Contacts of the helix formed by residues 67 - 87 (chain A) in PDB entry 1IXB
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA 4.9 1.4 + - - -
41A ALA* 2.8 43.9 + - + +
44A SER* 2.9 25.7 + - - +
45A LEU* 3.8 24.7 - - + -
63A LEU* 4.4 3.6 - - + -
64A PRO* 2.9 20.9 + - + +
66A ASP* 1.3 98.4 - - - +
68A LYS* 1.3 63.4 + - - +
69A THR 3.4 2.2 - - - -
70A VAL* 3.4 9.3 - - + +
71A LEU* 3.2 29.4 + - + +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.1 25.7 - - + +
61A ASP* 5.5 5.2 - - - +
63A LEU* 4.2 11.2 - - + +
64A PRO 3.4 6.7 + - - +
65A ALA* 3.4 15.6 + - - +
67A LYS* 1.3 76.8 - - - +
69A THR* 1.3 60.9 + - - +
71A LEU* 4.3 0.3 - - - +
72A ARG* 2.8 47.0 + - + +
155A ILE* 4.0 33.9 - - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 4.8 1.6 + - - -
66A ASP 5.4 0.8 - - - -
67A LYS 3.4 0.4 - - - -
68A LYS* 1.3 78.0 - - - +
70A VAL* 1.3 68.5 + - - +
72A ARG* 3.3 10.1 + - - +
73A ASN* 3.0 43.6 + - - +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 4.6 6.7 - - + +
41A ALA* 3.7 30.1 - - + -
66A ASP 4.6 5.5 + - - +
67A LYS* 3.4 23.3 - - + +
69A THR* 1.3 81.2 - - - +
71A LEU* 1.3 61.4 + - - +
73A ASN* 4.8 2.7 - - - +
74A ASN* 2.9 51.1 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.9 24.9 - - + +
41A ALA* 4.0 15.5 - - + -
42A LEU* 3.7 44.9 - - + -
45A LEU* 4.0 16.8 - - + -
56A LEU* 4.3 4.9 - - + -
60A LEU* 4.2 5.3 - - + +
63A LEU* 3.9 27.8 - - + -
67A LYS* 3.2 17.9 + - + +
69A THR 3.2 0.6 - - - -
70A VAL* 1.3 73.7 - - - +
72A ARG* 1.3 66.7 + - - +
73A ASN 3.2 1.1 - - - -
75A ALA* 2.8 38.8 + - + +
76A GLY 3.4 0.2 + - - -
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.0 20.4 - - + +
68A LYS* 2.8 35.6 + - + +
69A THR* 3.6 11.1 + - - +
71A LEU* 1.3 69.5 - - - +
73A ASN* 1.3 66.3 + - - +
76A GLY* 3.0 26.0 + - - -
146A GLN* 4.0 2.8 - - - +
147A ASP* 2.8 43.3 + - - +
151A MET* 3.4 18.7 - - - +
155A ILE* 3.1 38.7 + - - +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 4.2 0.7 - - - -
69A THR* 3.0 37.3 + - - +
70A VAL* 3.9 4.6 - - - +
72A ARG* 1.3 89.4 + - - +
74A ASN* 1.3 62.2 + - - +
77A GLY* 3.0 19.4 + - - -
145A ASN* 5.2 2.6 - - - +
146A GLN* 3.2 17.2 + - - +
147A ASP* 4.7 4.0 - - - +
124B PHE* 3.4 57.9 - - + +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.4 32.8 - - - +
37A ASN* 3.4 28.9 + - - +
38A ALA* 3.6 24.0 - - + +
70A VAL* 2.9 42.5 + - - +
73A ASN* 1.3 83.2 - - - +
75A ALA* 1.3 61.0 + - - +
76A GLY 3.3 0.9 - - - -
77A GLY 3.2 0.4 + - - +
78A HIS* 2.9 28.4 + - - +
124B PHE* 4.9 4.9 - - - -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 4.0 12.1 - - + +
38A ALA* 4.0 5.9 - - - +
53A VAL* 3.3 22.3 - - + +
56A LEU* 4.1 13.7 - - + -
57A ILE* 3.7 16.6 - - + -
60A LEU* 5.4 0.4 - - + -
71A LEU* 2.8 29.0 + - + +
74A ASN* 1.3 71.4 - - - +
76A GLY* 1.3 61.9 + - - +
78A HIS* 4.4 1.3 - - - -
79A ALA* 2.8 23.2 + - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 3.8 6.6 - - - +
71A LEU 3.4 0.2 + - - -
72A ARG 3.0 21.6 + - - -
75A ALA* 1.3 76.4 - - - +
77A GLY* 1.3 57.1 + - - +
79A ALA* 4.6 1.6 - - - -
80A ASN* 2.8 36.5 + - - +
146A GLN 3.3 18.2 - - - -
151A MET* 3.7 11.0 - - - -
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.9 14.1 - - - -
73A ASN 3.0 14.7 + - - -
74A ASN 3.2 3.3 + - - -
75A ALA 3.2 0.6 - - - -
76A GLY* 1.3 75.3 - - - +
78A HIS* 1.3 61.9 + - - +
81A HIS* 2.7 31.9 + - - -
146A GLN* 3.5 28.1 - - - +
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.5 43.4 - + + +
3A THR 3.3 24.0 + - - -
5A PRO* 4.2 2.7 - - + -
31A HIS* 2.8 32.7 + - - +
34A TYR* 3.9 4.5 - - + +
35A VAL* 3.5 15.2 - - + +
