Contacts of the helix formed by residues 72 - 90 (chain B) in PDB entry 1SXG
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 ASN 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP* 3.5 19.8 - - + +
70B ILE 3.2 2.7 + - - -
71B SER* 1.3 77.4 - - - +
73B ILE* 1.3 69.2 + - - +
74B PHE* 3.4 17.6 + - - +
75B TYR* 2.8 45.5 + - + +
76B ALA 3.1 7.9 + - - -
221B TYR* 5.2 18.7 - - - +
247B THR* 4.7 13.0 - - - +
249B GLU* 3.3 17.8 - - - +
278I ARG* 4.4 0.2 - - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER 4.2 0.2 - - - -
72B ASN* 1.3 70.9 + - - +
74B PHE* 1.3 56.4 + - - +
76B ALA* 4.1 7.9 - - + -
77B GLU* 2.8 43.9 + - + +
248B ASP* 6.2 0.2 - - + -
249B GLU* 3.1 21.3 - - - +
277B THR* 3.6 19.7 - - + -
278B ARG* 3.6 32.8 - - + +
279B LEU* 3.4 32.5 - - + -
71I SER 4.8 1.8 - - - +
73I ILE* 3.8 11.7 - - + -
278I ARG* 3.0 27.5 - - - +
279I LEU* 5.9 0.4 - - + -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 2.8 20.4 + - - +
73B ILE* 1.3 76.2 - - - +
75B TYR* 1.3 82.5 + + - +
78B LEU* 3.0 59.5 + - + +
146B ALA* 3.8 10.8 - - + -
247B THR* 5.5 1.6 - - + -
275B ASP* 3.4 34.8 - - + +
277B THR* 3.8 10.4 + - - +
292B GLN* 3.4 41.1 - - + -
294B MET* 3.9 27.7 - - + +
297B ILE* 5.4 0.2 - - + -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.5 31.4 - - + +
68B PRO* 3.3 33.6 - - + +
69B ASP* 3.2 30.3 - - + +
70B ILE* 4.8 0.7 - - - -
72B ASN* 2.8 38.1 + - + +
74B PHE* 1.3 97.1 - + - +
76B ALA* 1.3 59.3 + - - +
78B LEU* 3.6 7.0 - - + +
79B ALA* 2.9 30.8 + - - +
100B GLN* 5.2 7.8 + - - -
123B MET* 4.4 9.6 - - + -
124B SER 5.1 1.7 - - - -
125B GLY* 4.8 11.8 + - - -
146B ALA* 5.6 3.7 + - + -
147B SER* 5.6 2.1 + - - -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.5 22.6 + - - +
72B ASN 3.1 6.7 + - - +
73B ILE* 3.7 13.5 - - + +
75B TYR* 1.3 76.6 - - - +
77B GLU* 1.3 60.4 + - + +
79B ALA* 3.4 6.6 + - - +
80B ARG* 2.8 28.6 + - - +
70I ILE* 3.4 33.2 - - + +
71I SER* 4.6 5.8 - - - -
73I ILE* 6.5 0.4 - - + -
76I ALA* 5.5 0.7 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 2.8 28.1 + - + +
76B ALA* 1.3 70.1 - - + +
78B LEU* 1.3 66.3 + - - +
80B ARG* 3.1 8.5 + - - +
81B GLY* 3.0 19.4 + - - -
277B THR* 3.8 6.8 + - - +
278B ARG* 3.1 61.5 + - - +
294B MET* 3.8 31.8 - - + +
71I SER* 3.9 11.3 + - - +
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Residues in contact with LEU 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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74B PHE* 3.0 50.5 + - + +
75B TYR* 3.6 7.2 - - + +
77B GLU* 1.3 75.5 - - - +
79B ALA* 1.3 59.3 + - - +
81B GLY* 2.9 19.1 + - - -
82B ILE* 3.1 19.0 + - + +
123B MET* 3.4 30.5 - - - -
145B ALA* 5.1 1.3 - - + -
146B ALA* 3.7 11.7 - - + -
294B MET* 3.6 43.0 - - + +
297B ILE* 4.3 17.7 - - + -
298B GLY* 4.7 4.2 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.8 8.3 - - + -
75B TYR 2.9 19.2 + - - +
76B ALA 3.5 5.4 - - - +
78B LEU* 1.3 78.8 - - - +
80B ARG* 1.3 59.9 + - - +
82B ILE* 3.5 15.8 + - + +
83B GLU* 3.1 23.7 + - - +
95B LEU* 4.3 18.7 - - + +
123B MET* 5.1 0.6 - - + +
70I ILE* 4.0 23.9 - - + +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA 2.8 17.6 + - - +
77B GLU* 3.1 6.7 + - - +
79B ALA* 1.3 73.2 - - - +
81B GLY* 1.3 64.1 + - - +
83B GLU* 3.1 7.1 - - - +
84B ASP* 2.6 64.4 + - - +
69I ASP* 3.0 21.5 + - - -
70I ILE* 3.3 15.0 - - + -
71I SER* 3.7 18.6 - - - +
97I ASN* 3.0 21.4 - - - +
99I ASP* 2.7 38.1 + - - +
100I GLN* 4.3 11.7 - - - +
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Residues in contact with GLY 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 GLU 3.0 9.0 + - - -
78B LEU* 2.9 8.4 + - - -
