Contacts of the helix formed by residues 87 - 99 (chain B) in PDB entry 2J0Q
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 GLY 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.6 1.6 - - - -
65B GLN* 2.9 21.4 + - - -
85B GLY 3.4 2.6 - - - -
86B THR* 1.3 80.1 - - - +
88B LYS* 1.3 56.2 + - - +
89B THR 3.4 2.0 - - - -
90B ALA* 3.5 2.0 - - - +
91B THR* 2.8 28.9 + - - -
1413B ANP 3.1 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.2 9.9 - - + -
81B GLN* 4.4 2.0 - - - -
82B SER* 2.9 54.6 + - - +
83B GLN 3.1 15.0 + - - -
86B THR* 4.3 2.0 - - - +
87B GLY* 1.3 75.2 - - - +
89B THR* 1.3 62.9 - - - +
90B ALA 3.1 0.2 - - - -
91B THR* 2.8 31.2 + - - -
92B PHE* 3.1 12.9 + - - -
187B ASP* 5.3 1.3 - - - -
188B GLU* 5.5 0.2 - - - -
217B ILE* 3.6 24.6 - - + +
218B SER* 3.8 9.9 - - - +
219B ALA* 3.5 23.1 - - - +
1413B ANP 3.1 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 1.3 76.4 - - - +
90B ALA* 1.3 53.8 + - - +
92B PHE* 3.6 21.6 - - + -
93B SER* 2.5 35.4 + - - +
118B LEU* 5.4 4.0 - - + -
121B GLN* 5.8 4.9 - - + +
122B ILE* 3.8 18.8 - - + +
187B ASP* 2.9 16.6 + - - +
340B GLY 6.2 0.2 - - - +
1412B MG 2.2 33.1 - - - -
1413B ANP 2.7 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 4.1 17.0 - - + -
65B GLN* 3.7 12.8 - - - +
87B GLY 3.5 9.6 - - - +
88B LYS 3.1 0.2 - - - -
89B THR* 1.3 77.9 - - - +
91B THR* 1.3 58.8 - - - +
93B SER* 3.5 5.5 - - - -
94B ILE* 2.8 38.8 + - + +
129B LEU* 5.0 4.5 - - + -
1413B ANP 3.4 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.9 8.9 - - + +
65B GLN* 3.1 20.3 - - - +
68B ALA* 3.5 31.6 - - + -
69B ILE* 4.0 18.2 - - + +
72B ILE* 4.4 9.0 - - + -
87B GLY 2.8 20.9 + - - -
88B LYS* 2.8 20.3 + - - -
90B ALA* 1.3 74.9 - - - +
92B PHE* 1.3 55.6 + - - +
94B ILE* 3.5 3.7 + - - +
95B SER* 3.0 30.5 + - - -
217B ILE* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.6 7.6 - - + +
88B LYS 3.1 12.9 + - - -
89B THR* 3.6 25.8 - - + -
91B THR* 1.3 78.2 - - - +
93B SER* 1.3 70.7 + - - +
95B SER* 3.9 6.4 - - - -
96B VAL* 2.8 38.0 + - + +
111B ILE* 3.8 32.3 - - + -
122B ILE* 3.7 28.5 - - + -
185B VAL* 3.7 27.4 - - + -
187B ASP* 3.7 24.5 - - + -
215B VAL* 5.0 0.7 - - + -
217B ILE* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 2.5 26.1 + - - +
90B ALA* 3.5 6.2 - - - -
91B THR 3.3 0.2 - - - -
92B PHE* 1.3 89.1 - - - +
94B ILE* 1.3 67.2 + - - +
96B VAL* 3.3 1.6 + - - -
97B LEU* 3.0 29.5 + - - +
122B ILE* 4.6 5.5 + - - -
125B GLY* 5.3 1.9 - - - -
126B LEU* 3.5 30.3 + - - +
129B LEU* 4.1 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 4.0 22.2 - - + -
45B LEU* 4.0 23.8 - - + -
49B LEU* 3.3 12.4 - - + +
53B ILE* 3.5 28.3 - - + -
58B PHE* 4.5 14.1 - - + -
65B GLN* 5.3 2.2 - - - -
69B ILE* 4.0 26.5 - - + -
90B ALA* 2.8 25.3 + - + +
91B THR* 3.7 3.8 - - - +
93B SER* 1.3 73.3 - - - +
95B SER* 1.3 64.2 + - - +
97B LEU* 3.4 1.3 + - - -
98B GLN* 3.1 18.5 + - - +
129B LEU* 3.7 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.5 27.5 - - - +
72B ILE* 3.5 32.8 - - - +
73B ILE* 4.1 15.3 - - - -
91B THR 3.0 18.4 + - - -
92B PHE* 3.9 4.0 - - - -
93B SER 3.2 0.2 - - - -
94B ILE* 1.3 73.6 - - - +
96B VAL* 1.3 64.7 + - - +
98B GLN* 3.4 2.1 + - - +
99B CYS* 3.3 28.8 + - - -
183B MET* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 2.8 28.2 + - + +
93B SER* 3.7 5.4 - - - +
95B SER* 1.3 70.2 - - - +
97B LEU* 1.3 68.2 + - - +
99B CYS* 3.1 13.5 + - - +
100B LEU* 3.4 14.7 + - + +
109B ALA* 4.0 23.8 - - + -
111B ILE* 4.5 9.9 - - + -
126B LEU* 4.6 8.1 - - + -
159B VAL* 4.2 23.6 - - + -
183B MET* 3.7 30.6 - - - +
185B VAL* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.3 16.6 + - - -
49B LEU* 3.4 33.9 - - + -
93B SER 3.0 20.6 + - - +
94B ILE 3.7 0.7 - - - +
96B VAL* 1.3 78.3 - - + +
98B GLN* 1.3 62.4 + - - +
100B LEU* 3.3 15.1 + - + +
126B LEU* 3.5 27.1 - - + +
129B LEU* 3.7 12.1 - - + -
130B GLY* 3.5 23.8 - - - +
133B MET* 3.5 11.4 - - - +
135B VAL* 3.9 37.0 - - + -
159B VAL* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY 3.8 16.0 + - - -
45B LEU* 3.8 12.5 - - + -
46B ARG* 2.9 55.5 + - - +
49B LEU* 3.5 11.2 - - + +
73B ILE* 3.8 29.1 - - + +
94B ILE 3.1 13.7 + - - +
95B SER 3.6 9.9 - - - +
96B VAL 3.1 0.2 - - - -
97B LEU* 1.3 78.4 - - - +
99B CYS* 1.3 58.1 + - - +
100B LEU 4.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE 4.7 1.1 - - - -
73B ILE* 3.9 33.2 - - - -
95B SER 3.3 16.2 - - - +
96B VAL 3.1 8.2 + - - +
98B GLN* 1.3 78.8 - - - +
100B LEU* 1.3 68.5 + - - +
101B ASP* 5.1 0.9 - - - +
108B GLN* 4.8 4.2 - - - +
183B MET* 4.1 22.0 - - + -
213B GLN* 5.7 0.2 - - - -
----------------------------------------------------------
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