Contacts of the helix formed by residues 80 - 99 (chain C) in PDB entry 5I4A
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 ASP 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.9 17.7 - - + +
76C LYS 3.1 4.9 + - - +
77C GLU* 3.2 9.7 + - - +
79C GLU* 1.3 80.0 - - - +
81C LYS* 1.3 63.8 + - - +
82C LYS* 3.6 12.3 + - - +
83C LEU* 3.2 39.0 + - + +
84C PHE* 3.4 17.8 + - - +
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Residues in contact with LYS 81 (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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77C GLU* 3.0 34.8 + - - +
78C GLU* 5.2 4.4 + - - +
79C GLU 4.3 0.2 - - - -
80C ASP* 1.3 71.7 + - - +
82C LYS* 1.3 70.2 + - + +
84C PHE* 3.0 15.0 + - - +
85C VAL* 3.1 19.9 + - + +
136C ASN* 3.5 22.9 + - - +
139C ASN* 4.7 11.8 + - - -
141C TYR* 3.2 10.3 - - - +
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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
----------------------------------------------------------
80C ASP* 3.6 8.8 + - - +
81C LYS* 1.3 77.0 - - + +
83C LEU* 1.3 55.8 + - - +
85C VAL* 3.3 6.2 + - - +
86C LYS* 2.9 33.3 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.2 13.5 - - + -
16C ARG* 4.8 5.4 - - - +
51C GLU* 3.3 36.6 - - + +
75C ILE* 3.6 44.4 - - + +
80C ASP* 3.2 29.1 + - + +
82C LYS* 1.3 77.2 - - - +
84C PHE* 1.3 57.9 + - - +
86C LYS* 3.8 11.0 - - + +
87C THR* 2.8 42.9 + - - +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 5.4 0.9 - - + -
10C ILE* 3.3 35.0 - - + -
11C PRO 3.8 10.3 - - - -
12C LYS* 3.9 13.7 - - + -
13C LYS* 3.9 7.2 - - - -
14C ILE* 3.6 31.3 - - + +
53C PRO* 6.1 0.2 - - + -
77C GLU* 3.7 29.2 - - + -
80C ASP 3.4 10.5 + - - +
81C LYS 3.0 9.0 + - - +
83C LEU* 1.3 80.7 - - - +
85C VAL* 1.3 60.8 + - - +
87C THR* 3.4 2.3 + - - -
88C LEU* 2.9 45.6 + - + +
141C TYR* 3.8 37.9 - + - -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LYS* 3.1 18.0 + - + +
82C LYS* 3.9 5.6 - - - +
84C PHE* 1.3 77.0 - - - +
86C LYS* 1.3 64.3 + - - +
88C LEU* 3.2 5.9 + - - +
89C TYR* 2.9 48.2 + - + -
134C ILE* 4.2 15.0 - - + +
141C TYR* 3.7 32.8 - - + +
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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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49C TRP* 6.2 1.8 - - - -
51C GLU* 4.4 16.3 + - - +
82C LYS 2.9 18.8 + - - +
83C LEU* 3.8 10.3 - - + +
85C VAL* 1.3 78.0 - - - +
87C THR* 1.3 63.3 + - - +
89C TYR* 3.3 8.5 + - - +
90C LYS* 3.1 50.9 + - + +
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Residues in contact with THR 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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14C ILE* 3.6 28.3 - - + +
39C PHE* 4.2 1.0 - - + -
51C GLU* 3.3 30.4 + - - +
52C ILE* 3.6 24.0 - - - -
53C PRO* 3.7 6.5 - - + -
83C LEU* 2.8 30.3 + - - +
84C PHE 3.7 0.2 - - - -
86C LYS* 1.3 77.3 - - - +
88C LEU* 1.3 58.4 + - - +
90C LYS* 3.3 10.2 + - - +
91C TYR* 2.9 27.0 + - - +
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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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8C ILE* 3.5 37.2 - - + -
10C ILE* 5.0 7.4 - - + -
14C ILE* 5.3 0.4 - - - +
53C PRO* 4.8 9.2 - - + -
84C PHE* 2.9 41.6 + - + +
85C VAL* 3.7 4.9 - - - +
87C THR* 1.3 76.3 - - - +
89C TYR* 1.3 58.3 + - - +
91C TYR* 3.2 10.8 + - + +
92C ILE* 2.9 39.0 + - + +
134C ILE* 3.8 20.4 - - + -
141C TYR* 5.2 0.4 - - + -
247C ILE* 4.5 29.4 - - + -
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Residues in contact with TYR 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 VAL* 2.9 42.1 + - + +
86C LYS* 3.6 8.1 - - - +
87C THR 3.3 0.2 - - - -
88C LEU* 1.3 77.0 - - - +
90C LYS* 1.3 63.9 + - + +
92C ILE* 3.3 9.8 + - + +
93C LYS* 3.0 23.6 + - - +
107C ASN* 3.2 38.5 - - - +
109C PHE* 5.7 0.2 - - - -
132C ILE* 4.2 8.3 - - + -
133C LYS* 3.6 15.1 + - - +
134C ILE* 3.0 47.3 + - + +
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Residues in contact with LYS 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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38C ASN 4.6 1.4 - - - +
39C PHE* 3.5 35.4 - - + -
