Contacts of the helix formed by residues 72 - 89 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASP* 3.1 27.0 + - + +
70F ILE 3.1 7.2 - - - +
71F SER* 1.3 79.7 + - - +
73F ILE* 1.3 78.7 + - - +
74F PHE* 2.7 41.7 - - - +
75F TYR* 3.1 30.5 + - + -
76F ALA* 3.3 7.5 + - - +
221F TYR* 6.1 1.4 - - - +
249F GLU* 5.3 0.8 + - - -
278P ARG* 4.4 3.8 - - - +
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER 3.5 2.7 + - - +
72F ASN* 1.3 91.2 - - - +
74F PHE* 1.3 66.2 - - + +
76F ALA* 2.9 24.0 + - + +
77F GLU* 3.6 5.9 + - - +
249F GLU* 3.8 24.7 - - + +
277F THR* 3.6 29.3 - - + +
278F ARG* 3.8 30.3 - - + +
279F LEU* 3.8 23.1 - - + -
294F MET* 4.0 5.2 - - - +
73P ILE* 4.6 9.6 - - + -
278P ARG* 4.0 14.3 - - - +
279P LEU* 5.9 1.1 - - + -
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Residues in contact with PHE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ASN* 2.7 27.1 - - - +
73F ILE* 1.3 77.0 - - + +
75F TYR* 1.3 86.4 + + - +
76F ALA 3.4 0.3 + - - -
78F LEU* 3.8 36.3 + - + +
146F ALA* 4.4 7.0 - - + -
275F ASP* 3.3 32.5 - - + +
277F THR* 4.0 4.0 - - + -
292F GLN* 3.3 43.3 - - + -
294F MET* 3.3 39.9 - - + +
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Residues in contact with TYR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ILE* 4.4 20.0 - - + +
68F PRO* 3.3 37.3 - - + +
69F ASP* 3.4 28.3 - - + +
70F ILE* 4.8 6.8 - - + +
72F ASN* 3.1 25.6 + - + +
74F PHE* 1.3 100.9 - + - +
76F ALA* 1.3 63.5 + - - +
78F LEU* 3.9 5.1 - - + +
79F ALA* 3.1 24.1 + - - +
100F GLN* 4.2 8.1 + - - -
123F MET* 4.0 31.3 - - + +
124F SER 5.3 3.6 + - - -
125F GLY* 5.4 1.7 + - - -
146F ALA 5.7 4.5 + - - -
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 5.0 4.3 - - - +
72F ASN 3.3 7.0 + - - +
73F ILE* 2.9 18.6 + - - +
75F TYR* 1.3 74.9 - - - +
77F GLU* 1.3 70.1 + - + +
79F ALA* 3.0 6.4 + - - +
80F ARG* 2.9 21.6 + - - +
278F ARG* 5.6 2.9 - - - +
70P ILE* 3.9 37.1 - - + +
71P SER* 4.5 11.2 - - - +
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Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE 3.6 3.1 + - - +
76F ALA* 1.3 81.7 - - + +
78F LEU* 1.3 63.5 + - - +
80F ARG* 3.0 43.0 + - - +
81F GLY 3.0 10.0 + - - -
277F THR* 5.8 3.1 - - - -
278F ARG* 6.1 7.4 - - + +
294F MET* 3.4 46.9 - - + +
295F TYR* 4.0 18.0 - - - +
71P SER* 5.5 2.6 + - - -
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F PHE* 3.8 36.7 + - + +
75F TYR* 3.7 9.4 + - + +
76F ALA 3.2 0.8 - - - -
77F GLU* 1.3 78.1 - - - +
79F ALA* 1.3 64.4 + - - +
81F GLY* 2.9 13.9 + - - -
82F ILE* 3.1 16.5 + - - +
123F MET* 3.5 42.4 - - + -
145F ALA* 4.0 3.4 - - + -
146F ALA* 3.8 14.6 - - + -
294F MET* 3.4 19.9 + - + +
297F ILE* 3.6 12.3 - - + -
298F GLY* 3.5 32.5 - - - +
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ILE* 5.9 2.9 - - + -
70F ILE* 4.6 7.2 - - + -
75F TYR 3.1 15.9 + - - +
76F ALA* 3.0 7.2 + - - +
78F LEU* 1.3 79.6 - - - +
80F ARG* 1.3 55.4 + - - +
82F ILE* 3.6 13.0 - - + +
83F GLU* 3.1 35.8 + - - +
95F LEU* 4.2 25.4 - - + -
123F MET* 5.1 1.0 - - - +
70P ILE* 4.7 8.1 - - + -
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Residues in contact with ARG 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F ALA 2.9 11.3 + - - +
77F GLU* 3.0 35.1 + - - +
79F ALA* 1.3 74.3 - - - +
81F GLY* 1.3 67.6 + - - +
83F GLU* 3.3 4.3 + - - +
84F ASP* 2.7 48.5 + - - +
295F TYR* 3.5 32.5 - - + +
69P ASP* 6.1 0.9 - - - -
70P ILE* 5.7 2.0 - - + +
