Contacts of the helix formed by residues 80 - 98 (chain F) in PDB entry 1NZX
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 80 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ARG 3.4 3.0 + - - +
79F MET* 1.3 78.6 - - - +
81F ALA* 1.3 66.1 + - - +
82F SER* 3.8 7.6 - - - +
83F HIS* 2.9 20.5 + - + +
84F ARG* 3.2 9.2 + - - +
147G ASP* 3.5 26.2 - - - +
148G GLY* 2.8 33.5 + - - -
498G LYS* 3.1 15.5 + - - +
127H LYS* 5.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F MET 3.4 2.2 + - - -
80F ASP* 1.3 71.8 - - - +
82F SER* 1.3 61.9 + - - +
84F ARG* 3.0 42.1 + - - +
85F GLY 3.3 4.2 + - - -
136F ALA* 3.3 28.8 - - - +
137F ASP* 3.7 14.8 - - + -
145G PRO* 3.9 25.7 + - + +
146G ILE 5.5 0.2 + - - -
147G ASP* 4.8 0.6 + - - -
498G LYS* 5.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ASP* 3.8 3.3 - - - +
81F ALA* 1.3 79.2 - - - +
83F HIS* 1.3 60.5 + - - +
85F GLY* 3.1 5.4 + - - +
86F ARG* 3.0 28.6 + - - +
136F ALA* 5.1 0.2 - - - -
137F ASP* 3.4 28.3 - - - +
147G ASP* 2.9 34.3 + - - -
127H LYS* 5.4 7.3 - - - +
462H GLN* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F MET* 3.7 35.3 - - + +
80F ASP* 2.9 19.1 + - + +
82F SER* 1.3 78.6 + - - +
84F ARG* 1.3 60.5 + - - +
85F GLY 3.0 1.6 - - - -
86F ARG* 2.9 22.0 + - + +
87F LEU* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F TRP* 3.7 31.8 + - + -
79F MET* 4.0 20.6 + - + +
80F ASP 3.2 9.5 + - - +
81F ALA* 3.0 27.7 + - - +
83F HIS* 1.3 75.3 - - - +
85F GLY* 1.3 61.7 + - - +
87F LEU* 3.3 7.1 + - - +
88F LEU* 3.1 27.3 + - - +
136F ALA* 3.3 21.9 + - + -
183F LEU 3.5 18.2 - - - +
184F ALA 3.0 25.2 + - - -
185F THR* 3.9 8.1 + - - +
186F GLY* 3.5 16.9 - - - +
213F PHE* 4.8 1.7 - - - -
145G PRO* 5.8 1.0 - - - +
500G SER* 3.8 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ALA 3.3 3.8 + - - -
82F SER 3.1 8.5 + - - -
83F HIS 3.0 0.8 - - - -
84F ARG* 1.3 77.7 - - - +
86F ARG* 1.3 65.9 + - - +
88F LEU 3.1 1.6 + - - -
89F ASN* 3.0 30.6 + - - -
133F ALA* 3.4 31.4 - - - +
136F ALA* 3.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F SER* 3.0 18.8 + - - +
83F HIS* 2.9 30.6 + - + +
85F GLY* 1.3 75.1 - - - +
87F LEU* 1.3 58.0 + - + +
89F ASN* 3.1 29.6 + - - +
90F ARG* 2.9 29.0 + - - +
89H ASN* 4.8 3.6 + - - -
93H ASP* 4.3 4.6 + - - -
96H GLU* 4.7 2.8 + - - -
130H ARG* 3.2 62.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F TRP* 4.0 3.1 - - + -
79F MET* 3.5 39.7 - - + -
83F HIS* 2.8 26.9 + - + +
84F ARG* 3.7 5.8 - - - +
85F GLY 3.2 0.2 - - - -
86F ARG* 1.3 76.6 - - + +
88F LEU* 1.3 56.9 + - - +
90F ARG* 3.2 6.7 + - + +
91F LEU* 2.9 29.3 + - - +
211F ALA* 3.4 25.8 - - - +
212F GLY* 4.2 11.7 - - - +
213F PHE* 3.5 44.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ARG 3.1 17.1 + - - +
85F GLY* 3.1 9.4 + - - +
87F LEU* 1.3 76.0 - - - +
89F ASN* 1.3 60.6 + - - +
91F LEU* 3.4 8.5 + - + +
92F ALA* 3.1 22.3 + - - +
129F LEU* 4.2 32.5 - - + +
132F TYR* 4.0 0.7 - - + -
133F ALA* 3.5 33.4 - - + +
180F GLY* 3.9 21.3 - - - +
183F LEU* 4.1 28.9 - - + -
184F ALA* 4.0 20.0 - - + +
213F PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLY 3.0 20.0 + - - -
