Contacts of the helix formed by residues 135 - 151 (chain G) in PDB entry 3PUY
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 LEU 135 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PRO 4.8 0.3 - - - +
85F CYS* 5.3 0.2 - - - +
86F THR* 3.5 29.1 + - + +
89F ILE* 4.1 24.8 - - + +
94F TYR* 4.8 2.9 - - + -
476F PHE* 4.9 1.1 - - + -
484F PHE* 3.8 46.7 - - + +
487F ALA* 4.3 8.1 - - + -
488F ALA* 4.4 12.3 - - + +
134G VAL* 1.3 102.3 - - + +
136G SER* 1.3 60.7 + - - +
137G LEU 3.4 2.0 - - - -
138G VAL* 3.6 34.4 + - + +
139G ALA* 3.6 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PRO* 3.9 25.7 - - - +
86F THR* 4.2 2.6 + - - -
133G ALA* 3.3 38.0 + - - +
134G VAL 3.3 1.2 - - - +
135G LEU* 1.3 77.0 - - - +
137G LEU* 1.3 66.3 + - - +
139G ALA* 3.0 5.2 + - - +
140G LEU* 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G VAL 4.8 4.4 + - - +
135G LEU* 3.4 0.6 - - - +
136G SER* 1.3 85.3 + - - +
138G VAL* 1.3 62.2 + - + +
140G LEU* 4.2 13.4 - - + +
141G TYR* 3.3 24.9 + - - +
231G PRO* 4.3 20.4 - - + +
232G VAL* 4.2 26.0 - - + +
235G LEU* 4.1 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLN* 3.3 36.6 - - + +
89F ILE* 5.3 8.1 - - + -
94F TYR* 3.7 21.5 - - + +
484F PHE* 5.5 4.7 - - + -
134G VAL 5.5 0.9 - - - +
135G LEU* 3.8 34.8 - - + +
136G SER 3.2 0.6 - - - -
137G LEU* 1.3 78.8 - - + +
139G ALA* 1.3 60.4 + - - +
141G TYR* 4.6 3.4 - - - +
142G ALA* 4.0 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PHE* 3.7 15.1 - - + -
82F PRO* 4.0 15.9 - - + -
85F CYS* 3.8 36.3 - - + -
135G LEU 3.6 6.4 + - - +
136G SER 3.0 9.8 + - - +
138G VAL* 1.3 78.6 - - - +
140G LEU* 1.3 64.1 + - - +
141G TYR 3.4 0.2 - - - -
142G ALA* 3.3 9.1 + - - +
143G LEU 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F PHE* 4.1 26.0 - - + +
81F PHE* 6.0 0.2 - - + -
82F PRO* 4.7 15.3 - - + -
136G SER* 2.8 24.4 + - - +
137G LEU* 3.6 16.1 + - + +
139G ALA* 1.3 74.1 - - - +
141G TYR* 1.3 65.8 + - - +
143G LEU* 3.0 19.0 + - + +
144G PHE* 3.1 45.4 + - + -
165G ALA* 5.1 3.1 - - + -
232G VAL* 3.9 30.1 - - + -
235G LEU* 4.7 7.2 - - + -
236G LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLN* 4.9 13.5 - - + -
50E VAL* 3.3 32.5 - - + +
53E THR* 5.5 4.0 - - - -
55E ASP* 5.4 7.8 + - - +
137G LEU 3.3 15.7 + - - +
138G VAL* 4.6 4.0 - - - +
139G ALA 3.4 0.2 - - - -
140G LEU* 1.3 77.9 - - - +
142G ALA* 1.3 59.0 + - - +
144G PHE 3.9 0.2 - - - -
145G ASP* 2.9 42.8 + - + +
156G LEU* 3.7 42.5 - - + +
235G LEU* 3.7 38.7 - - + +
236G LEU* 5.0 0.2 - - - -
238G ARG* 4.9 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PHE* 5.7 4.5 - - + -
138G VAL 4.0 11.6 + - - +
139G ALA* 3.3 12.4 + - - +
140G LEU 3.2 0.4 - - - -
141G TYR* 1.3 82.4 - - - +
143G LEU* 1.3 58.9 + - - +
145G ASP* 3.9 2.8 - - - +
146G ARG* 3.0 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.7 28.7 - - + -