40C LYS* 3.1 46.8 + - - +
51C GLU* 5.1 9.5 + - - +
86C LYS* 3.1 45.7 + - + +
87C THR* 3.7 5.8 - - - +
89C TYR* 1.3 75.6 - - + +
91C TYR* 1.3 57.4 + - - +
93C LYS* 3.4 12.5 + - + +
94C LYS* 2.9 28.1 + - - +
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.5 8.5 - - + -
53C PRO* 3.8 23.3 - - + -
55C ILE* 4.4 14.1 - - + +
56C ASP 4.5 9.0 + - - -
57C PHE* 3.8 37.5 - + - -
87C THR 2.9 17.3 + - - +
88C LEU* 3.7 9.4 - - + +
89C TYR 3.2 0.2 - - - -
90C LYS* 1.3 75.8 - - - +
92C ILE* 1.3 64.9 + - - +
94C LYS* 3.3 9.7 + - + +
95C LEU* 3.1 46.0 + - + +
246C LYS* 3.1 31.3 + - + +
247C ILE* 3.7 32.1 - - + -
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Residues in contact with ILE 92 (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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88C LEU* 2.9 28.2 + - + +
89C TYR* 3.7 8.5 - - + +
91C TYR* 1.3 73.9 - - - +
93C LYS* 1.3 65.6 + - - +
95C LEU* 3.2 8.5 + - - +
96C PHE* 3.0 53.4 + - + -
109C PHE* 4.4 6.3 - - + -
132C ILE* 4.0 15.7 - - + -
134C ILE* 3.8 17.3 - - + -
143C LEU* 3.5 31.6 - - + -
244C LEU* 4.6 4.9 - - + -
247C ILE* 3.9 22.4 - - + -
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN 5.3 2.9 - - - +
89C TYR 3.0 13.4 + - - +
90C LYS* 3.5 14.6 - - + +
91C TYR 3.3 0.2 - - - -
92C ILE* 1.3 76.9 - - - +
94C LYS* 1.3 55.7 + - - +
96C PHE* 3.4 2.1 + - - +
97C LEU* 2.9 50.9 + - + +
103C PHE* 3.9 40.9 - - + -
107C ASN* 5.5 2.2 - - - +
109C PHE* 3.8 26.2 - - + -
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Residues in contact with LYS 94 (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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37C ASN* 2.8 36.7 + - - +
38C ASN* 3.3 21.1 + - - +
39C PHE* 3.9 7.9 - - + -
57C PHE* 3.6 42.4 - - + -
58C GLN 5.2 5.1 + - - -
90C LYS 2.9 16.2 + - - +
91C TYR* 3.6 12.3 - - + +
92C ILE 3.2 0.4 - - - -
93C LYS* 1.3 77.4 - - - +
95C LEU* 1.3 55.1 + - + +
97C LEU* 3.2 0.5 + - - +
98C ASP* 2.7 69.3 + - - +
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Residues in contact with LEU 95 (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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91C TYR* 3.1 50.6 + - + +
92C ILE* 3.7 6.3 - - - +
94C LYS* 1.3 78.3 - - + +
96C PHE* 1.3 62.3 + - - +
98C ASP* 3.3 10.5 + - + +
99C ASN* 2.6 34.2 + - - +
243C PHE* 3.7 29.6 - - + +
244C LEU* 4.1 16.2 - - + -
246C LYS* 3.7 35.9 - - + +
247C ILE* 5.0 3.8 - - + -
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Residues in contact with PHE 96 (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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92C ILE* 3.0 46.6 + - + +
95C LEU* 1.3 76.7 - - - +
97C LEU* 1.3 61.1 + - - +
99C ASN 3.2 8.1 + - - -
100C ASP 3.3 0.2 + - - -
101C PHE* 2.9 44.8 + + + +
109C PHE* 3.4 50.5 - + + -
130C TYR* 4.8 3.4 - - + -
132C ILE* 3.8 31.0 - - + -
241C LEU* 3.6 31.6 - - + -
243C PHE* 3.6 14.4 - + - -
244C LEU* 4.1 15.9 - - + -
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Residues in contact with LEU 97 (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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38C ASN* 3.7 44.3 + - + +
93C LYS* 2.9 48.8 + - + +
94C LYS 3.8 0.9 - - - +
96C PHE* 1.3 77.2 - - + +
98C ASP* 1.3 58.3 + - - +
100C ASP* 3.0 18.7 + - - -
101C PHE 3.4 20.1 - - - +
102C TYR* 4.9 1.1 - - + -
103C PHE* 4.4 18.6 - - + +
109C PHE* 5.5 1.3 - - + -
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL 5.5 0.5 - - - +
37C ASN 4.7 0.5 - - - -
38C ASN* 2.9 28.9 + - - +
94C LYS* 2.7 56.4 + - - +
95C LEU* 3.7 11.4 - - + +
97C LEU* 1.3 72.3 - - - +
99C ASN* 1.3 62.6 + - - +
100C ASP* 3.3 1.9 + - - +
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Residues in contact with ASN 99 (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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95C LEU* 2.6 31.1 + - - +
96C PHE 3.2 3.3 + - - +
97C LEU 3.1 0.2 - - - -
98C ASP* 1.3 82.3 - - - +
100C ASP* 1.3 69.3 + - - +
101C PHE* 3.3 13.1 + - + -
243C PHE* 3.3 50.2 - - + +
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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