71P SER* 6.0 6.3 - - - -
97P ASN* 6.4 0.2 - - - +
99P ASP* 5.8 3.6 - - - +
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Residues in contact with GLY 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F GLU 3.0 7.2 + - - -
78F LEU 2.9 8.1 + - - -
80F ARG* 1.3 79.4 - - - +
82F ILE* 1.3 62.2 + - - +
84F ASP* 3.7 1.7 + - - +
85F ILE* 3.5 25.8 + - - +
295F TYR* 3.5 38.3 - - - -
299F ALA* 3.6 9.0 - - - +
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Residues in contact with ILE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F VAL* 3.9 26.5 - - + -
78F LEU* 3.1 12.7 + - + +
79F ALA* 3.6 13.5 - - - +
80F ARG 3.2 0.2 - - - -
81F GLY* 1.3 78.7 - - - +
83F GLU* 1.3 57.8 + - - +
85F ILE 3.4 0.5 + - - -
86F ALA* 2.9 27.4 + - - +
93F ILE* 3.7 27.1 - - + -
121F ILE* 4.2 15.7 - - + -
123F MET* 3.6 31.2 - - + -
298F GLY* 3.9 16.1 - - - +
302F MET* 3.4 23.7 - - - +
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Residues in contact with GLU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ALA* 3.1 22.7 + - - +
80F ARG* 3.8 5.8 - - - +
82F ILE* 1.3 79.5 - - - +
84F ASP* 1.3 59.7 + - - +
86F ALA* 3.1 6.0 + - - +
87F THR* 2.8 42.3 + - + +
93F ILE* 3.3 41.5 - - + +
95F LEU* 5.5 2.3 - - - +
97P ASN* 3.6 42.9 + - - +
99P ASP* 4.1 21.1 - - - +
104P LYS* 5.5 2.3 - - - +
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Residues in contact with ASP 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 2.7 45.0 + - - +
81F GLY 3.9 2.2 - - - +
83F GLU* 1.3 78.2 - - - +
85F ILE* 1.3 59.5 + - + +
87F THR* 2.5 25.5 + - - -
88F MET* 2.9 15.2 + - - +
295F TYR* 3.4 30.4 + - - +
99P ASP* 5.5 3.3 - - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLY 3.5 13.2 + - - +
82F ILE 3.4 1.4 + - - +
84F ASP* 1.3 77.0 - - + +
86F ALA* 1.3 63.7 + - - +
88F MET* 3.2 24.2 + - + +
89F TYR* 2.9 45.1 + - + -
295F TYR* 5.2 4.7 - - - +
299F ALA* 3.6 29.6 - - + +
302F MET* 3.8 26.2 - - + -
303F ARG* 4.2 34.1 - - + +
306F THR* 4.9 0.2 - - - +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ILE 2.9 15.7 + - - +
83F GLU 3.1 9.4 - - - +
85F ILE* 1.3 76.5 - - - +
87F THR* 1.3 59.7 + - + +
89F TYR* 2.9 4.4 + - - -
90F LYS 2.8 24.3 + - - -
91F TYR* 2.8 29.7 + - + +
93F ILE* 3.6 31.2 - - + -
302F MET* 3.9 8.5 - - + +
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Residues in contact with THR 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F GLU* 2.8 29.8 + - + +
84F ASP* 2.5 26.3 + - - -
86F ALA* 1.3 72.9 - - + +
88F MET* 1.3 62.1 + - - +
90F LYS* 3.3 16.4 + - - +
91F TYR 4.2 5.8 + - - +
99P ASP* 4.9 3.6 - - - +
104P LYS* 3.5 32.3 - - - +
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Residues in contact with MET 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASP 2.9 10.7 + - - +
85F ILE* 3.2 31.2 - - + +
87F THR* 1.3 85.2 + - - +
89F TYR* 1.3 71.4 + - + +
90F LYS* 3.2 6.5 + - - +
303F ARG* 5.8 5.6 - - - +
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Residues in contact with TYR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F THR 4.4 1.7 + - - -
85F ILE* 2.9 43.3 + - + +
86F ALA 2.9 3.5 + - - -
88F MET* 1.3 90.1 - - + +
90F LYS* 1.3 76.7 + - - +
91F TYR* 3.3 27.8 + + + -
302F MET* 5.9 0.2 - - + -
303F ARG* 5.0 12.9 - - + +
306F THR* 3.6 33.6 - - + +
310F ASN* 5.2 4.7 - - - -
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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