Contacts of the helix formed by residues 70 - 91 (chain C) in PDB entry 1S0V
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 ALA 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL* 3.9 19.1 - - + +
65C ALA* 4.4 2.2 - - - -
67C ASN 2.7 8.9 + - - +
69C ALA* 1.3 79.9 - - - +
71C LYS* 1.3 56.8 + - - +
72C PRO* 2.9 5.8 - - - -
73C LEU* 3.0 15.5 - - + +
74C ILE* 2.9 37.3 + - + +
123C LEU* 5.1 7.9 - - + -
254C ILE* 4.2 20.4 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA 4.1 20.6 - - - +
66C ASP* 5.0 5.4 - - - +
67C ASN 3.6 9.3 + - - +
68C ALA* 4.5 24.8 - - + +
70C ALA* 1.3 73.8 - - - +
72C PRO* 1.4 69.7 - - + +
73C LEU 2.9 1.8 - - - -
74C ILE* 4.0 8.1 - - + -
75C THR* 2.7 30.4 + - - +
754C GLN* 4.6 24.9 + - - +
755C PHE* 4.3 29.1 - - + -
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA 3.8 8.3 - - - +
69C ALA 3.4 20.0 - - - +
70C ALA 2.9 7.2 - - - -
71C LYS* 1.4 92.8 - - + +
73C LEU* 1.3 80.2 + - + +
75C THR* 3.6 9.3 + - - +
76C THR* 3.5 22.2 + - - +
253C ALA 5.7 1.1 - - - +
257C ARG* 4.3 20.6 - - + +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA 4.6 0.9 - - - +
70C ALA* 3.0 13.2 - - + +
72C PRO* 1.3 94.0 - - + +
74C ILE* 1.3 57.4 + - + +
75C THR 3.1 1.3 - - - -
76C THR* 3.0 11.0 + - - +
77C LEU* 2.6 45.5 + - + +
250C TYR* 3.8 33.9 - - + +
253C ALA* 3.8 19.7 - - + -
254C ILE* 3.7 31.4 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA* 3.6 41.5 - - + +
70C ALA* 2.9 21.7 + - + +
71C LYS* 3.0 7.4 + - - +
73C LEU* 1.3 77.7 - - + +
75C THR* 1.3 59.7 + - - +
77C LEU* 3.8 9.6 - - + -
78C LEU* 3.2 25.7 + - + +
116C TYR* 4.2 20.4 - - + +
119C ILE* 4.7 21.3 - - + -
123C LEU* 4.6 11.0 - - + -
755C PHE* 3.4 27.7 - - + -
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LYS* 2.7 27.2 + - - +
72C PRO* 3.9 8.2 + - - +
73C LEU 3.0 0.4 + - - -
74C ILE* 1.3 75.4 - - - +
76C THR* 1.3 62.4 + - + +
78C LEU* 5.1 1.1 - - - +
79C PRO* 3.5 15.1 - - - +
755C PHE* 3.8 24.2 - - + -
756C ARG 5.0 10.5 - - - +
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PRO 3.5 14.7 + - - +
73C LEU* 3.0 17.6 + - - +
75C THR* 1.3 78.4 - - + +
77C LEU* 1.3 61.3 + - - +
79C PRO* 2.8 25.0 - - - +
80C LYS* 4.2 13.0 + - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 2.6 28.6 + - + +
74C ILE* 4.0 7.4 - - + +
76C THR* 1.3 72.1 + - - +
78C LEU* 1.3 61.6 + - - +
79C PRO* 3.0 7.1 - - - +
80C LYS* 3.4 13.5 + - - +
81C MET* 3.5 10.6 + - - +
119C ILE* 3.4 31.6 - - + -
123C LEU* 6.0 0.4 - - + -
220C LEU* 5.0 4.5 - - + -
224C THR* 3.7 37.3 + - + +
226C MET* 3.5 22.7 - - + -
250C TYR* 4.0 25.6 - - + +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 3.2 22.8 + - + +
75C THR 5.1 0.4 - - - +
77C LEU* 1.3 72.7 - - - +
79C PRO* 1.3 66.7 - - + +
81C MET* 4.0 3.4 - - - -
82C ILE* 2.9 43.8 + - + +
112C GLU 3.9 3.4 - - - +
115C ALA* 3.1 36.6 - - + -
116C TYR* 3.4 22.9 - - + +
119C ILE* 4.5 8.7 - - + +
746C ARG* 4.6 24.2 - - - +
755C PHE* 5.7 2.2 - - + +
756C ARG 5.7 7.6 - - - -
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Residues in contact with PRO 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C THR 3.5 14.4 - - - +
76C THR* 2.8 28.5 - - - +
77C LEU 3.0 3.1 - - - -
78C LEU* 1.3 92.5 - - + +
80C LYS* 1.3 60.4 + - + +
82C ILE* 3.2 6.2 + - + +
83C ALA* 2.7 37.7 + - - +
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR 4.2 14.4 + - - +
77C LEU 3.6 6.7 - - - +
79C PRO* 1.3 77.7 - - + +
81C MET* 1.3 58.7 + - - +
83C ALA* 3.1 9.2 - - - +
84C ARG* 2.9 29.1 + - - +
223C SER* 3.5 17.8 - - - +
224C THR* 3.0 33.0 - - + -
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Residues in contact with MET 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU 3.5 8.8 + - - +
78C LEU 3.9 6.7 - - - +
79C PRO 3.2 0.2 - - - -
80C LYS* 1.3 75.8 - - - +
82C ILE* 1.3 67.3 + - - +
84C ARG* 3.1 4.0 + - - +
85C ILE* 2.8 38.8 + - + +
114C VAL* 5.4 1.3 - - + -
115C ALA* 3.4 28.7 - - + +
118C THR* 4.4 16.4 - - - +
