Contacts of the helix formed by residues 71 - 94 (chain A) in PDB entry 1AX8
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 ARG 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 1.3 75.1 - - - +
72A ASN* 1.3 87.0 + - - +
74A ILE* 4.3 4.6 - - - +
75A GLN* 3.3 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 4.5 5.8 + - + +
23A ASP* 5.9 1.8 - - - +
24A ILE* 3.4 41.0 - - + +
70A SER* 3.4 4.7 + - - +
71A ARG* 1.3 106.7 + - - +
73A VAL* 1.3 55.3 + - - +
75A GLN* 3.3 20.8 + - - +
76A ILE* 2.7 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 5.7 0.2 - - + -
65A LEU* 3.1 50.9 - - + +
68A MET* 3.4 28.7 - - + +
69A PRO* 4.1 3.1 - - + -
70A SER* 3.2 18.9 + - - +
72A ASN* 1.3 73.4 - - - +
74A ILE* 1.3 58.4 + - + +
76A ILE* 3.5 6.1 - - - +
77A SER* 2.6 34.7 + - - -
122A GLU* 6.1 1.8 - - + -
126A LEU* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 4.0 27.6 - - + -
70A SER 3.1 23.0 + - - +
71A ARG* 4.3 4.5 - - - +
73A VAL* 1.3 73.4 - - + +
75A GLN* 1.3 67.5 + - - +
77A SER* 3.4 6.7 + - - -
78A ASN* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 2.7 53.7 - - - +
71A ARG* 3.3 16.9 + - - +
72A ASN* 3.3 25.5 + - - +
74A ILE* 1.3 82.6 - - - +
76A ILE* 1.3 61.4 + - - +
78A ASN* 3.2 12.9 + - - +
79A ASP* 3.2 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.9 14.1 - - + -
20A ARG* 3.5 20.4 - - + -
21A ILE* 3.7 23.6 - - + -
24A ILE* 3.7 22.7 - - + -
65A LEU* 3.7 17.3 - - + -
72A ASN 2.7 28.9 + - - +
73A VAL* 3.6 5.8 - - - +
75A GLN* 1.3 72.1 - - - +
77A SER* 1.3 57.0 + - - +
79A ASP* 2.9 11.4 + - - +
80A LEU* 2.9 40.8 + - + +
126A LEU* 3.8 11.7 - - + -
129A LEU* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.5 16.1 + - - +
65A LEU* 3.9 27.1 - - - +
66A THR* 4.2 12.0 + - - -
73A VAL* 2.6 23.9 + - - -
74A ILE* 3.7 7.9 - - - -
76A ILE* 1.3 73.4 - - - +
78A ASN* 1.3 61.9 + - - +
80A LEU* 3.3 8.0 + - - +
81A GLU* 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 3.1 12.7 + - - +
75A GLN* 3.5 11.4 - - - +
76A ILE 3.2 0.2 - - - -
77A SER* 1.3 75.9 - - - +
79A ASP* 1.3 64.0 + - - +
81A GLU* 3.1 22.0 + - - +
82A ASN* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 15.7 - - + +
16A THR* 5.3 0.9 - - - +
17A ILE* 3.4 24.0 - - + +
20A ARG* 2.5 42.1 + - - -
75A GLN* 3.2 13.2 + - - +
76A ILE* 2.9 9.1 + - - +
78A ASN* 1.3 81.6 - - - +
80A LEU* 1.3 56.2 + - - +
82A ASN* 3.1 17.4 + - - +
83A LEU* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.1 17.0 - - + -
58A LEU* 4.2 18.6 - - + +
61A TYR* 3.8 26.0 - - + -
62A GLN* 3.4 27.4 - - + +
65A LEU* 4.0 19.1 - - + -
76A ILE* 2.9 29.1 + - + +
77A SER* 3.5 10.3 - - - +
78A ASN 3.2 0.2 - - - -
79A ASP* 1.3 75.6 - - - +
81A GLU* 1.3 57.3 + - - +
83A LEU* 3.3 6.8 + - + +
84A ARG* 2.9 32.7 + - - +
129A LEU* 4.1 16.4 - - + -
133A LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.1 31.6 + - - +
77A SER 3.3 3.5 + - - +
78A ASN* 3.1 17.5 + - - +
80A LEU* 1.3 74.3 - - - +
82A ASN* 1.3 66.6 + - - +
84A ARG* 3.4 20.4 + - - +
85A ASP* 3.1 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 16.3 - - + +
78A ASN* 3.2 23.7 + - - +
79A ASP* 3.1 21.1 + - - +
81A GLU* 1.3 78.9 - - - +
83A LEU* 1.3 62.2 + - - +
85A ASP* 3.5 13.8 - - - +
86A LEU* 3.2 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.5 35.7 - - + +
13A LEU* 3.5 14.8 - - + +
14A ILE* 3.7 21.3 - - + -
17A ILE* 4.5 7.6 - - + -
58A LEU* 3.8 23.1 - - + -
79A ASP 2.9 15.0 + - - +
80A LEU* 3.6 8.1 - - + +
81A GLU 3.2 0.2 - - - -
