Contacts of the helix formed by residues 74 - 93 (chain B) in PDB entry 3PEJ
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 SER 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET 4.1 0.6 + - - -
73B GLU* 1.4 75.8 - - - +
75B HIS* 1.3 67.3 + - - +
76B GLN* 3.5 14.1 + - - +
77B TYR* 3.9 15.4 - - - +
78B GLN* 3.2 26.3 + - - +
166B ALA* 5.7 2.2 - - - -
226B PHE* 4.3 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 1.3 73.7 + - - +
76B GLN* 1.4 65.4 + - - +
78B GLN* 3.3 8.5 + - + +
79B THR* 2.9 46.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 3.5 9.0 + - - +
75B HIS* 1.4 80.5 - - - +
77B TYR* 1.4 55.9 + - - +
79B THR* 3.5 6.2 + - - -
80B GLU* 3.1 28.8 + - - +
166B ALA* 3.3 22.9 - - + +
167B LYS* 3.3 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 5.0 1.6 - - + -
74B SER* 3.8 20.4 + - - +
75B HIS 3.3 0.2 - - - -
76B GLN* 1.4 75.7 - - - +
78B GLN* 1.3 59.2 + - - +
80B GLU* 4.5 0.4 - - - -
81B VAL* 2.9 58.9 + - + +
162B LEU* 3.4 50.3 - - + +
165B ILE* 4.2 5.6 - - + -
166B ALA* 3.7 16.8 - - + +
195B TYR* 2.7 34.2 + - - -
218B TRP* 3.7 8.8 + - - -
220B SER* 4.7 2.6 + - - -
224B ALA 4.1 14.1 - - - -
226B PHE* 3.3 35.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 5.4 3.6 - - + -
74B SER 3.2 17.3 + - - +
75B HIS* 3.3 11.2 + - - +
77B TYR* 1.3 77.6 - - - +
79B THR* 1.4 55.7 + - - +
82B THR* 2.5 31.9 + - - -
223B ASP 5.4 1.3 - - - +
224B ALA* 3.3 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 2.9 37.3 + - - -
76B GLN* 3.9 5.6 - - - -
77B TYR 3.2 0.2 - - - -
78B GLN* 1.4 75.3 - - - +
80B GLU* 1.3 63.3 + - - +
82B THR* 3.5 5.3 + - - -
83B ARG* 3.2 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN 3.1 18.2 + - - +
77B TYR 3.9 2.9 - - - +
79B THR* 1.3 72.9 - - - +
81B VAL* 1.3 60.2 + - + +
83B ARG* 3.1 10.7 + - - +
84B LEU* 2.8 45.6 + - + +
165B ILE* 3.4 26.6 - - + +
166B ALA* 4.1 11.7 - - - +
169B GLY* 3.5 11.9 - - - -
170B THR* 3.0 15.4 + - - -
171B SER* 2.6 47.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 2.9 58.2 + - + +
80B GLU* 1.3 68.3 - - + +
82B THR* 1.4 56.3 + - - +
84B LEU* 3.5 7.1 - - + +
85B MET* 2.8 62.4 + - + +
165B ILE* 4.2 9.2 - - + -
195B TYR* 3.7 27.6 - - + -
224B ALA* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN 2.5 25.5 + - - -
79B THR* 3.6 6.3 - - - -
80B GLU 3.3 0.2 - - - -
81B VAL* 1.4 75.7 - - - +
83B ARG* 1.3 58.7 + - + +
85B MET* 3.8 6.4 - - - +
86B ASP* 2.9 50.9 + - - +
223B ASP* 4.5 4.8 + - - -
224B ALA* 3.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.2 28.1 + - + +
80B GLU* 3.1 10.2 + - - +
82B THR* 1.3 74.6 - - + +
84B LEU* 1.4 64.4 + - - +
86B ASP* 3.1 7.7 + - - +
87B ILE* 2.9 38.3 + - + +
171B SER* 3.0 30.2 + - - -
172B ASN* 2.6 36.1 + - - +
175B GLU* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 2.8 38.0 + - + +
81B VAL* 3.5 15.7 - - + +
83B ARG* 1.4 71.9 - - - +
85B MET* 1.3 57.4 + - - +
87B ILE* 3.9 1.5 - - - +