80B ARG* 1.3 73.5 - - - +
82B ILE* 1.3 52.1 + - - +
83B GLU 2.8 13.7 + - - -
84B ASP* 2.9 9.4 + - - +
85B ILE* 2.8 40.5 + - - +
294B MET 5.7 1.1 - - - -
295B TYR* 5.0 15.9 - - - -
298B GLY* 6.1 0.2 - - - -
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.9 30.3 - - + -
78B LEU* 3.1 19.0 + - + +
79B ALA* 3.6 11.0 - - - +
81B GLY* 1.3 73.6 - - - +
83B GLU* 1.3 56.5 + - - +
85B ILE* 4.4 8.2 - - - +
86B ALA* 3.1 26.4 + - - +
93B ILE* 4.4 3.8 - - + +
121B ILE* 4.2 15.9 - - + -
123B MET* 3.3 35.7 - - + -
145B ALA* 5.5 1.3 - - + -
298B GLY* 4.0 23.5 - - - +
302B MET* 3.4 20.6 - - + +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.1 13.5 + - - +
80B ARG* 3.1 17.0 - - - +
81B GLY 2.8 1.0 + - - -
82B ILE* 1.3 76.8 - - - +
84B ASP* 1.3 65.7 + - - +
86B ALA* 3.0 15.8 + - - +
87B THR* 3.0 15.9 + - - +
91B TYR 5.6 0.9 - - - +
93B ILE* 3.2 37.9 + - - +
95B LEU* 5.8 1.4 - - - +
70I ILE* 5.6 0.7 - - + +
97I ASN* 3.3 50.2 + - + +
99I ASP* 4.5 9.6 - - - +
104I LYS* 4.4 7.8 + - - -
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Residues in contact with ASP 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 ARG* 2.6 48.3 + - - +
81B GLY* 2.9 8.8 + - - +
83B GLU* 1.3 71.2 - - - +
85B ILE* 1.3 68.2 + - + +
87B THR* 3.1 18.5 + - - -
88B MET* 3.3 12.9 + - - +
295B TYR* 5.0 10.4 - - + -
99I ASP* 4.2 3.7 - - - +
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Residues in contact with ILE 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 GLY 2.8 26.5 + - - +
82B ILE* 4.3 4.7 - - - +
84B ASP* 1.3 75.8 - - - +
86B ALA* 1.3 56.6 + - - +
88B MET* 3.2 12.7 + - + +
89B TYR* 3.0 49.7 + - + -
295B TYR* 3.4 43.1 - - + +
298B GLY 3.7 4.3 - - - -
299B ALA* 3.2 46.7 - - + +
302B MET* 4.2 8.3 - - + -
5256B 171 5.2 5.8 - - + -
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Residues in contact with ALA 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 ILE 3.1 21.2 + - - +
83B GLU* 3.0 11.3 + - - +
85B ILE* 1.3 75.4 - - - +
87B THR* 1.3 61.0 + - - +
89B TYR* 3.4 2.6 + - - +
90B LYS 2.8 8.5 + - - -
91B TYR* 2.8 39.5 + - + +
93B ILE* 3.3 29.2 - - + -
302B MET* 3.8 9.6 - - + +
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Residues in contact with THR 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 GLU* 3.0 13.5 + - - -
84B ASP* 3.1 12.7 + - - +
86B ALA* 1.3 76.3 - - - +
88B MET* 1.3 67.0 + - + +
90B LYS* 3.1 17.9 + - - +
91B TYR 5.1 1.8 - - - -
99I ASP* 4.3 13.3 + - - -
104I LYS* 4.4 8.8 + - - +
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Residues in contact with MET 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 ASP 3.3 7.3 + - - +
85B ILE* 3.2 15.4 + - + +
86B ALA 3.1 0.2 - - - -
87B THR* 1.3 78.9 - - + +
89B TYR* 1.3 67.7 + - + +
90B LYS* 2.9 26.1 + - - +
295B TYR* 4.4 8.7 - - - +
303B ARG* 5.8 1.1 - - - +
5256B 171 3.9 37.2 - - + +
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.0 38.4 + - + +
86B ALA 4.0 0.9 - - - +
88B MET* 1.3 85.2 - - + +
90B LYS* 1.3 71.4 + - - +
91B TYR* 3.2 47.5 - + + -
299B ALA 5.0 1.3 - - - -
302B MET* 3.9 16.8 - - + -
303B ARG* 2.7 58.0 + - - +
306B THR* 3.3 26.0 - - + -
5256B 171 4.3 4.5 + - + -
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Residues in contact with LYS 90 (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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60B THR* 4.1 17.0 - - - +
61B THR* 4.9 1.4 + - - -
86B ALA 2.8 8.4 + - - -
87B THR* 3.1 11.4 + - - +
88B MET 2.9 17.8 + - - +
89B TYR* 1.3 81.3 - - - +
91B TYR* 1.3 60.3 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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