Contacts of the helix formed by residues 145 - 156 (chain F) in PDB entry 5YUS
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 145 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ARG* 3.7 7.2 - - - +
4F ILE* 3.4 11.7 - - - -
143F ALA* 3.3 0.7 - - - +
144F PRO* 1.3 87.1 - - + +
146F LYS* 1.3 67.3 + - - +
147F PHE* 3.7 31.9 - - + -
148F LEU* 3.9 19.7 - - + -
149F ALA* 3.2 22.5 + - - +
228F GLY 4.0 15.0 - - - +
230F ASP* 3.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ARG* 5.2 0.2 - - - +
4F ILE* 3.8 13.9 - - + +
98F GLU* 2.9 34.5 + - - -
106F TYR* 3.3 48.3 - - + -
145F VAL* 1.3 75.0 - - - +
147F PHE* 1.3 64.2 + - - +
149F ALA* 3.1 3.1 + - - +
150F LYS 3.0 18.0 + - - -
230F ASP* 3.4 12.0 + - - +
232F ARG* 3.6 45.7 - - + +
233F ASP 3.2 27.9 + - - -
234F VAL* 3.9 8.5 - - + +
235F ASN* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F TYR* 4.4 4.7 - - - -
145F VAL* 3.4 9.6 - - + -
146F LYS* 1.3 73.4 - - - +
148F LEU* 1.3 89.8 + - + +
150F LYS* 3.2 4.2 + - - +
151F ILE* 2.9 49.9 + - + +
173F LEU* 4.4 1.3 - - + -
176F LEU* 4.6 8.3 - - + -
181F ILE* 4.6 6.5 - - + -
182F PRO* 4.2 20.6 - - + +
225F ARG* 3.2 54.3 - - + +
228F GLY* 4.1 14.1 - - - -
230F ASP* 2.9 37.6 + - + +
232F ARG* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ALA* 3.5 17.5 - - + -
144F PRO* 5.0 2.9 - - + -
145F VAL* 3.6 17.2 + - + -
146F LYS 3.3 0.4 - - - -
147F PHE* 1.3 110.4 - - + +
149F ALA* 1.3 57.4 + - - +
151F ILE* 3.5 6.0 + - + +
152F ALA* 2.8 30.1 + - - +
164F ILE* 3.8 9.1 - - + +
169F VAL* 3.9 38.4 - - + -
172F PHE* 3.9 32.8 - - + -
173F LEU* 4.4 6.5 - - + -
176F LEU* 4.6 0.2 - - + -
228F GLY* 4.4 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.7 32.8 - - + +
6F HIS* 3.7 12.4 - - + +
106F TYR* 4.6 0.2 - - + -
141F GLY* 3.4 18.0 - - - +
143F ALA* 3.2 10.2 - - + +
145F VAL 3.2 13.4 + - - +
146F LYS 3.1 10.2 + - - +
148F LEU* 1.3 76.4 - - - +
150F LYS* 1.3 58.5 + - - +
152F ALA* 3.2 4.7 + - - -
153F SER 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F HIS* 3.6 21.3 + - + +
8F ASP* 5.7 0.7 - - - -
100F LEU* 4.0 5.4 - - + +
104F GLU* 2.2 36.8 + - - -
106F TYR* 3.4 28.7 - - + +
146F LYS 3.0 5.4 + - - +
147F PHE* 3.2 8.9 + - - +
149F ALA* 1.3 75.1 - - - +
151F ILE* 1.3 67.5 + - + +
153F SER* 2.9 18.0 + - - -
154F ASP* 3.7 8.7 + - - +
182F PRO* 4.1 25.1 - - + -
872H C 4.6 1.3 - - - -
873H C 2.3 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 2.9 42.5 + - + +
148F LEU* 3.8 6.1 - - + +
150F LYS* 1.3 75.7 - - + +
152F ALA* 1.3 64.2 + - - +
154F ASP* 3.1 19.6 + - - +
155F MET* 3.5 15.2 - - + +
172F PHE* 3.8 26.7 - - + -
176F LEU* 4.0 29.6 - - + -
180F LYS* 3.6 42.1 + - + +
181F ILE* 4.5 1.6 - - - -
182F PRO* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F ALA 4.0 1.4 - - - +
141F GLY* 3.6 5.2 - - - -
142F VAL 4.0 4.9 - - - +
148F LEU 2.8 22.3 + - - +
149F ALA* 3.2 6.3 + - - +
151F ILE* 1.3 73.5 - - - +
153F SER* 1.3 61.8 + - - +
155F MET* 3.1 22.1 + - - -
156F ASN 4.3 1.0 + - - -
162F PHE* 3.4 47.9 - - + +
164F ILE* 4.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F HIS* 2.8 39.2 + - - -
8F ASP* 4.1 13.0 + - - +
139F SER* 3.7 21.5 - - - -
140F ALA* 3.5 8.5 + - - +
141F GLY* 3.3 24.2 - - - +
149F ALA 3.0 6.7 + - - -
150F LYS 2.9 11.4 + - - -
151F ILE 3.2 0.2 - - - -
152F ALA* 1.3 76.6 - - - +
154F ASP* 1.3 63.0 + - - +
155F MET 3.7 0.3 + - - -
156F ASN 4.4 2.1 + - - -
157F LYS* 4.2 4.9 - - - +
160F GLY 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ASP* 4.6 9.7 - - - +
150F LYS* 4.4 8.4 - - - +
151F ILE* 3.1 14.1 + - - +
153F SER* 1.3 84.3 + - - +
155F MET* 1.3 62.9 + - + +
156F ASN 3.3 1.6 + - - -
157F LYS* 3.3 47.9 + - - +
180F LYS* 5.0 13.0 + - - +
900F TTP 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ILE* 3.5 19.7 - - + +
152F ALA* 3.1 10.8 + - - +
154F ASP* 1.3 79.8 - - + +
156F ASN* 1.3 65.3 + - - +
157F LYS 3.7 0.6 - - - +
162F PHE* 3.6 45.1 - - + -
172F PHE* 3.6 35.0 - - + -
180F LYS* 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F ALA 4.3 2.6 + - - -
153F SER 4.4 1.5 + - - -
154F ASP 3.3 0.4 - - - -
155F MET* 1.3 83.8 - - - +
157F LYS* 1.3 60.5 + - - +
158F PRO 3.6 2.4 - - - +
160F GLY* 3.1 27.5 + - - -
161F GLN* 3.0 41.0 + - - +
162F PHE* 4.5 8.8 - - + -
----------------------------------------------------------
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