - +
147C VAL* 1.3 57.0 + - + +
149C GLU* 3.5 17.9 + - - +
150C ARG* 3.2 60.4 + - - +
159C ALA* 5.0 0.9 - - - +
190C VAL* 6.0 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 4.5 17.9 - - + +
123C ALA* 5.6 0.4 - - + -
124C THR* 3.8 22.0 - - - +
143C VAL* 3.5 26.7 - - + -
144C GLN* 3.0 25.2 + - + +
146C GLU* 1.3 74.8 - - - +
148C ALA* 1.3 64.5 + - - +
150C ARG* 3.3 30.5 + - - +
151C MET* 3.1 35.4 + - + +
163C LEU* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C VAL* 3.5 22.2 - - + +
144C GLN 3.1 3.9 + - - +
145C LYS 3.4 8.1 - - - +
147C VAL* 1.3 80.1 - - - +
149C GLU* 1.3 53.4 + - - +
151C MET* 3.4 4.4 + - - +
152C THR* 2.7 38.3 + - - +
175C ARG* 4.1 7.0 - - - -
193C SER* 3.7 19.7 - - - +
195C VAL* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LYS* 2.9 48.2 + - - +
146C GLU* 3.6 19.3 - - - +
148C ALA* 1.3 68.9 - - - +
150C ARG* 1.3 61.1 + - - +
152C THR* 3.3 6.1 + - - -
153C ALA* 2.8 35.3 + - - +
159C ALA* 3.8 13.1 - - + +
175C ARG* 3.3 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 5.3 4.4 + - - -
124C THR* 5.1 3.4 + - - -
146C GLU* 3.2 45.8 + - - +
147C VAL* 3.4 36.8 - - - +
149C GLU* 1.3 81.8 - - - +
151C MET* 1.3 57.5 + - - +
152C THR 3.4 0.5 + - - -
159C ALA* 3.4 31.1 - - + +
163C LEU* 4.2 24.7 - - + +
164C THR* 2.5 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C THR* 4.3 13.9 - - - +
127C VAL* 4.1 27.8 - - + -
141C PHE* 3.6 36.3 - - + -
143C VAL* 4.8 1.3 - - + -
147C VAL* 3.1 34.0 + - + +
148C ALA* 3.6 11.9 - - - +
149C GLU 3.3 0.4 - - - -
150C ARG* 1.3 75.8 - - - +
152C THR* 1.3 64.4 + - + +
163C LEU* 3.9 18.2 - - + -
164C THR* 4.5 8.5 - - - +
167C VAL* 3.5 39.2 - - + +
173C ALA* 3.8 3.5 - - - +
195C VAL* 4.6 8.1 - - + -
197C LEU* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ALA 2.7 23.3 + - - +
149C GLU* 3.6 6.2 + - - -
151C MET* 1.3 85.7 - - + +
153C ALA* 1.3 68.3 + - - +
154C ARG* 3.7 5.2 + - - +
164C THR* 4.5 1.1 - - - -
173C ALA* 4.1 21.8 - - + +
174C GLU 4.1 4.0 - - - +
175C ARG* 4.0 37.5 + - + +
195C VAL* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLU 2.8 16.8 + - - +
151C MET 3.7 1.4 - - - -
152C THR* 1.3 82.6 - - - +
154C ARG* 1.3 62.6 + - - +
155C PRO* 4.5 0.7 - - - +
157C THR* 3.8 7.0 - - - +
159C ALA* 3.6 8.1 - - + -
160C TYR* 3.5 36.9 - - - +
164C THR* 3.3 23.4 - - - +
----------------------------------------------------------
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