Contacts of the helix formed by residues 92 - 102 (chain X) in PDB entry 1NJI
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 ASP 92 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81X ASP* 2.9 25.7 - - + +
84X VAL* 3.4 16.3 - - - +
90X TYR* 3.5 1.5 - - - +
91X ASP* 1.3 90.7 + - + +
93X ILE* 1.3 64.3 + - - +
94X SER* 3.4 23.2 + - - -
95X GLY* 3.0 21.5 + - - -
96X LEU 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X GLU* 3.9 33.4 - - + +
66X LEU* 4.0 15.5 - - + -
67X ALA* 3.3 35.2 - - + -
79X VAL* 3.7 12.6 - - + +
80X ASP* 4.0 8.5 - - - -
81X ASP* 2.9 24.0 + - - +
84X VAL* 3.6 24.8 - - + +
92X ASP* 1.3 70.3 - - - +
94X SER* 1.3 54.4 + - - +
96X LEU* 2.9 6.3 + - + +
97X ALA* 2.7 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X GLN* 3.2 7.3 + - - -
63X GLU* 2.6 40.7 + - - -
81X ASP* 4.6 0.4 + - - -
92X ASP* 3.3 17.2 + - - -
93X ILE* 1.3 78.3 - - - +
95X GLY* 1.3 56.7 + - - +
98X PHE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X TYR* 3.1 27.3 - - - -
91X ASP 5.3 0.4 - - - -
92X ASP* 3.0 19.1 + - - -
94X SER* 1.3 80.7 - - - +
96X LEU* 1.3 61.6 + - - +
98X PHE* 3.7 5.9 + - - +
99X ALA 3.2 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66X LEU* 4.4 11.9 - - + -
79X VAL* 5.4 1.3 - - + -
84X VAL* 4.2 24.0 - - + -
88X THR* 4.5 5.4 - - + +
90X TYR* 3.7 26.1 - - + +
92X ASP 3.1 9.1 + - - +
93X ILE* 2.9 9.8 + - + +
95X GLY* 1.3 74.1 - - - +
97X ALA* 1.3 68.4 + - - +
99X ALA* 2.9 13.9 + - - +
100X LEU* 2.9 26.4 + - + +
105X THR* 4.3 8.5 - - + -
106X THR 5.9 0.2 - - - -
107X LEU* 5.1 3.4 - - + -
110X GLN* 4.0 19.5 - - + -
112X LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X GLN* 3.1 21.3 - - - +
62X LEU* 3.9 15.3 - - + -
63X GLU* 3.7 15.3 - - + +
66X LEU* 3.9 20.4 - - + +
93X ILE 2.7 17.8 + - - +
96X LEU* 1.3 73.3 - - - +
98X PHE* 1.3 65.0 + - - +
100X LEU* 2.9 14.4 + - - +
101X LEU* 3.0 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X GLN* 3.2 21.4 - - - +
90X TYR* 6.5 0.2 - + - -
94X SER 3.0 18.0 + - - +
95X GLY* 3.9 6.7 - - - +
97X ALA* 1.3 76.4 - - - +
99X ALA* 1.3 56.5 + - + +
101X LEU* 3.4 4.7 + - + +
102X SER* 2.6 57.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X TYR* 3.2 46.0 - - + +
95X GLY 3.2 2.2 + - - +
96X LEU 2.9 9.2 + - - +
98X PHE* 1.3 81.9 - - + +
100X LEU* 1.3 59.5 + - - +
102X SER* 3.2 7.4 + - - -
103X GLU 3.1 2.4 + - - -
104X GLU* 2.8 37.4 + - + -
105X THR* 3.7 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X MET* 3.7 22.3 - - + +
34X LEU* 3.4 28.3 - - + -
62X LEU* 4.1 3.4 - - + -
66X LEU* 3.8 27.4 - - + -
96X LEU* 2.9 21.6 + - + +
97X ALA 2.9 6.3 + - - +
99X ALA* 1.3 76.9 - - - +
101X LEU* 1.3 56.1 + - - +
103X GLU* 2.6 30.3 + - - +
105X THR* 3.8 12.8 - - + +
106X THR* 3.8 31.4 - - - -
107X LEU* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X MET* 3.6 33.9 + - + +
56X GLU* 4.5 13.6 - - - +
57X PRO* 3.8 28.7 - - + +
58X SER 4.3 0.9 - - - +
59X GLN* 3.7 46.2 - - + +
62X LEU* 3.8 15.7 - - + -
97X ALA 3.0 12.9 + - - +
98X PHE* 3.7 7.0 - - + +
100X LEU* 1.3 76.9 - - - +
102X SER* 1.3 58.3 + - - +
103X GLU* 3.0 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98X PHE* 2.6 47.6 + - - -
99X ALA* 3.2 11.6 + - - -
101X LEU* 1.3 74.0 - - - +
103X GLU* 1.3 70.9 + - - +
104X GLU* 3.2 15.6 + - - +
----------------------------------------------------------
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