53A VAL* 3.6 24.3 - - + +
74A ASN 2.9 16.7 + - - +
75A ALA* 3.8 4.3 - - - +
77A GLY* 1.3 76.4 - - - +
79A ALA* 1.3 62.4 + - - +
82A SER* 2.8 45.8 + - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.9 22.4 - - + +
54A GLU* 4.6 6.7 - - + -
57A ILE* 3.6 30.3 - - + -
75A ALA 2.8 21.1 + - - +
76A GLY 3.8 1.6 - - - +
78A HIS* 1.3 74.2 - - - +
80A ASN* 1.3 65.9 + - - +
82A SER* 3.3 3.4 + - - -
83A LEU* 3.1 23.9 + - - +
150A LEU* 5.9 0.7 - - + -
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 5.0 0.2 - - - +
76A GLY 2.8 15.3 + - - +
79A ALA* 1.3 79.5 - - - +
81A HIS* 1.3 57.6 + - - +
83A LEU* 3.3 6.2 + - - +
84A PHE* 2.9 27.9 + - - +
128A TRP* 3.5 31.8 - - + +
130A TRP* 3.4 24.9 - - + -
146A GLN* 3.0 41.3 + - - +
147A ASP 3.4 11.7 + - - -
148A SER* 3.4 17.2 + - - -
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Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A HIS* 3.1 19.6 + + - -
30A HIS* 5.2 0.6 - - - +
31A HIS* 3.4 31.6 - + + +
34A TYR* 3.5 26.5 - + - -
77A GLY* 2.7 31.3 + - - +
80A ASN* 1.3 72.9 - - - +
82A SER* 1.3 65.7 + - - +
84A PHE* 3.1 6.9 + + - +
85A TRP* 3.0 40.3 + + - +
128A TRP* 3.8 9.8 - + - -
146A GLN* 3.5 6.7 - - - -
167A ASP* 3.5 2.6 + - - -
171A HIS* 3.8 0.4 + - - -
206A MH2 2.1 46.2 + - - -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.9 10.1 - - - +
31A HIS* 3.6 8.5 - - - -
53A VAL* 5.1 4.5 - - - +
78A HIS* 2.8 43.7 + - - -
79A ALA* 3.6 6.5 - - - -
81A HIS* 1.3 77.4 - - - +
83A LEU* 1.3 62.3 + - - +
85A TRP* 3.6 7.0 + - - +
86A LYS* 3.5 30.9 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 3.1 13.4 + - - +
80A ASN* 3.6 9.0 - - - +
82A SER* 1.3 74.6 - - - +
84A PHE* 1.3 70.3 + - + +
86A LYS* 3.2 9.8 + - - +
87A GLY* 2.9 21.9 + - - -
128A TRP* 5.7 0.9 - - + -
130A TRP* 4.1 14.8 - - + -
150A LEU* 6.1 0.7 - - + -
162A PRO* 3.7 27.4 - - + +
163A ILE 5.3 0.4 - - - +
164A MET* 4.3 6.7 - - - -
165A GLY* 4.0 24.9 - - - +
200A ARG* 3.6 35.2 - - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.0 11.0 - + - -
23A MET* 5.8 0.9 - - - -
26A HIS* 4.0 25.1 - + - -
80A ASN 2.9 17.4 + - - +
81A HIS* 3.1 6.7 + + - +
83A LEU* 1.3 81.0 - - - +
85A TRP* 1.4 84.6 + + - +
87A GLY* 3.0 12.1 + - - +
88A LEU* 3.3 46.9 - - + +
128A TRP* 3.8 18.2 - + + -
165A GLY 3.5 21.5 - - - -
166A LEU* 4.0 7.6 - - + -
167A ASP* 3.6 20.4 - - + -
172A ALA* 5.4 0.2 - - + -
184A TYR* 3.7 20.6 - - - -
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Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.4 7.0 - - + -
7A LEU* 3.4 30.3 - - + -
8A PRO* 3.7 7.2 - - + +
9A TYR* 2.7 44.7 + - - +
23A MET* 3.8 27.6 - - + -
26A HIS* 3.5 41.5 - + + -
27A HIS* 3.8 32.6 - + + -
31A HIS* 2.9 31.4 + + - -
81A HIS* 3.0 30.3 + + - +
82A SER* 4.2 6.7 - - - +
83A LEU 3.3 0.2 - - - -
84A PHE* 1.4 94.9 - + - +
86A LYS* 1.3 63.2 + - + +
87A GLY 3.3 0.5 + - - -
88A LEU* 3.4 4.1 + - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 6.4 1.8 - - - -
8A PRO* 4.1 16.8 - - + +
82A SER* 3.5 17.8 + - - +
83A LEU* 3.2 10.2 + - - +
85A TRP* 1.3 78.0 - - + +
87A GLY* 1.3 56.0 + - - +
88A LEU 3.3 1.7 - - - +
193A ASN* 3.2 24.1 + - - -
196A GLU* 3.5 30.6 - - + +
200A ARG* 6.3 1.3 - - - +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 2.9 16.9 + - - -
84A PHE* 3.0 9.3 + - - -
86A LYS* 1.3 77.7 - - - +
88A LEU* 1.3 59.8 + - - +
164A MET* 5.3 9.3 - - - +
165A GLY 5.6 2.0 - - - +
188A PHE* 4.8 2.1 - - - -
192A VAL* 3.7 10.6 - - - +
193A ASN* 2.9 28.3 + - - +
196A GLU* 4.6 6.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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