Contacts of the helix formed by residues 79 - 88 (chain A) in PDB entry 1NZ8
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 ASN 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.7 1.4 - - - +
34A LYS* 3.4 35.3 - - + +
71A ASP 3.8 5.3 + - - -
72A LEU* 3.0 31.3 - - - +
74A ASP* 3.7 19.5 + - - +
78A PRO* 1.3 78.6 - - - +
80A GLU* 1.3 73.9 + - - +
81A ALA* 2.6 36.2 + - - +
82A TRP* 3.1 15.6 + - - +
83A GLU* 4.1 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.3 27.7 - - + +
34A LYS* 5.5 5.0 + - - +
79A ASN* 1.3 82.7 - - - +
81A ALA* 1.3 64.4 + - - +
82A TRP 3.1 0.4 - - - -
83A GLU* 2.8 26.9 + - + +
84A VAL* 3.1 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.9 0.7 - - - +
31A LEU* 4.4 13.0 - - + -
34A LYS* 4.8 9.2 - - + -
35A ILE* 4.9 15.9 - - + -
70A MET* 5.4 4.9 - - + -
72A LEU* 4.2 7.6 - - + -
79A ASN* 2.6 33.6 + - - +
80A GLU* 1.3 72.9 - - - +
82A TRP* 1.3 61.5 + - - +
84A VAL* 3.3 10.1 + - - +
85A VAL* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 5.2 1.3 - + + -
8A VAL* 3.3 42.6 - - + -
70A MET* 4.9 10.3 - - + -
72A LEU* 4.4 17.5 - - + +
78A PRO* 3.9 29.8 - - + +
79A ASN 3.1 10.6 + - - +
80A GLU 3.1 0.8 - - - -
81A ALA* 1.3 75.9 - - - +
83A GLU* 1.3 61.5 + - + +
85A VAL* 3.4 15.2 + - + +
86A ARG* 2.9 49.2 + - + +
91A ILE* 6.0 0.9 - - + -
93A GLY 6.0 0.4 - - - -
94A PHE* 5.8 0.7 - - + -
100A ARG* 3.6 32.0 - - + +
101A PRO* 3.6 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN 4.1 1.3 + - - +
80A GLU* 2.8 20.4 + - + +
82A TRP* 1.3 80.3 - - + +
84A VAL* 1.3 63.0 + - + +
86A ARG* 3.3 7.2 + - - +
87A GLY* 2.9 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.8 32.3 - - + -
26A ILE* 4.1 14.4 - - + -
29A PHE* 4.6 14.8 - - + -
31A LEU* 3.4 28.9 - - + -
80A GLU* 3.1 18.1 + - + +
81A ALA 3.6 5.6 - - - +
82A TRP 3.3 0.2 - - - -
83A GLU* 1.3 77.0 - - + +
85A VAL* 1.3 52.6 + - - +
87A GLY* 3.0 2.3 + - - -
88A THR* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.0 7.2 - - + -
22A LEU* 3.9 27.8 - - + -
26A ILE* 4.6 9.2 - - + -
35A ILE* 5.6 1.8 - - + -
68A ILE* 5.9 5.8 - - + -
70A MET* 5.2 11.9 - - + -
81A ALA 3.2 17.6 + - - +
82A TRP* 3.8 24.5 - - + +
84A VAL* 1.3 74.3 - - - +
86A ARG* 1.3 57.9 + - - +
88A THR* 2.5 20.2 + - - +
90A GLY 6.0 0.4 - - - +
91A ILE* 3.0 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 2.9 43.2 + - + +
83A GLU* 3.7 7.0 - - - +
85A VAL* 1.3 77.5 - - - +
87A GLY* 1.3 57.4 + - - +
91A ILE* 3.2 25.8 + - + +
92A THR 3.8 25.1 + - - -
93A GLY* 4.3 11.4 - - - -
94A PHE* 6.0 2.7 - - - -
100A ARG* 4.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 2.9 13.9 + - - -
84A VAL* 3.5 3.4 - - - -
86A ARG* 1.3 79.1 - - - +
88A THR* 1.3 65.2 + - - +
89A PRO* 3.6 4.2 - - - +
91A ILE* 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 5.5 0.4 - - - -
22A LEU* 3.4 36.7 - - + +
25A ARG* 3.7 28.0 - - - +
84A VAL* 2.7 23.8 + - + +
85A VAL* 2.5 32.6 + - - +
87A GLY* 1.3 73.4 - - - +
89A PRO* 1.3 64.1 - - + +
90A GLY* 2.9 12.0 + - - -
91A ILE* 2.7 32.7 + - - +
----------------------------------------------------------
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