88B ILE* 2.9 44.6 + - + +
165B ILE* 4.2 11.7 - - + -
170B THR 4.2 1.1 - - - -
171B SER* 3.7 25.8 - - - +
174B LEU* 3.8 23.1 - - + -
192B VAL* 3.8 32.5 - - + -
195B TYR* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 2.8 47.3 + - + +
82B THR* 3.8 5.6 - - - +
84B LEU* 1.3 70.5 - - - +
86B ASP* 1.3 60.6 + - - +
88B ILE* 4.6 4.5 - - - -
89B VAL* 2.9 39.7 + - + +
195B TYR* 4.5 12.6 - - + +
198B PHE* 3.5 46.2 - - + -
220B SER* 5.8 1.3 - - - -
221B THR 3.4 22.7 - - - +
222B ALA* 3.3 28.3 - - - +
224B ALA* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 2.9 44.7 + - - +
83B ARG* 3.1 8.2 + - - +
85B MET* 1.3 73.8 - - - +
87B ILE* 1.4 58.4 + - + +
89B VAL* 3.9 3.9 - - - +
90B ASN* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 2.9 38.3 + - + +
84B LEU* 4.0 2.7 - - - +
86B ASP* 1.4 71.7 - - + +
88B ILE* 1.4 54.8 + - - +
90B ASN* 3.3 6.4 + - - +
91B SER* 2.9 39.5 + - - -
171B SER* 3.4 33.4 - - - +
174B LEU* 3.8 31.9 - - + +
175B GLU* 3.7 17.0 - - + +
178B SER* 4.2 11.9 - - - +
184B MET* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 2.9 29.3 + - + +
85B MET* 4.0 3.6 - - - +
87B ILE* 1.4 72.8 - - - +
89B VAL* 1.3 58.5 + - + +
91B SER 3.8 0.2 - - - -
92B LEU* 2.9 38.7 + - + +
174B LEU* 4.2 17.9 - - + -
184B MET* 4.4 9.4 - - + -
187B ILE* 4.1 25.8 - - + -
192B VAL* 4.0 22.0 - - + +
195B TYR* 4.3 13.7 - - + +
196B SER* 3.8 32.1 - - - +
199B LEU* 4.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 2.9 26.1 + - + +
86B ASP* 4.1 3.4 - - - +
88B ILE* 1.3 79.2 - - + +
90B ASN* 1.4 62.5 + - - +
93B TYR* 3.1 33.4 + - + +
96B LYS* 5.6 4.3 - - - -
195B TYR 5.8 0.7 - - - +
198B PHE* 3.6 31.9 - - + +
199B LEU* 3.7 18.6 - - + +
248B LYS* 5.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 2.9 20.4 + - - +
87B ILE* 3.7 5.8 + - - +
89B VAL* 1.4 76.4 - - - +
91B SER* 1.3 58.1 + - - +
93B TYR* 3.1 30.6 - - - -
178B SER* 4.2 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE 2.9 17.6 + - - -
88B ILE 4.0 0.2 - - - -
90B ASN* 1.3 78.7 + - - +
92B LEU* 1.3 59.8 + - - +
93B TYR* 3.7 2.3 + - - -
94B THR* 4.4 4.9 + - - -
95B GLN* 3.9 10.4 - - - +
178B SER* 3.0 26.0 + - - -
182B GLY 5.4 1.2 + - - -
183B ASP* 6.3 0.2 - - - -
184B MET* 3.5 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 2.9 31.6 + - + +
91B SER* 1.3 78.2 - - - +
93B TYR* 1.4 56.2 + - - +
94B THR 3.1 5.8 - - - +
95B GLN* 2.9 35.4 + - + +
96B LYS* 2.9 26.5 + - - -
98B VAL* 3.9 27.8 - - + -
101B ARG* 6.1 0.7 - - - +
184B MET* 3.7 34.3 - - + +
187B ILE* 4.5 10.8 - - + -
196B SER* 5.3 0.2 - - - -
199B LEU* 3.5 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 3.1 18.9 + - + +
90B ASN* 3.1 35.0 - - - -
91B SER 3.7 1.7 - - - -
92B LEU* 1.4 74.7 - - - +
94B THR* 1.3 80.0 + - + +
95B GLN 3.4 0.2 - - - -
96B LYS* 3.4 41.7 + - - +
199B LEU* 4.1 0.9 - - - -
----------------------------------------------------------
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