Contacts of the helix formed by residues 76 - 89 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLU* 4.9 10.5 + - - +
41A SER* 3.9 7.0 + - - +
42A SER* 5.6 9.6 - - - +
67B THR* 2.9 29.7 + - - -
68B GLY 4.2 0.2 - - - -
69B ASP* 2.9 42.4 + - + +
74B GLY 3.3 2.3 + - - -
75B SER* 1.3 72.1 + - - +
77B ASN* 1.3 69.5 + - - +
79B TYR* 3.2 13.1 + - - +
80B ASP* 3.1 28.3 + - - +
12C LYS* 5.7 0.2 - - - +
59C ASP* 5.3 3.0 + - - -
60C HIS* 5.5 5.5 + - - -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA 5.3 0.2 + - - -
67B THR 5.1 0.8 + - - -
68B GLY* 3.6 5.5 - - - -
69B ASP* 2.7 31.8 + - - +
75B SER* 3.1 10.6 + - - +
76B ARG* 1.3 80.0 - - - +
78B TYR* 1.3 60.0 + - - +
80B ASP* 3.7 17.7 + - + +
81B LEU* 3.0 28.9 + - - +
306B GLY 3.6 4.9 - - - +
309B MET* 3.9 10.4 - - + +
310B ALA* 3.4 44.4 - - - +
313B VAL* 4.2 2.4 - - - +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER* 3.1 14.3 + - - +
77B ASN* 1.3 76.1 - - - +
79B TYR* 1.3 93.5 + + - +
81B LEU* 3.2 4.3 + - - +
82B LYS* 3.0 41.6 + - + +
94B ILE* 3.8 34.5 + - + +
96B PRO* 4.3 10.1 - - + -
285B PHE* 5.1 1.7 - - - -
289B ARG* 3.2 24.9 + - - -
299B VAL 3.8 16.2 - - - -
300B THR* 3.4 51.4 - - + +
309B MET* 4.1 8.8 - - - -
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 4.6 5.0 + - - -
39A LEU 4.4 1.7 - - - -
40A PRO* 3.7 32.3 - - + +
74B GLY* 3.4 29.9 - - - -
75B SER 3.2 20.6 - - - -
76B ARG* 3.2 10.5 + - - +
78B TYR* 1.3 102.9 - + - +
80B ASP* 1.3 61.8 + - - +
82B LYS* 3.4 12.7 + - + +
83B ASP* 3.0 30.7 + - - +
300B THR* 5.3 1.9 - - - +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.1 18.1 + - - +
77B ASN* 3.7 21.4 + - + +
78B TYR 3.4 0.2 - - - -
79B TYR* 1.3 76.3 - - - +
81B LEU* 1.3 58.3 + - - +
83B ASP* 3.4 10.8 + - - +
84B LYS* 2.8 28.2 + - - +
313B VAL* 3.9 24.1 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASN 3.0 17.2 + - - +
78B TYR 3.6 4.0 - - - +
80B ASP* 1.3 74.4 - - - +
82B LYS* 1.3 65.8 + - - +
84B LYS* 3.1 3.4 + - - +
85B ALA* 2.9 24.4 + - - +
94B ILE* 3.9 17.7 - - + -
96B PRO* 4.5 10.5 - - + -
275B LEU* 4.2 16.6 - - + -
309B MET* 4.4 25.6 - - + +
312B MET* 3.8 35.4 - - + -
313B VAL* 3.7 14.6 - - + +
316B LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR* 3.0 40.0 + - + +
79B TYR* 3.6 13.5 - - + +
81B LEU* 1.3 78.2 - - - +
83B ASP* 1.3 67.2 + - - +
85B ALA* 3.4 2.8 + - - +
86B LYS* 3.1 21.9 + - + +
91B TYR 4.9 1.4 - - - +
92B ASP* 3.9 23.5 + - - +
93B TYR* 5.3 5.2 - - - +
94B ILE* 3.5 26.0 - - + +
285B PHE* 6.5 0.9 - - - -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.0 23.7 + - - +
80B ASP* 3.7 11.9 - - - +
82B LYS* 1.3 78.8 + - - +
84B LYS* 1.3 66.2 + - - +
86B LYS* 3.3 7.9 + - - +
87B GLU* 3.0 23.8 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASP 2.8 18.5 + - - +
81B LEU* 3.1 8.9 + - - +
83B ASP* 1.3 78.0 - - - +
85B ALA* 1.3 57.6 + - - +
87B GLU* 3.2 31.3 + - - +
88B LEU* 2.9 38.1 + - + +
247B LYS* 4.3 0.2 - - - +
313B VAL* 3.9 22.4 - - + +
316B LEU* 3.9 27.6 - - + -
317B GLU* 2.7 52.8 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 2.9 12.0 + - + +
82B LYS 3.8 0.9 - - - +
84B LYS* 1.3 73.4 - - - +
86B LYS* 1.3 66.0 + - - +
89B PHE* 3.0 46.4 + - + +
90B ASN 3.4 3.6 + - - -
91B TYR* 3.7 7.5 + - + +
94B ILE* 3.5 32.3 - - + -
275B LEU* 4.7 9.0 - - + -
277B ALA* 4.7 4.9 - - + -
316B LEU* 5.4 1.5 - - + +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS* 3.1 14.5 + - + +
83B ASP* 3.5 11.4 - - - +
84B LYS 3.2 0.2 - - - -
85B ALA* 1.3 76.9 - - - +
87B GLU* 1.3 59.1 + - - +
90B ASN* 2.8 59.2 + - - +
91B TYR 3.4 14.1 + - - +
92B ASP* 2.7 32.7 + - - +
251B PHE* 4.9 1.4 - - - -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP 3.0 13.2 + - - +
84B LYS* 3.2 37.5 + - - +
86B LYS* 1.3 78.3 - - - +
88B LEU* 1.3 65.2 + - + +
247B LYS* 3.0 34.7 + - + +
251B PHE* 4.0 13.5 - - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 2.9 30.6 + - + +
87B GLU* 1.3 85.6 - - - +
89B PHE* 1.3 84.2 + - + +
227B PHE* 4.7 5.6 - - + -
247B LYS* 4.1 38.2 - - + +
250B ILE* 3.7 22.5 - - + +
251B PHE* 3.8 16.0 + - - +
316B LEU* 3.9 44.0 - - + +
320B THR* 4.2 10.3 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.0 37.8 + - + +
88B LEU* 1.3 96.9 - - + +
90B ASN* 1.3 71.8 + - - +
91B TYR* 3.1 31.8 - - + -
227B PHE* 3.5 35.4 - + - -
250B ILE* 4.1 1.3 - - + -
251B PHE* 4.6 5.3 - - - +
254B TYR* 3.6 43.3 - + + +
260B LEU* 3.7 17.3 - - + -
262B MET* 3.5 27.1 - - + -
275B LEU* 4.8 6.7 - - + -
277B ALA* 5.0 1.1 - - + -
316B 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