77F LEU* 3.7 41.7 - - + +
78F PHE* 3.8 26.7 - - + -
81F PHE* 4.1 19.9 - - + -
139G ALA 3.2 10.7 + - - +
140G LEU* 3.0 13.0 + - + +
142G ALA* 1.3 75.7 - - - +
144G PHE* 1.3 62.2 + - + +
146G ARG* 3.1 6.9 + - - +
147G LEU* 2.7 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F PHE* 3.5 28.9 - + - -
140G LEU* 3.1 38.4 + - + +
143G LEU* 1.3 79.8 - - + +
145G ASP* 1.3 59.3 + - - +
147G LEU* 4.0 15.9 - - + -
148G GLY* 3.1 23.7 + - - -
154G ILE 3.3 24.7 - - - -
155G GLY* 3.6 11.9 - - - -
156G LEU* 3.7 23.5 + - + -
161G GLY* 3.2 33.2 - - - -
164G PHE* 4.3 7.6 - + - -
165G ALA* 3.6 18.4 - - + -
232G VAL* 5.8 0.2 - - + -
236G LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASP* 5.4 6.3 - - - +
141G TYR* 2.9 30.9 + - + +
142G ALA* 3.9 6.1 - - - +
144G PHE* 1.3 78.1 - - - +
146G ARG* 1.3 81.9 + - - +
148G GLY* 3.6 6.4 + - - -
149G GLU* 3.4 13.8 + - - +
156G LEU* 3.9 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E THR* 6.2 2.2 - - - +
39F GLU* 3.2 37.4 + - - +
42F PHE* 4.4 24.0 - - + -
142G ALA* 3.0 40.2 + - - +
143G LEU 3.1 7.5 + - - +
145G ASP* 1.3 87.8 + - - +
147G LEU* 1.3 68.8 + - - +
148G GLY 2.8 3.4 + - - -
149G GLU* 3.0 30.2 + - - +
150G TYR* 3.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F MET* 6.2 0.7 - - + -
42F PHE* 4.2 24.9 - - + -
77F LEU* 6.1 2.2 - - + -
143G LEU* 2.7 30.2 + - + +
144G PHE* 4.0 20.2 - - + -
146G ARG* 1.3 73.0 - - - +
148G GLY* 1.3 55.8 + - - +
150G TYR* 3.0 10.0 + - + +
151G ILE* 2.9 48.1 + - + +
154G ILE* 3.4 44.6 - - + +
164G PHE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE 3.1 19.7 + - - -
145G ASP 3.9 3.4 - - - -
146G ARG 2.8 6.3 + - - -
147G LEU* 1.3 73.7 - - - +
149G GLU* 1.3 56.7 + - - -
151G ILE 3.3 7.6 - - - +
152G PRO* 3.1 28.1 - - - +
155G GLY* 3.6 14.3 - - - -
156G LEU 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 6.0 0.2 - - - +
37F GLN* 4.6 7.9 + - - +
39F GLU* 3.6 19.6 - - - +
145G ASP* 3.4 19.7 + - - +
146G ARG* 3.0 19.5 + - - +
148G GLY* 1.3 76.2 - - - +
150G TYR* 1.3 86.8 + - + +
152G PRO* 5.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F LEU* 4.0 23.0 - - + +
33F LEU* 3.6 35.2 - - + -
34F MET* 3.5 44.2 - - + +
37F GLN* 3.5 17.0 + - - -
39F GLU* 3.1 34.5 - - + +
42F PHE* 4.5 9.9 - + + -
146G ARG* 3.5 19.1 - - - -
147G LEU* 3.0 4.8 + - - +
149G GLU* 1.3 103.0 + - + +
151G ILE* 1.3 69.2 + - + +
152G PRO* 3.7 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F LEU* 4.9 16.2 - - + -
34F MET* 6.0 2.2 - - + -
147G LEU* 2.9 37.4 + - + +
148G GLY* 3.3 8.6 - - - +
150G TYR* 1.3 85.7 - - + +
152G PRO* 1.3 66.2 - - + +
153G PHE* 3.9 16.4 - - + +
154G ILE* 3.6 36.2 + - + +
155G GLY 3.9 1.2 + - - -
----------------------------------------------------------
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