86F ARG* 3.5 30.2 - - - +
88F LEU* 1.3 74.9 - - - +
90F ARG* 1.3 64.8 + - - +
92F ALA* 3.3 6.2 + - - +
93F ASP* 3.0 31.2 + - - +
130F ARG* 3.9 23.6 + - - +
133F ALA* 3.7 19.0 - - - +
86H ARG* 4.9 4.4 + - - +
89H ASN* 4.6 20.9 + - - +
130H ARG* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG 2.9 13.0 + - - +
87F LEU* 3.4 13.2 - - + +
89F ASN* 1.3 74.6 - - - +
91F LEU* 1.3 66.0 + - - +
93F ASP* 3.1 26.3 + - - +
94F LEU* 2.9 56.9 + - + +
97F ARG* 5.3 1.4 - - - +
210F GLU* 4.6 9.7 + - - +
211F ALA* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU 2.9 12.4 + - - +
88F LEU* 3.6 14.4 - - + +
89F ASN 3.3 0.2 - - - -
90F ARG* 1.3 76.4 - - - +
92F ALA* 1.3 57.0 + - - +
94F LEU* 3.2 5.6 + - - +
95F ILE* 2.9 38.0 + - + +
129F LEU* 4.0 26.9 - - + -
179F LEU* 5.1 7.0 - - + -
183F LEU* 5.2 2.9 - - + -
204F VAL* 4.3 9.9 - - + +
207F LEU* 3.8 15.3 - - + +
208F ILE* 3.6 50.0 - - + +
211F ALA* 4.0 5.5 - - + +
213F PHE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU 3.1 14.4 + - - +
89F ASN 3.5 9.2 - - - +
91F LEU* 1.3 77.3 - - - +
93F ASP* 1.3 56.5 + - - +
95F ILE* 3.0 2.6 + - - -
96F GLU* 2.8 25.6 + - - +
126F LEU* 3.1 19.7 - - + +
129F LEU* 4.3 15.7 - - + +
130F ARG* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ASN* 3.0 23.2 + - - +
90F ARG* 3.1 26.5 + - - +
92F ALA* 1.3 75.3 - - - +
94F LEU* 1.3 58.9 + - - +
96F GLU* 3.3 5.0 + - - +
97F ARG* 2.9 28.1 + - - +
130F ARG* 2.9 25.4 + - - +
86H ARG* 4.5 7.8 + - - -
93H ASP* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ARG* 2.9 40.4 + - + +
91F LEU* 3.5 7.4 - - - +
93F ASP* 1.3 75.6 - - - +
95F ILE* 1.3 63.5 + - - +
97F ARG* 3.2 23.6 + - - +
98F ASP* 3.1 26.7 + - - +
207F LEU* 3.3 41.7 - - + +
210F GLU* 3.3 32.5 - - + +
211F ALA* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 2.9 20.3 + - + +
92F ALA 3.5 7.4 - - - +
94F LEU* 1.3 76.6 - - - +
96F GLU* 1.3 56.0 + - - +
98F ASP 3.2 4.2 + - - -
99F ARG* 2.9 25.6 + - - +
102F LEU* 3.8 11.0 - - + +
122F LEU* 3.8 24.5 - - + -
125F VAL* 4.0 16.4 - - + -
126F LEU* 4.0 11.9 - - + -
129F LEU* 3.7 28.9 - - + -
172F LEU* 6.0 0.9 - - + -
204F VAL* 4.3 24.0 - - + -
207F LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ALA 2.8 14.7 + - - +
93F ASP* 3.7 6.2 - - - +
95F ILE* 1.3 74.6 - - - +
97F ARG* 1.3 66.8 + - - +
99F ARG* 3.1 36.0 + - - +
126F LEU* 3.8 25.0 - - + +
130F ARG* 2.9 28.2 + - - +
86H ARG* 4.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ARG* 5.3 1.6 - - - +
93F ASP 2.9 14.3 + - - +
94F LEU* 3.2 23.2 + - - +
96F GLU* 1.3 80.5 - - - +
98F ASP* 1.3 89.0 + - - +
99F ARG 3.4 2.1 + - - -
100F THR* 5.0 1.6 + - - -
203F TYR* 4.3 2.4 + - - -
207F LEU* 3.6 8.3 - - - +
210F GLU* 2.7 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU 3.1 8.5 + - - +
95F ILE 3.2 5.4 + - - +
97F ARG* 1.3 115.6 + - - +
99F ARG* 1.3 56.9 + - - +
100F THR 3.4 2.5 - - - -
101F TYR* 3.3 13.1 + - + +
102F LEU* 2.9 33.0 + - + +
203F TYR* 2.7 38.5 + - + +
207F LEU* 3.4 9.2 - - + +
----------------------------------------------------------
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