Contacts of the helix formed by residues 76 - 89 (chain A) in PDB entry 1AX4
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A THR* 2.9 30.5 + - - -
68A GLY 4.2 0.4 + - - -
69A ASP* 2.9 42.9 + - + +
74A GLY 3.4 2.2 + - - -
75A SER* 1.3 72.1 + - - +
77A ASN* 1.3 70.7 + - - +
79A TYR* 3.2 14.3 + - - +
80A ASP* 3.1 28.3 + - - +
15B GLU* 4.9 9.9 + - - +
41B SER* 3.9 5.8 + - - +
42B SER* 5.6 8.7 - - - -
10D ARG* 6.1 0.6 - - - +
12D LYS* 5.5 0.2 - - - +
59D ASP* 5.3 3.2 + - - -
60D HIS* 5.8 3.4 + - - -
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Residues in contact with ASN 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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67A THR 5.1 1.2 + - - -
68A GLY* 3.5 4.8 - - - -
69A ASP* 2.7 32.8 + - - +
75A SER* 3.1 9.8 + - - +
76A ARG* 1.3 79.8 - - - +
78A TYR* 1.3 59.8 + - - +
80A ASP* 3.3 17.5 + - - +
81A LEU* 2.9 30.5 + - - +
306A GLY 3.7 4.4 - - - +
309A MET* 3.8 24.0 - - + +
310A ALA* 3.4 31.5 - - - +
313A VAL* 4.2 2.4 - - - +
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Residues in contact with TYR 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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75A SER* 3.0 14.9 + - - +
77A ASN* 1.3 77.9 - - - +
79A TYR* 1.3 93.5 + + - +
81A LEU* 3.3 4.9 + - - +
82A LYS* 3.0 44.5 + - + +
94A ILE* 3.8 31.8 + - + +
96A PRO* 4.3 9.9 - - + -
285A PHE* 5.2 1.7 - - - -
289A ARG* 3.3 23.9 + - - -
299A VAL 3.8 15.5 - - - -
300A THR* 3.3 50.5 - - + +
309A MET* 4.0 9.3 - - - -
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Residues in contact with TYR 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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74A GLY* 3.4 31.3 - - - -
75A SER 3.2 19.7 - - - -
76A ARG* 3.2 11.4 + - - +
78A TYR* 1.3 99.0 - + - +
80A ASP* 1.3 63.3 + - - +
82A LYS* 3.3 12.3 + - + +
83A ASP* 3.0 30.2 + - - +
300A THR* 5.4 1.7 - - - +
38B LEU 4.6 4.5 + - - -
39B LEU 4.4 1.6 - - - -
40B PRO* 3.6 34.3 - - + +
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Residues in contact with ASP 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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76A ARG* 3.1 21.5 + - - +
77A ASN* 3.6 21.9 + - - +
78A TYR 3.3 0.2 - - - -
79A TYR* 1.3 75.5 - - - +
81A LEU* 1.3 58.3 + - - +
83A ASP* 3.3 10.9 + - - +
84A LYS* 2.9 28.6 + - - +
313A VAL* 3.9 22.6 - - + +
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Residues in contact with LEU 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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77A ASN 2.9 15.9 + - - +
78A TYR* 3.6 4.7 - - - +
80A ASP* 1.3 75.0 - - - +
82A LYS* 1.3 65.3 + - - +
84A LYS* 3.2 2.3 + - + +
85A ALA* 2.9 24.7 + - - +
94A ILE* 3.8 17.0 - - + -
96A PRO* 4.5 9.4 - - + -
275A LEU* 4.1 18.2 - - + -
309A MET* 4.3 24.9 - - + +
312A MET* 3.8 36.3 - - + -
313A VAL* 3.6 15.5 - - + +
316A LEU* 3.9 21.8 - - + -
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Residues in contact with LYS 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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78A TYR* 3.0 39.3 + - + +
79A TYR* 3.6 16.6 - - + +
81A LEU* 1.3 77.6 - - - +
83A ASP* 1.3 67.7 + - - +
85A ALA* 3.4 2.8 + - - +
86A LYS* 3.1 22.2 + - + +
91A TYR 4.9 1.2 - - - +
92A ASP 3.8 24.4 + - - +
93A TYR* 5.3 5.8 - - - +
94A ILE* 3.5 25.6 - - + +
285A PHE* 6.6 0.2 - - - -
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Residues in contact with ASP 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 TYR* 3.0 23.0 + - - +
80A ASP* 3.6 12.2 - - - +
82A LYS* 1.3 80.1 + - - +
84A LYS* 1.3 59.2 + - - +
86A LYS* 3.1 8.2 + - - +
87A GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 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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80A ASP 2.9 17.2 + - - +
81A LEU* 3.2 9.4 + - - +
83A ASP* 1.3 77.0 - - - +
85A ALA* 1.3 61.4 + - - +
87A GLU* 3.2 33.2 + - - +
88A LEU* 3.0 34.2 + - + +
313A VAL* 4.0 22.6 - - + +
316A LEU* 4.0 27.6 - - + -
317A GLU* 2.8 50.6 + - - +
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Residues in contact with ALA 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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81A LEU* 2.9 11.2 + - + +
82A LYS 3.8 1.3 - - - +
84A LYS* 1.3 75.7 - - - +
86A LYS* 1.3 63.6 + - - +
89A PHE* 3.0 47.4 + - + +
90A ASN 3.4 3.3 + - - -
91A TYR* 3.8 7.0 + - + +
94A ILE* 3.5 32.3 - - + -
275A LEU* 4.7 9.2 - - + -
277A ALA* 4.7 4.0 - - + -
316A LEU* 5.5 1.9 - - - +
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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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82A LYS* 3.1 14.2 + - + +
83A ASP* 3.1 12.1 + - - +
85A ALA* 1.3 78.0 - - - +
87A GLU* 1.4 59.4 + - - +
90A ASN* 2.8 57.6 + - - +
91A TYR 3.4 14.1 + - - +
92A ASP* 2.7 32.9 + - - +
251A PHE* 5.0 1.0 - - - -
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Residues in contact with GLU 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 ASP 2.9 13.2 + - - +
84A LYS* 3.2 37.6 + - - +
86A LYS* 1.4 79.5 - - - +
88A LEU* 1.3 64.6 + - - +
247A LYS* 3.0 33.8 + - - +
251A PHE* 4.2 13.5 - - - -
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Residues in contact with LEU 88 (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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84A LYS* 3.0 29.3 + - + +
87A GLU* 1.3 86.4 - - - +
89A PHE* 1.3 83.1 + - + +
227A PHE* 4.7 5.2 - - + -
247A LYS* 4.2 33.1 - - + +
250A ILE* 3.7 22.9 - - + +
251A PHE* 3.9 15.8 + - - +
316A LEU* 3.9 44.0 - - + +
320A THR* 4.3 13.0 - - + -
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Residues in contact with PHE 89 (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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85A ALA* 3.0 38.0 + - + +
88A LEU* 1.3 97.4 - - + +
90A ASN* 1.3 70.7 + - - +
91A TYR* 3.2 30.4 - - + -
227A PHE* 3.6 29.4 - + - -
250A ILE* 4.2 0.9 - - + -
251A PHE* 4.6 5.7 - - - +
254A TYR* 3.6 51.1 - + + +
260A LEU* 3.7 17.5 - - + -
262A MET* 3.5 27.1 - - + -
275A LEU* 4.8 6.3 - - + -
277A ALA* 5.0 1.8 - - + -
316A LEU* 4.8 3.4 - - + -
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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