82A ASN* 1.3 75.4 - - - +
84A ARG* 1.3 64.1 + - - +
86A LEU* 3.3 2.8 + - + -
87A LEU* 3.0 25.7 + - + +
133A LEU* 3.6 30.7 - - + -
136A MET* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 2.8 41.5 + - - +
58A LEU* 3.8 24.7 - - + +
59A ALA* 3.6 25.5 - - - +
62A GLN* 3.3 28.7 + - - -
80A LEU 2.9 17.8 + - - +
81A GLU* 3.4 19.3 + - - +
83A LEU* 1.3 75.2 - - - +
85A ASP* 1.3 64.1 + - - +
87A LEU* 3.1 8.7 + - - +
88A HIS* 3.0 36.5 + - + +
101A ALA* 3.8 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.1 29.1 + - - +
82A ASN* 3.5 18.5 - - - +
84A ARG* 1.3 77.1 - - - +
86A LEU* 1.3 53.5 + - + +
88A HIS* 2.9 9.5 + - - +
89A VAL* 2.7 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.7 19.3 - - + +
9A ASP* 3.5 43.3 - - + +
10A THR* 3.6 27.9 + - + +
13A LEU* 4.0 17.7 - - + -
82A ASN* 3.2 14.5 + - + +
83A LEU* 3.3 8.0 + - + +
85A ASP* 1.3 80.7 - - + +
87A LEU* 1.3 61.4 + - - +
89A VAL* 4.3 8.7 - - + -
90A LEU* 3.2 22.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
10A THR* 4.5 14.6 - - + -
51A LEU* 4.3 19.1 - - + +
54A MET* 3.9 14.1 - - + -
55A ASP* 3.8 24.5 - - + +
58A LEU* 3.5 32.3 - - + -
83A LEU* 3.0 13.8 + - + +
84A ARG* 3.1 10.5 + - - +
86A LEU* 1.3 78.9 - - - +
88A HIS* 1.3 58.3 + - - +
90A LEU* 3.4 9.0 - - + +
91A ALA* 3.2 20.8 + - - +
98A LEU* 3.7 12.1 - - + +
136A MET* 5.3 3.4 - - - -
140A LEU* 4.4 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 3.0 36.6 + - - -
84A ARG* 3.0 29.4 + - + +
85A ASP* 2.9 11.1 + - - +
87A LEU* 1.3 73.9 - - - +
89A VAL* 1.3 61.0 + - + +
90A LEU 3.1 1.3 - - - -
91A ALA* 3.8 2.6 - - + +
92A PHE* 3.0 26.7 + - - +
98A LEU* 3.7 35.5 + - + +
99A PRO 5.0 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 25.4 - - + -
85A ASP* 2.7 28.9 + - + +
86A LEU* 4.0 13.5 - - + +
87A LEU 3.5 0.2 - - - -
88A HIS* 1.3 73.9 - - + +
90A LEU* 1.3 57.2 + - - +
92A PHE* 3.2 13.6 - - + +
93A SER* 3.1 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.7 27.6 - - + -
6A VAL* 4.0 16.1 - - + +
7A GLN* 4.8 17.7 - - + +
10A THR* 5.7 3.8 - - + +
51A LEU* 3.9 26.7 - - + -
86A LEU 3.2 11.9 + - - +
87A LEU* 3.4 12.8 - - + +
88A HIS 3.1 0.2 - - - -
89A VAL* 1.3 76.4 - - - +
91A ALA* 1.3 65.1 + - - +
92A PHE 3.0 1.1 - - - -
93A SER* 2.8 19.6 + - - -
94A LYS* 2.9 34.8 + - + +
140A LEU* 5.0 10.3 - - + -
144A PRO* 5.7 3.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
51A LEU* 4.0 9.8 - - + +
87A LEU 3.2 4.3 + - - +
88A HIS* 3.8 5.6 - - + +
90A LEU* 1.3 77.8 - - - +
92A PHE* 1.3 60.8 + - - +
94A LYS* 3.0 2.1 + - - -
95A SER 2.9 4.5 + - - -
96A CYS* 2.9 44.8 + - - +
98A LEU* 3.5 43.3 - - + +
146A CYS* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS 3.0 15.3 + - - +
89A VAL* 3.2 18.6 - - + +
91A ALA* 1.3 76.4 - - - +
93A SER* 1.3 62.0 - - - +
95A SER* 2.8 24.5 + - - +
96A CYS 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.8 26.1 - - - +
6A VAL* 5.3 3.6 - - - +
89A VAL* 3.1 9.0 + - - -
90A LEU* 2.8 31.0 + - - +
92A PHE* 1.3 83.3 - - - +
94A LYS* 1.3 57.8 + - - +
95A SER* 3.1 5.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
3A ILE* 4.4 11.9 - - + -
51A LEU* 3.8 14.7 - - - +
90A LEU* 2.9 36.3 + - + +
91A ALA 3.0 5.6 + - - +
93A SER* 1.3 77.4 - - - +
95A SER* 1.3 69.7 + - - +
96A CYS* 3.0 41.8 + - - +
143A SER* 5.6 4.0 - - - +
144A PRO 3.6 23.7 + - - -
145A GLY* 4.2 0.4 - - - -
146A CYS* 3.8 13.1 - - - +
----------------------------------------------------------
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