Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 1AZ1
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 LYS 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS 3.4 2.4 + - - -
84A GLU* 1.3 71.6 - - - +
86A GLY* 1.3 61.2 + - - +
87A LEU 3.3 0.5 + - - -
88A VAL* 3.5 14.6 + - - +
89A LYS* 4.7 1.7 + - - +
135A THR* 5.4 0.2 - - - +
139A ASP* 3.5 55.3 + - + +
142A ALA* 3.9 16.2 - - - -
143A ALA* 4.0 21.6 - - + +
146A GLU* 4.6 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.2 3.6 - - - +
85A LYS* 1.3 77.9 - - - +
87A LEU* 1.3 66.0 + - - +
88A VAL 3.5 0.4 - - - -
89A LYS* 5.1 3.5 + - - +
90A GLY* 5.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR 3.7 17.0 - - - +
82A TYR* 4.0 23.1 - - + +
84A GLU* 2.9 37.2 + - + +
86A GLY* 1.3 82.6 - - - +
88A VAL* 1.3 63.8 + - - +
89A LYS 3.5 1.3 - - - -
90A GLY* 3.5 4.4 + - - +
91A ALA* 3.1 23.7 + - - +
117A PRO* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.1 19.9 - - + +
82A TYR 3.5 18.6 - - - +
83A HIS 4.1 6.1 - - - +
84A GLU 3.5 10.8 - - - +
85A LYS 3.5 8.6 + - - +
87A LEU* 1.3 74.2 - - - +
89A LYS* 1.3 68.5 + - - +
91A ALA* 3.3 4.2 + - - +
92A CYS* 3.1 20.3 + - - +
140A THR* 4.7 3.6 - - + -
143A ALA* 3.6 35.4 - - + +
144A MET* 4.2 10.1 - - - -
147A LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS 4.7 1.8 + - - -
86A GLY 5.1 2.4 - - - +
87A LEU 3.5 0.4 - - - -
88A VAL* 1.3 78.8 - - - +
90A GLY* 1.3 59.1 + - - +
92A CYS* 3.3 2.4 + - - +
93A GLN* 2.9 59.5 + - - +
147A LEU* 3.9 16.3 - - + +
150A GLU* 3.3 32.9 + - - +
152A LEU* 4.1 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 5.2 1.8 + - - -
87A LEU* 3.5 7.7 + - - +
88A VAL 3.3 0.6 - - - -
89A LYS* 1.3 81.3 - - - +
91A ALA* 1.3 54.9 + - - +
93A GLN* 3.9 13.6 - - - +
94A LYS* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS* 5.8 2.3 + - + +
78A LEU* 3.7 25.8 - - + -
79A TRP 5.8 0.2 - - - +
82A TYR* 3.8 28.2 - - + -
87A LEU 3.1 17.6 + - - +
88A VAL 3.3 0.8 + - - +
90A GLY* 1.3 73.2 - - - +
92A CYS* 1.3 64.8 + - - +
94A LYS* 3.3 8.2 + - - +
95A THR* 3.2 23.4 + - - -
107A TYR* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL 3.1 13.2 + - - +
89A LYS* 3.5 8.3 - - - +
91A ALA* 1.3 75.8 - - - +
93A GLN* 1.3 58.1 + - - +
95A THR* 3.3 4.6 + - - +
96A LEU* 2.9 36.8 + - - +
104A LEU* 4.3 8.7 - - - -
107A TYR* 3.4 27.7 + - + -
147A LEU* 4.1 14.8 - - + -
152A LEU* 4.2 14.1 - - + -
153A VAL* 3.8 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 2.9 55.5 + - - +
90A GLY* 3.9 9.7 - - - +
92A CYS* 1.3 72.5 - - - +
94A LYS* 1.3 60.7 + - - +
96A LEU* 3.3 13.2 + - + +
97A SER* 2.9 32.2 + - - -
152A LEU* 4.1 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS* 4.4 22.8 - - + +
90A GLY 3.1 14.7 + - - +
91A ALA* 3.4 12.1 - - - +
93A GLN* 1.3 75.7 - - - +
95A THR* 1.3 59.3 + - - +
97A SER* 3.2 11.4 + - - -
98A ASP* 3.0 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS* 3.8 13.9 - - - +
51A GLU* 2.7 27.4 + - - +
76A SER* 3.6 25.2 + - - +
77A LYS 5.2 0.5 + - - -
91A ALA 3.2 10.1 + - - -
92A CYS* 3.6 8.7 - - - -
94A LYS* 1.3 79.4 - - - +
96A LEU* 1.3 57.4 + - - +
98A ASP* 3.3 4.0 + - - +
99A LEU* 2.9 47.1 + - + +
104A LEU* 4.0 13.2 - - + -
107A TYR* 4.9 5.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A CYS* 2.9 20.9 + - - +
93A GLN* 3.6 16.8 - - + +
94A LYS 3.3 0.2 - - - -
95A THR* 1.3 76.8 - - - +
97A SER* 1.3 56.5 + - - +
99A LEU* 4.7 2.2 - - - -
100A LYS* 2.9 23.6 + - - -
101A LEU* 3.1 32.4 + - + +
102A ASP* 3.9 17.0 - - - +
103A TYR* 3.7 17.7 - - - +
104A LEU* 3.6 33.0 - - + +
152A LEU* 4.3 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN* 5.3 0.5 - - - +
93A GLN* 2.9 15.7 + - - +
94A LYS* 3.2 16.0 + - - -
96A LEU* 1.3 76.8 - - - +
98A ASP* 1.3 64.7 + - - +
100A LYS* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS* 4.6 7.3 + - - -
51A GLU* 3.4 18.6 - - + +
52A ASN* 3.3 37.4 + - - +
94A LYS* 3.0 51.4 + - - +
95A THR 3.7 4.3 - - - +
97A SER* 1.3 76.5 - - - +
99A LEU* 1.3 56.8 + - - +
100A LYS* 2.9 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS* 4.1 10.5 - - - -
51A GLU* 3.4 35.9 - - + +
54A VAL* 4.1 22.2 - - + -
55A GLY* 3.5 19.3 - - - +
58A ILE* 4.8 7.2 - - + +
59A GLN* 5.0 0.9 - - - +
74A ILE* 4.0 14.1 - - + -
76A SER* 4.7 2.0 - - - -
95A THR* 2.9 38.6 + - + +
96A LEU* 4.2 2.0 - - - +
98A ASP* 1.3 75.8 - - - +
100A LYS* 1.3 69.2 + - - +
101A LEU* 3.5 22.2 + - + +
104A LEU* 3.8 19.3 - - + -
----------------------------------------------------------
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