Contacts of the helix formed by residues 76 - 89 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ASP* 5.1 3.8 + - - -
60B HIS* 5.5 6.0 + - - -
67C THR* 2.8 30.9 + - - -
68C GLY 4.0 0.4 + - - -
69C ASP* 2.9 41.8 + - + +
74C GLY 3.3 2.5 + - - -
75C SER* 1.3 72.8 + - - +
77C ASN* 1.3 65.5 + - - +
79C TYR* 3.2 13.6 + - - +
80C ASP* 3.1 32.2 + - - +
15D GLU* 4.9 11.1 + - - +
41D SER* 4.5 5.8 + - - +
42D SER* 5.6 8.7 - - - -
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Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR 5.1 1.0 + - - -
68C GLY* 3.5 5.7 - - - -
69C ASP* 2.7 35.2 + - - +
75C SER* 3.2 7.3 + - - +
76C ARG* 1.3 80.5 - - - +
78C TYR* 1.3 59.0 + - - +
80C ASP* 3.7 17.4 + - - +
81C LEU* 2.9 29.6 + - - +
306C GLY 3.6 3.8 - - - +
309C MET* 3.8 23.1 - - + +
310C ALA* 3.5 30.2 - - - +
313C VAL* 4.2 3.2 - - + +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 3.1 13.7 + - - +
77C ASN* 1.3 75.0 - - - +
79C TYR* 1.4 89.2 + + - +
81C LEU* 3.2 5.0 + - + +
82C LYS* 2.9 47.4 + - + +
94C ILE* 3.8 36.3 + - + +
96C PRO* 4.3 7.9 - - + -
285C PHE* 5.1 1.6 - - - -
289C ARG* 3.2 21.6 + - - -
299C VAL 3.7 15.0 - - - -
300C THR* 3.3 55.6 - - + +
309C MET* 4.0 9.0 - - - -
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Residues in contact with TYR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLY* 3.4 31.5 - - - -
75C SER 3.2 20.4 - - - -
76C ARG* 3.2 11.2 + - - +
78C TYR* 1.4 101.3 - + - +
80C ASP* 1.3 63.9 + - - +
82C LYS* 3.4 11.5 + - + +
83C ASP* 3.0 30.5 + - - +
300C THR* 5.3 1.7 - - - +
38D LEU 4.5 5.7 + - - -
39D LEU 4.4 1.9 - - - -
40D PRO* 3.6 32.6 - - + +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 3.1 21.5 + - - +
77C ASN* 3.7 21.1 + - - +
78C TYR 3.3 0.2 - - - -
79C TYR* 1.3 78.1 - - - +
81C LEU* 1.3 58.2 + - - +
83C ASP* 3.3 11.1 + - - +
84C LYS* 2.9 27.2 + - - +
313C VAL* 3.9 21.5 - - + +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASN 2.9 17.8 + - - +
78C TYR 3.5 4.7 - - - +
80C ASP* 1.3 72.5 - - - +
82C LYS* 1.3 66.2 + - - +
84C LYS* 3.0 3.9 + - + +
85C ALA* 2.9 24.5 + - + +
94C ILE* 3.9 17.7 - - + -
96C PRO* 4.4 9.6 - - + -
275C LEU* 4.1 16.6 - - + -
309C MET* 4.4 25.1 - - + +
312C MET* 3.7 36.8 - - + -
313C VAL* 3.6 15.9 - - + +
316C LEU* 3.9 21.3 - - + -
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 2.9 40.5 + - + +
79C TYR* 3.6 12.8 - - + +
81C LEU* 1.3 76.6 - - - +
83C ASP* 1.3 67.7 + - - +
85C ALA* 3.3 2.9 + - - +
86C LYS* 3.1 21.3 + - + +
91C TYR 5.0 1.0 - - - +
92C ASP* 3.7 25.2 + - - +
93C TYR* 5.2 5.4 - - - +
94C ILE* 3.6 26.2 - - + +
285C PHE* 6.5 0.9 - - - -
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 3.0 23.7 + - - +
80C ASP* 3.6 12.7 - - - +
82C LYS* 1.3 82.5 + - - +
84C LYS* 1.3 62.3 + - - +
86C LYS* 3.4 7.1 + - - +
87C GLU* 3.0 22.7 + - - +
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Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASP 2.9 14.6 + - - +
81C LEU* 3.0 11.6 + - - +
83C ASP* 1.3 75.5 - - - +
85C ALA* 1.3 59.1 + - - +
87C GLU* 3.1 32.6 + - - +
88C LEU* 2.9 41.0 + - + +
247C LYS* 4.4 0.2 - - - +
313C VAL* 4.0 20.8 - - + +
316C LEU* 4.1 25.6 - - + -
317C GLU* 2.7 53.4 + - - +
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 2.9 11.2 + - + +
82C LYS 3.7 1.6 - - - +
84C LYS* 1.3 76.2 - - - +
86C LYS* 1.3 62.0 + - - +
88C LEU* 5.5 0.2 - - - -
89C PHE* 3.0 46.4 + - + +
90C ASN 3.4 4.2 + - - -
91C TYR* 3.7 6.9 + - + +
94C ILE* 3.5 32.8 - - + -
275C LEU* 4.8 7.2 - - + -
277C ALA* 4.7 5.8 - - + -
316C LEU* 5.5 2.2 - - + +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LYS* 3.1 13.6 + - + +
83C ASP* 3.6 11.7 - - - +
84C LYS 3.2 0.2 - - - -
85C ALA* 1.3 79.2 - - - +
87C GLU* 1.3 59.0 + - - +
90C ASN* 2.8 55.0 + - - +
91C TYR 3.5 14.5 + - - +
92C ASP* 2.7 33.1 + - - +
251C PHE* 5.0 1.6 - - - -
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ASP 3.0 13.9 + - - +
84C LYS* 3.1 38.0 + - - +
86C LYS* 1.3 79.4 - - - +
88C LEU* 1.3 65.5 + - + +
247C LYS* 3.0 34.5 + - - +
251C PHE* 4.1 12.6 - - - -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LYS* 2.9 36.6 + - + +
87C GLU* 1.3 84.3 - - - +
89C PHE* 1.3 82.7 + - + +
227C PHE* 4.7 5.4 - - + -
247C LYS* 4.2 36.7 - - + +
250C ILE* 3.7 23.2 - - + +
251C PHE* 3.8 16.7 + - - +
316C LEU* 3.9 43.3 - - + +
320C THR* 4.2 10.1 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ALA* 3.0 37.0 + - + +
88C LEU* 1.3 95.8 - - + +
90C ASN* 1.3 70.0 + - - +
91C TYR* 3.2 31.3 - - + -
227C PHE* 3.6 29.4 - + - -
250C ILE* 4.1 1.1 - - + -
251C PHE* 4.6 5.3 - - - +
254C TYR* 3.6 49.8 - + + +
260C LEU* 3.7 18.8 - - + -
262C MET* 3.6 28.0 - - + -
275C LEU* 4.8 7.2 - - + -
277C ALA* 5.0 1.8 - - + -
316C LEU* 4.8 3.1 - - + -
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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