119C ILE* 4.1 13.9 - - + -
216C CYS* 4.0 15.7 - - + +
219C MET* 4.0 24.2 - - + -
220C LEU* 3.7 37.2 - - + +
223C SER* 3.7 11.1 - - - +
224C THR* 5.5 0.2 - - - +
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 2.9 49.3 + - + +
79C PRO* 3.8 5.2 - - + +
81C MET* 1.3 71.5 - - - +
83C ALA* 1.3 68.6 + - - +
85C ILE* 2.9 21.6 + - - +
86C ASN* 3.2 18.1 + - - +
111C PRO* 4.3 4.3 - - + +
112C GLU* 3.3 53.2 - - + +
115C ALA* 3.3 17.5 - - + -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PRO 2.7 18.6 + - - +
80C LYS* 3.1 13.7 - - - +
82C ILE* 1.3 71.8 - - - +
84C ARG* 1.3 53.7 + - - +
85C ILE 2.6 12.1 + - - -
86C ASN* 2.8 19.8 + - - +
87C ASP* 3.3 15.6 + - - +
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Residues in contact with ARG 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 LYS 2.9 9.5 + - - +
81C MET* 3.6 4.5 - - - +
83C ALA* 1.3 71.0 - - - +
85C ILE* 1.3 61.1 + - + +
87C ASP* 2.7 37.9 + - - +
88C TRP* 3.4 18.1 - - - +
91C GLU* 3.6 22.4 + - - -
219C MET* 4.2 12.6 - - + +
222C GLU* 2.9 34.5 + - + +
223C SER* 3.4 41.3 - - - +
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Residues in contact with ILE 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 MET* 2.8 39.5 - - + +
82C ILE* 3.2 10.3 - - - +
83C ALA 2.6 6.3 + - - -
84C ARG* 1.3 76.5 - - - +
86C ASN* 1.3 59.8 + - - +
87C ASP 3.2 0.4 - - - -
88C TRP* 3.3 4.1 + - - +
89C PHE* 2.9 60.9 + - + -
111C PRO* 3.9 21.1 - - + +
114C VAL* 4.4 9.4 - - + -
115C ALA* 3.5 41.1 - - + +
219C MET* 4.4 13.2 - - + -
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Residues in contact with ASN 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 ILE* 3.2 20.8 + - - +
83C ALA* 2.8 9.6 + - - +
85C ILE* 1.3 80.7 + - - +
87C ASP* 1.3 61.7 + - - +
89C PHE* 3.3 15.6 + - - +
90C GLU* 3.3 26.9 + - - +
111C PRO* 4.1 26.2 - - - +
112C GLU* 4.9 1.7 - - - +
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Residues in contact with ASP 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 ALA* 3.3 11.6 + - - +
84C ARG* 2.7 30.2 + - - +
85C ILE 3.2 0.6 - - - -
86C ASN* 1.3 74.6 - - - +
88C TRP* 1.3 59.8 + - - +
90C GLU* 3.2 8.1 + - - +
91C GLU* 2.9 48.1 + - - +
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Residues in contact with TRP 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 ARG* 3.4 24.0 + - - +
85C ILE* 3.3 6.0 + - - +
87C ASP* 1.3 82.4 - - - +
89C PHE* 1.3 70.2 + + - +
91C GLU* 3.6 27.9 + - + -
92C VAL* 3.0 42.0 + - + +
95C LYS* 6.0 4.3 - - - -
100C PRO* 4.5 13.0 - - + +
103C PHE* 4.7 13.1 - - + +
106C LEU* 5.8 1.8 - - + -
215C ARG* 2.8 55.0 - - + +
219C MET* 4.4 10.3 - - + -
222C GLU* 5.6 2.5 - - - -
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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 ILE* 2.9 48.8 + - + +
86C ASN* 3.7 18.8 - - - +
87C ASP 3.2 0.6 - - - -
88C TRP* 1.3 89.2 - + - +
90C GLU* 1.3 66.3 + - - +
93C LYS* 3.3 25.3 + - - +
103C PHE* 3.4 23.1 - + + -
106C LEU* 2.7 47.3 - - + -
107C GLN* 2.8 41.7 - - + +
109C ILE 5.3 1.8 - - - -
111C PRO* 5.0 12.8 - - + -
114C VAL* 5.4 1.1 - - + -
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Residues in contact with GLU 90 (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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86C ASN 3.3 12.0 + - - +
87C ASP* 3.2 12.0 + - - +
89C PHE* 1.3 77.0 - - - +
91C GLU* 1.3 60.1 + - + +
92C VAL 3.1 6.6 + - - -
93C LYS* 2.9 47.2 + - - +
94C ALA* 3.3 25.8 + - - +
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Residues in contact with GLU 91 (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 ARG* 3.6 14.2 + - - -
87C ASP* 2.9 43.0 + - - +
88C TRP* 3.6 25.7 + - + +
89C PHE 3.5 0.4 - - - -
90C GLU* 1.3 78.0 - - + +
92C VAL* 1.3 59.5 + - - +
94C ALA* 4.6 4.7 - - - -
95C LYS* 3.6 30.3 + - - +
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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